From 826f6b3f95ac9885204e9065a5dce4dd8fc8661d Mon Sep 17 00:00:00 2001
From: Aayam Bansal <aayambansal@gmail.com>
Date: Wed, 29 Jul 2026 05:44:48 +0800
Subject: [PATCH 01/40] feat: detect scientific file formats

---
 frontend/workspace/src/science/files.test.ts | 82 ++++++++++++++++
 frontend/workspace/src/science/files.ts      | 99 ++++++++++++++++++++
 2 files changed, 181 insertions(+)
 create mode 100644 frontend/workspace/src/science/files.test.ts
 create mode 100644 frontend/workspace/src/science/files.ts

diff --git a/frontend/workspace/src/science/files.test.ts b/frontend/workspace/src/science/files.test.ts
new file mode 100644
index 00000000..ad55b5fc
--- /dev/null
+++ b/frontend/workspace/src/science/files.test.ts
@@ -0,0 +1,82 @@
+import { describe, expect, test } from "bun:test"
+import { detectScientificFile } from "./files"
+
+describe("detectScientificFile", () => {
+  test("routes small-molecule structures into the 3D chemistry renderer", () => {
+    expect(detectScientificFile("xyz", "2\nwater\nO 0 0 0\nH 0 0 1")).toEqual({
+      kind: "chem-3d",
+      data: {
+        data: "2\nwater\nO 0 0 0\nH 0 0 1",
+        format: "xyz",
+      },
+      format: "xyz",
+    })
+  })
+
+  test("routes macromolecular structures case-insensitively", () => {
+    expect(detectScientificFile("PDB", "ATOM      1")).toEqual({
+      kind: "protein-structure",
+      data: {
+        data: "ATOM      1",
+        format: "pdb",
+      },
+      format: "pdb",
+    })
+  })
+
+  test("does not infer a scientific renderer from file contents alone", () => {
+    expect(detectScientificFile("txt", "ATOM      1")).toBeUndefined()
+  })
+
+  test("does not render empty scientific files", () => {
+    expect(detectScientificFile("sdf", "   \n")).toBeUndefined()
+  })
+
+  test("uses the first SMILES record for two-dimensional chemistry", () => {
+    expect(detectScientificFile("smi", "# compounds\n\nCCO ethanol\nCCC propane")).toEqual({
+      kind: "chem-2d",
+      data: {
+        smiles: "CCO",
+        records: 2,
+      },
+      format: "smiles",
+    })
+  })
+
+  test("combines wrapped FASTA lines into a single sequence", () => {
+    expect(detectScientificFile("fasta", ">alpha human sample\nAC GT\nTG\n")).toEqual({
+      kind: "sequence",
+      data: {
+        id: "alpha human sample",
+        sequence: "ACGTTG",
+        records: 1,
+      },
+      format: "fasta",
+    })
+  })
+
+  test("routes equal-length FASTA records into the alignment viewer", () => {
+    expect(detectScientificFile("FA", ">alpha\nACGT\n>beta\nAC-T")).toEqual({
+      kind: "msa",
+      data: {
+        sequences: [
+          { id: "alpha", seq: "ACGT" },
+          { id: "beta", seq: "AC-T" },
+        ],
+      },
+      format: "fasta",
+    })
+  })
+
+  test("does not pretend unequal FASTA records form an alignment", () => {
+    expect(detectScientificFile("faa", ">alpha\nMKT\n>beta\nMKTA")).toEqual({
+      kind: "sequence",
+      data: {
+        id: "alpha",
+        sequence: "MKT",
+        records: 2,
+      },
+      format: "fasta",
+    })
+  })
+})
diff --git a/frontend/workspace/src/science/files.ts b/frontend/workspace/src/science/files.ts
new file mode 100644
index 00000000..4860636b
--- /dev/null
+++ b/frontend/workspace/src/science/files.ts
@@ -0,0 +1,99 @@
+import type { ArtifactKind } from "./renderers/registry"
+
+export interface ScientificFile {
+  kind: ArtifactKind
+  data: unknown
+  format: string
+}
+
+const protein: Record<string, string> = {
+  pdb: "pdb",
+  ent: "pdb",
+  cif: "mmcif",
+  mmcif: "mmcif",
+  pdbqt: "pdbqt",
+  gro: "gro",
+}
+
+const molecule: Record<string, string> = {
+  xyz: "xyz",
+  sdf: "sdf",
+  mol: "mol",
+  mol2: "mol2",
+}
+
+const fasta = new Set(["fa", "fasta", "faa", "fna", "ffn", "frn"])
+
+export function detectScientificFile(extension: string, content: string): ScientificFile | undefined {
+  if (!content.trim()) return
+
+  const ext = extension.toLowerCase()
+  const proteinFormat = protein[ext]
+  if (proteinFormat) {
+    return {
+      kind: "protein-structure",
+      data: { data: content, format: proteinFormat },
+      format: proteinFormat,
+    }
+  }
+
+  const moleculeFormat = molecule[ext]
+  if (moleculeFormat) {
+    return {
+      kind: "chem-3d",
+      data: { data: content, format: moleculeFormat },
+      format: moleculeFormat,
+    }
+  }
+
+  if (ext === "smi" || ext === "smiles") {
+    const records = content
+      .split(/\r?\n/)
+      .map((line) => line.trim())
+      .filter((line) => line && !line.startsWith("#"))
+    const smiles = records[0]?.split(/\s+/)[0]
+    if (!smiles) return
+    return {
+      kind: "chem-2d",
+      data: { smiles, records: records.length },
+      format: "smiles",
+    }
+  }
+
+  if (!fasta.has(ext)) return
+  const records = content.split(/\r?\n/).reduce<{ id: string; seq: string }[]>((all, line) => {
+    const value = line.trim()
+    if (!value) return all
+    if (value.startsWith(">")) {
+      all.push({ id: value.slice(1).trim() || `sequence_${all.length + 1}`, seq: "" })
+      return all
+    }
+    const record = all[all.length - 1]
+    if (record) {
+      record.seq += value.replace(/\s+/g, "")
+      return all
+    }
+    all.push({ id: "sequence_1", seq: value.replace(/\s+/g, "") })
+    return all
+  }, [])
+  const sequences = records.filter((record) => record.seq)
+  const first = sequences[0]
+  if (!first) return
+  const aligned = sequences.length > 1 && sequences.every((record) => record.seq.length === first.seq.length)
+  if (aligned) {
+    return {
+      kind: "msa",
+      data: { sequences },
+      format: "fasta",
+    }
+  }
+  return {
+    kind: "sequence",
+    data: {
+      id: first.id,
+      sequence: first.seq,
+      records: sequences.length,
+    },
+    format: "fasta",
+  }
+}

From ee0e014c6af4557b98a6b439363d905bb7e9b817 Mon Sep 17 00:00:00 2001
From: Aayam Bansal <aayambansal@gmail.com>
Date: Wed, 29 Jul 2026 05:47:10 +0800
Subject: [PATCH 02/40] feat: render scientific files in document tabs

---
 frontend/workspace/src/atlas/FilePreview.tsx | 30 ++++++++++++++++++--
 frontend/workspace/src/science/files.test.ts | 15 ++++++++++
 2 files changed, 42 insertions(+), 3 deletions(-)

diff --git a/frontend/workspace/src/atlas/FilePreview.tsx b/frontend/workspace/src/atlas/FilePreview.tsx
index ab372e7c..6e4934d3 100644
--- a/frontend/workspace/src/atlas/FilePreview.tsx
+++ b/frontend/workspace/src/atlas/FilePreview.tsx
@@ -17,6 +17,8 @@ import { useSync } from "@/context/sync"
 import { usePlatform } from "@/context/platform"
 import { FONT_MONO, FONT_SANS, FONT_CODE } from "@/styles/tokens"
 import { PdfViewer } from "@/science/renderers/documents/PdfViewer"
+import { ScienceArtifact } from "@/science/ScienceArtifact"
+import { detectScientificFile } from "@/science/files"
 import { toast } from "@/atlas/Toast"
 import { IconFile, IconX, IconCopy, IconDownload, IconBookOpen, IconBraces, IconRefresh } from "@/atlas/shared/Icon"
 
@@ -26,6 +28,7 @@ import { IconFile, IconX, IconCopy, IconDownload, IconBookOpen, IconBraces, Icon
  * A file's extension picks the renderer:
  *   .md / .markdown  → formatted markdown (@synsci/ui Markdown)
  *   .pdf             → PdfViewer (pdfjs page rasterizer)
+ *   molecular/FASTA  → scientific artifact renderer, with editable source
  *   .tex / .latex    → highlighted LaTeX source (a .tex is a source FILE, not a
  *                      math expression — the KaTeX LatexView is reserved for
  *                      kind:"latex" math ARTIFACTS with a single math string)
@@ -98,7 +101,7 @@ const LANG: Record<string, string> = {
   log: "text",
 }
 
-type Kind = "markdown" | "pdf" | "image" | "code" | "binary"
+type Kind = "markdown" | "pdf" | "image" | "science" | "code" | "binary"
 
 type FileData = { content?: string; encoding?: string; mimeType?: string }
 
@@ -150,6 +153,7 @@ export function FileView(props: {
   const dataUrl = () => `data:${mime() || "application/octet-stream"};base64,${b64()}`
   const text = () => (!data() || isBinary() ? "" : (data()!.content ?? ""))
   const dirty = () => draft() !== savedText()
+  const scientific = createMemo(() => (isBinary() ? undefined : detectScientificFile(e(), draft())))
 
   const kind = createMemo<Kind>(() => {
     const x = e()
@@ -160,6 +164,7 @@ export function FileView(props: {
     }
     if (x === "md" || x === "markdown" || x === "mdx") return "markdown"
     if (x === "pdf") return "pdf"
+    if (scientific()) return "science"
     // .tex / .latex / .sty / .cls are source files → highlighted "code" view
     // (LANG maps them to the shiki `latex` grammar). They are NEVER routed to
     // KaTeX, which blanks on a full \documentclass document.
@@ -169,6 +174,7 @@ export function FileView(props: {
   const badge = () => {
     const k = kind()
     if (k === "code") return LANG[e()] ?? e() ?? "text"
+    if (k === "science") return scientific()?.format ?? e()
     return k
   }
 
@@ -213,7 +219,7 @@ export function FileView(props: {
     } catch {}
   }
 
-  const toggleable = () => kind() === "markdown" || kind() === "code"
+  const toggleable = () => kind() === "markdown" || kind() === "science" || kind() === "code"
 
   return (
     <div
@@ -426,6 +432,24 @@ export function FileView(props: {
                 </div>
               </Match>
 
+              {/* scientific file */}
+              <Match when={kind() === "science" && !showSource()}>
+                <Show when={scientific()}>
+                  {(artifact) => (
+                    <div
+                      style={{
+                        padding: "14px",
+                        height: "100%",
+                        "min-height": "420px",
+                        "box-sizing": "border-box",
+                      }}
+                    >
+                      <ScienceArtifact kind={artifact().kind} data={artifact().data} height={560} />
+                    </div>
+                  )}
+                </Show>
+              </Match>
+
               {/* binary */}
               <Match when={kind() === "binary"}>
                 <div
@@ -453,7 +477,7 @@ export function FileView(props: {
               </Match>
 
               {/* code / text — editable source, or highlighted read view */}
-              <Match when={kind() === "code" && showSource()}>
+              <Match when={(kind() === "code" || kind() === "science") && showSource()}>
                 <textarea
                   value={draft()}
                   spellcheck={false}
diff --git a/frontend/workspace/src/science/files.test.ts b/frontend/workspace/src/science/files.test.ts
index ad55b5fc..a078aab9 100644
--- a/frontend/workspace/src/science/files.test.ts
+++ b/frontend/workspace/src/science/files.test.ts
@@ -1,6 +1,10 @@
 import { describe, expect, test } from "bun:test"
+import { readFileSync } from "node:fs"
+import { fileURLToPath } from "node:url"
 import { detectScientificFile } from "./files"
 
+const read = (path: string) => readFileSync(fileURLToPath(new URL(path, import.meta.url)), "utf8")
+
 describe("detectScientificFile", () => {
   test("routes small-molecule structures into the 3D chemistry renderer", () => {
     expect(detectScientificFile("xyz", "2\nwater\nO 0 0 0\nH 0 0 1")).toEqual({
@@ -80,3 +84,14 @@ describe("detectScientificFile", () => {
     })
   })
 })
+
+describe("scientific file viewer integration", () => {
+  test("routes recognized files through the shared science artifact dispatcher", () => {
+    const preview = read("../atlas/FilePreview.tsx")
+
+    expect(preview).toContain('import { detectScientificFile } from "@/science/files"')
+    expect(preview).toContain('import { ScienceArtifact } from "@/science/ScienceArtifact"')
+    expect(preview).toContain('type Kind = "markdown" | "pdf" | "image" | "science" | "code" | "binary"')
+    expect(preview).toContain("<ScienceArtifact")
+  })
+})

From e9d2b4f1ea2e303b1976892bbc3c1a94f8b6e072 Mon Sep 17 00:00:00 2001
From: Aayam Bansal <aayambansal@gmail.com>
Date: Wed, 29 Jul 2026 05:49:31 +0800
Subject: [PATCH 03/40] test: cover scientific file previews

---
 .../e2e/science-file-viewers.spec.ts          | 32 +++++++++++++++++++
 .../workspace/e2e/science/alignment.fasta     |  4 +++
 frontend/workspace/e2e/science/example.pdb    |  7 ++++
 frontend/workspace/e2e/science/ligand.sdf     |  9 ++++++
 frontend/workspace/e2e/science/water.xyz      |  5 +++
 5 files changed, 57 insertions(+)
 create mode 100644 frontend/workspace/e2e/science/alignment.fasta
 create mode 100644 frontend/workspace/e2e/science/example.pdb
 create mode 100644 frontend/workspace/e2e/science/ligand.sdf
 create mode 100644 frontend/workspace/e2e/science/water.xyz

diff --git a/frontend/workspace/e2e/science-file-viewers.spec.ts b/frontend/workspace/e2e/science-file-viewers.spec.ts
index cd875e12..fb10f8da 100644
--- a/frontend/workspace/e2e/science-file-viewers.spec.ts
+++ b/frontend/workspace/e2e/science-file-viewers.spec.ts
@@ -56,3 +56,35 @@ test("PDF files rasterize their pages without an error", async ({ page, director
   expect(await canvas.evaluate((node: HTMLCanvasElement) => node.width * node.height)).toBeGreaterThan(0)
   await expect(viewer.locator('[data-slot="pdf-error"]')).toHaveCount(0)
 })
+
+test("XYZ files open as interactive 3D chemistry with source access", async ({ page, directory, gotoSession }) => {
+  await gotoSession()
+  await openFile(page, directory, "frontend/workspace/e2e/science/water.xyz")
+
+  const artifact = page.locator('[data-component="science-artifact"][data-kind="chem-3d"]')
+  await expect(artifact).toBeVisible()
+  await expect(artifact.locator('[data-component="mol-structure"]')).toBeVisible()
+
+  await page.getByTitle("raw source", { exact: true }).click()
+  await expect(page.getByTitle("rendered view", { exact: true })).toBeVisible()
+  await expect(page.locator("textarea")).toHaveValue(/water/)
+})
+
+test("PDB and SDF files select their molecular renderers", async ({ page, directory, gotoSession }) => {
+  await gotoSession()
+  await openFile(page, directory, "frontend/workspace/e2e/science/example.pdb")
+  await expect(page.locator('[data-component="science-artifact"][data-kind="protein-structure"]')).toBeVisible()
+
+  await openFile(page, directory, "frontend/workspace/e2e/science/ligand.sdf")
+  await expect(page.locator('[data-component="science-artifact"][data-kind="chem-3d"]')).toBeVisible()
+})
+
+test("aligned FASTA files open in the sequence alignment viewer", async ({ page, directory, gotoSession }) => {
+  await gotoSession()
+  await openFile(page, directory, "frontend/workspace/e2e/science/alignment.fasta")
+
+  const artifact = page.locator('[data-component="science-artifact"][data-kind="msa"]')
+  await expect(artifact).toBeVisible()
+  await expect(artifact.locator('[data-component="science-msa"]')).toBeVisible()
+  await expect(artifact).toContainText("2 seqs")
+})
diff --git a/frontend/workspace/e2e/science/alignment.fasta b/frontend/workspace/e2e/science/alignment.fasta
new file mode 100644
index 00000000..3c69fca5
--- /dev/null
+++ b/frontend/workspace/e2e/science/alignment.fasta
@@ -0,0 +1,4 @@
+>human
+MKTAYIAKQRQI
+>mouse
+MKTAYIAKQKQI
diff --git a/frontend/workspace/e2e/science/example.pdb b/frontend/workspace/e2e/science/example.pdb
new file mode 100644
index 00000000..9cf25c80
--- /dev/null
+++ b/frontend/workspace/e2e/science/example.pdb
@@ -0,0 +1,7 @@
+HEADER    MINIMAL GLYCINE
+ATOM      1  N   GLY A   1       0.000   0.000   0.000  1.00 20.00           N
+ATOM      2  CA  GLY A   1       1.458   0.000   0.000  1.00 20.00           C
+ATOM      3  C   GLY A   1       1.958   1.420   0.000  1.00 20.00           C
+ATOM      4  O   GLY A   1       1.220   2.390   0.000  1.00 20.00           O
+TER
+END
diff --git a/frontend/workspace/e2e/science/ligand.sdf b/frontend/workspace/e2e/science/ligand.sdf
new file mode 100644
index 00000000..444667e8
--- /dev/null
+++ b/frontend/workspace/e2e/science/ligand.sdf
@@ -0,0 +1,9 @@
+ethane
+OpenScience
+
+  2  1  0  0  0  0            999 V2000
+    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.5400    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0  0  0  0
+M  END
+$$$$
diff --git a/frontend/workspace/e2e/science/water.xyz b/frontend/workspace/e2e/science/water.xyz
new file mode 100644
index 00000000..401cfafa
--- /dev/null
+++ b/frontend/workspace/e2e/science/water.xyz
@@ -0,0 +1,5 @@
+3
+water
+O 0.000000 0.000000 0.000000
+H 0.758602 0.000000 0.504284
+H -0.758602 0.000000 0.504284

From 9c91233a800a9782fa32b683c5852597e72f69b9 Mon Sep 17 00:00:00 2001
From: Aayam Bansal <aayambansal@gmail.com>
Date: Wed, 29 Jul 2026 06:05:53 +0800
Subject: [PATCH 04/40] feat: add native notebook workbench

---
 backend/cli/src/server/routes/notebook.ts     | 137 ++++
 backend/cli/src/server/server.ts              |   2 +
 backend/cli/src/tool/notebook.ts              |   4 +
 backend/cli/src/tool/rkernel.ts               |   4 +
 backend/cli/test/server/notebook.test.ts      |  81 +++
 frontend/workspace/e2e/notebook.spec.ts       |  76 ++
 frontend/workspace/src/atlas/FilePreview.tsx  |  20 +-
 .../workspace/src/notebook/NotebookView.tsx   | 678 ++++++++++++++++++
 frontend/workspace/src/notebook/model.test.ts | 175 +++++
 frontend/workspace/src/notebook/model.ts      | 145 ++++
 frontend/workspace/src/science/files.test.ts  |   4 +-
 11 files changed, 1322 insertions(+), 4 deletions(-)
 create mode 100644 backend/cli/src/server/routes/notebook.ts
 create mode 100644 backend/cli/test/server/notebook.test.ts
 create mode 100644 frontend/workspace/e2e/notebook.spec.ts
 create mode 100644 frontend/workspace/src/notebook/NotebookView.tsx
 create mode 100644 frontend/workspace/src/notebook/model.test.ts
 create mode 100644 frontend/workspace/src/notebook/model.ts

diff --git a/backend/cli/src/server/routes/notebook.ts b/backend/cli/src/server/routes/notebook.ts
new file mode 100644
index 00000000..e95dedef
--- /dev/null
+++ b/backend/cli/src/server/routes/notebook.ts
@@ -0,0 +1,137 @@
+import { Hono } from "hono"
+import { describeRoute, validator } from "hono-openapi"
+import z from "zod"
+import { Instance } from "../../project/instance"
+import { pythonKernels } from "../../tool/notebook"
+import { rKernels } from "../../tool/rkernel"
+import type { ExecuteResult, KernelOutput } from "../../science/kernel/types"
+import { Provenance } from "../../science/provenance/store"
+import { lazy } from "../../util/lazy"
+
+const Language = z.enum(["python", "r"])
+const Key = z.object({
+  id: z.string().trim().min(1).max(1024),
+  language: Language,
+})
+const Execute = Key.extend({
+  code: z.string().max(2_000_000),
+  timeout: z.number().int().min(5_000).max(600_000).optional(),
+})
+
+type Language = z.infer<typeof Language>
+
+const manager = (language: Language) => (language === "r" ? rKernels : pythonKernels)
+
+const key = (id: string) => `notebook-${Bun.hash(`${Instance.directory}\0${id}`).toString(36)}`
+
+function output(value: KernelOutput, execution: number | null) {
+  if (value.type === "stream") {
+    return {
+      output_type: "stream",
+      name: value.name ?? "stdout",
+      text: value.data?.["text/plain"] ?? "",
+    }
+  }
+  if (value.type === "error") {
+    return {
+      output_type: "error",
+      ename: value.error?.name ?? "Error",
+      evalue: value.error?.message ?? "Kernel execution failed",
+      traceback: value.error?.traceback ?? [],
+    }
+  }
+  return {
+    output_type: value.type === "result" ? "execute_result" : "display_data",
+    data: value.data ?? {},
+    metadata: {},
+    ...(value.type === "result" ? { execution_count: execution } : {}),
+  }
+}
+
+function response(result: ExecuteResult) {
+  const execution = result.executionCount ?? null
+  return {
+    ok: result.ok,
+    execution_count: execution,
+    outputs: result.outputs.map((value) => output(value, execution)),
+  }
+}
+
+export const NotebookRoutes = lazy(() =>
+  new Hono()
+    .post(
+      "/execute",
+      describeRoute({
+        summary: "Execute a notebook cell",
+        description: "Execute code in a persistent project-scoped Python or R kernel.",
+        operationId: "notebook.execute",
+        responses: { 200: { description: "Jupyter-compatible cell outputs" } },
+      }),
+      validator("json", Execute),
+      async (c) => {
+        const body = c.req.valid("json")
+        const kernel = await manager(body.language).get(key(body.id), { cwd: Instance.directory })
+        const result = await kernel.execute(body.code, { timeout: body.timeout })
+        const node = await Provenance.record({
+          kind: "run",
+          label: `${body.language} cell · ${body.id}`.slice(0, 140),
+          tool: "notebook",
+          sessionID: body.id,
+          inputs: {
+            path: body.id,
+            language: body.language,
+            code: body.code,
+          },
+          status: result.ok ? "ok" : "error",
+          meta: {
+            directory: Instance.directory,
+            executionCount: result.executionCount ?? null,
+            outputTypes: result.outputs.map((value) => value.type),
+          },
+        } as Parameters<typeof Provenance.record>[0])
+        return c.json({ ...response(result), provenance_id: node.id })
+      },
+    )
+    .get(
+      "/status",
+      describeRoute({
+        summary: "Get notebook kernel status",
+        operationId: "notebook.status",
+        responses: { 200: { description: "Kernel state" } },
+      }),
+      validator("query", Key),
+      (c) => {
+        const query = c.req.valid("query")
+        return c.json({ active: manager(query.language).active(key(query.id)), language: query.language })
+      },
+    )
+    .post(
+      "/restart",
+      describeRoute({
+        summary: "Restart a notebook kernel",
+        operationId: "notebook.restart",
+        responses: { 200: { description: "Kernel state" } },
+      }),
+      validator("json", Key),
+      async (c) => {
+        const body = c.req.valid("json")
+        await manager(body.language).release(key(body.id))
+        return c.json({ active: false, language: body.language })
+      },
+    )
+    .post(
+      "/interrupt",
+      describeRoute({
+        summary: "Interrupt a notebook kernel",
+        description: "Stop the running cell and release its kernel. The next execution starts a fresh kernel.",
+        operationId: "notebook.interrupt",
+        responses: { 200: { description: "Kernel state" } },
+      }),
+      validator("json", Key),
+      async (c) => {
+        const body = c.req.valid("json")
+        await manager(body.language).release(key(body.id))
+        return c.json({ active: false, language: body.language })
+      },
+    ),
+)
diff --git a/backend/cli/src/server/server.ts b/backend/cli/src/server/server.ts
index b95e192b..ea076f02 100644
--- a/backend/cli/src/server/server.ts
+++ b/backend/cli/src/server/server.ts
@@ -29,6 +29,7 @@ import { SessionRoutes } from "./routes/session"
 import { PtyRoutes } from "./routes/pty"
 import { McpRoutes } from "./routes/mcp"
 import { FileRoutes } from "./routes/file"
+import { NotebookRoutes } from "./routes/notebook"
 import { ConfigRoutes } from "./routes/config"
 import { ExperimentalRoutes } from "./routes/experimental"
 import { ProviderRoutes } from "./routes/provider"
@@ -278,6 +279,7 @@ export namespace Server {
         .route("/question", QuestionRoutes())
         .route("/provider", ProviderRoutes())
         .route("/", FileRoutes())
+        .route("/notebook", NotebookRoutes())
         .route("/mcp", McpRoutes())
         .route("/settings/skills", SettingsSkillsRoutes())
         .route("/settings/memory", MemorySettingsRoutes())
diff --git a/backend/cli/src/tool/notebook.ts b/backend/cli/src/tool/notebook.ts
index 75c7b8b5..d111d7af 100644
--- a/backend/cli/src/tool/notebook.ts
+++ b/backend/cli/src/tool/notebook.ts
@@ -418,6 +418,10 @@ class PythonKernelManager implements KernelManager {
     this.kernels.delete(sessionID)
   }
 
+  active(sessionID: string): boolean {
+    return this.kernels.get(sessionID)?.ready ?? false
+  }
+
   async shutdownAll(): Promise<void> {
     for (const [id, k] of this.kernels) {
       await k.shutdown()
diff --git a/backend/cli/src/tool/rkernel.ts b/backend/cli/src/tool/rkernel.ts
index 6774cffc..4d859f5a 100644
--- a/backend/cli/src/tool/rkernel.ts
+++ b/backend/cli/src/tool/rkernel.ts
@@ -382,6 +382,10 @@ class RKernelManager implements KernelManager {
     this.kernels.delete(sessionID)
   }
 
+  active(sessionID: string): boolean {
+    return this.kernels.get(sessionID)?.ready ?? false
+  }
+
   async shutdownAll(): Promise<void> {
     for (const [id, k] of this.kernels) {
       await k.shutdown()
diff --git a/backend/cli/test/server/notebook.test.ts b/backend/cli/test/server/notebook.test.ts
new file mode 100644
index 00000000..851ad11e
--- /dev/null
+++ b/backend/cli/test/server/notebook.test.ts
@@ -0,0 +1,81 @@
+import { describe, expect, test } from "bun:test"
+import { NotebookRoutes } from "../../src/server/routes/notebook"
+import { Instance } from "../../src/project/instance"
+import { tmpdir } from "../fixture/fixture"
+import { Provenance } from "../../src/science/provenance/store"
+
+describe("/notebook routes", () => {
+  test("executes cells in a persistent project-scoped Python kernel", async () => {
+    await using tmp = await tmpdir({ git: true })
+    await Instance.provide({
+      directory: tmp.path,
+      fn: async () => {
+        const app = NotebookRoutes()
+        const first = await app.request("/execute", {
+          method: "POST",
+          headers: { "Content-Type": "application/json" },
+          body: JSON.stringify({ id: "analysis.ipynb", language: "python", code: "value = 41" }),
+        })
+        expect(first.status).toBe(200)
+
+        const second = await app.request("/execute", {
+          method: "POST",
+          headers: { "Content-Type": "application/json" },
+          body: JSON.stringify({ id: "analysis.ipynb", language: "python", code: "value + 1" }),
+        })
+        const result = (await second.json()) as {
+          ok: boolean
+          provenance_id: string
+          execution_count: number
+          outputs: Array<{
+            output_type: string
+            data?: Record<string, string>
+            execution_count?: number
+            metadata?: object
+          }>
+        }
+
+        expect(second.status).toBe(200)
+        expect(result.ok).toBe(true)
+        expect(result.provenance_id).toMatch(/^[a-f0-9]{16}$/)
+        expect(result.execution_count).toBe(2)
+        expect(result.outputs).toContainEqual({
+          output_type: "execute_result",
+          execution_count: 2,
+          data: { "text/plain": "42" },
+          metadata: {},
+        })
+        expect(await Provenance.get(result.provenance_id)).toMatchObject({
+          kind: "run",
+          tool: "notebook",
+          status: "ok",
+          inputs: {
+            path: "analysis.ipynb",
+            language: "python",
+            code: "value + 1",
+          },
+        })
+
+        const status = await app.request("/status?id=analysis.ipynb&language=python")
+        expect(await status.json()).toEqual({ active: true, language: "python" })
+
+        const restart = await app.request("/restart", {
+          method: "POST",
+          headers: { "Content-Type": "application/json" },
+          body: JSON.stringify({ id: "analysis.ipynb", language: "python" }),
+        })
+        expect(await restart.json()).toEqual({ active: false, language: "python" })
+      },
+    })
+  }, 30_000)
+
+  test("validates notebook execution input", async () => {
+    const response = await NotebookRoutes().request("/execute", {
+      method: "POST",
+      headers: { "Content-Type": "application/json" },
+      body: JSON.stringify({ id: "", language: "julia", code: "" }),
+    })
+
+    expect(response.status).toBe(400)
+  })
+})
diff --git a/frontend/workspace/e2e/notebook.spec.ts b/frontend/workspace/e2e/notebook.spec.ts
new file mode 100644
index 00000000..76f6091e
--- /dev/null
+++ b/frontend/workspace/e2e/notebook.spec.ts
@@ -0,0 +1,76 @@
+import { mkdtempSync, readFileSync, rmSync, writeFileSync } from "node:fs"
+import { tmpdir } from "node:os"
+import path from "node:path"
+import { test, expect } from "./fixtures"
+
+test("opens, executes, edits, and saves a native Jupyter notebook", async ({ page, gotoSession }) => {
+  const directory = mkdtempSync(path.join(tmpdir(), "openscience-notebook-e2e-"))
+  const filename = "analysis.ipynb"
+  const filepath = path.join(directory, filename)
+  writeFileSync(
+    filepath,
+    JSON.stringify(
+      {
+        cells: [
+          { cell_type: "markdown", id: "intro", metadata: {}, source: ["# Experiment\n", "Persistent kernel"] },
+          {
+            cell_type: "code",
+            id: "setup",
+            metadata: {},
+            source: ["value = 41"],
+            execution_count: null,
+            outputs: [],
+          },
+          {
+            cell_type: "code",
+            id: "result",
+            metadata: {},
+            source: ["value + 1"],
+            execution_count: null,
+            outputs: [],
+          },
+        ],
+        metadata: { kernelspec: { display_name: "Python 3", language: "python", name: "python3" } },
+        nbformat: 4,
+        nbformat_minor: 5,
+      },
+      null,
+      2,
+    ),
+  )
+
+  try {
+    await gotoSession()
+    await page.getByRole("tab", { name: "Files", exact: true }).click()
+    const location = page.getByPlaceholder("/absolute/path")
+    await location.fill(directory)
+    await location.press("Enter")
+    await page.getByPlaceholder("filter this folder…").fill(filename)
+    await page.getByRole("button", { name: new RegExp(`^${filename}\\b`) }).click()
+
+    const notebook = page.locator('[data-component="notebook"]')
+    await expect(notebook).toBeVisible()
+    await expect(notebook.getByText("Experiment", { exact: true })).toBeVisible()
+    await expect(notebook.locator('[data-cell-type="code"]')).toHaveCount(2)
+
+    await notebook.locator('[data-action="run-all"]').click()
+    await expect(notebook.getByText("42", { exact: true })).toBeVisible({ timeout: 20_000 })
+    await expect(notebook.getByLabel("Kernel ready")).toBeVisible()
+
+    const result = notebook.getByLabel("code cell 3")
+    await result.fill("value + 2")
+    await notebook.locator('[data-cell-id="result"] [data-action="run-cell"]').click()
+    await expect(notebook.getByText("43", { exact: true })).toBeVisible()
+
+    await page.getByRole("button", { name: "save", exact: true }).click()
+    await expect.poll(() => JSON.parse(readFileSync(filepath, "utf8")).cells[2].source).toEqual(["value + 2"])
+    await expect
+      .poll(() => JSON.parse(readFileSync(filepath, "utf8")).cells[2].outputs[0].data["text/plain"])
+      .toBe("43")
+    await expect
+      .poll(() => JSON.parse(readFileSync(filepath, "utf8")).cells[2].metadata.openscience.provenance_id)
+      .toMatch(/^[a-f0-9]{16}$/)
+  } finally {
+    rmSync(directory, { recursive: true, force: true })
+  }
+})
diff --git a/frontend/workspace/src/atlas/FilePreview.tsx b/frontend/workspace/src/atlas/FilePreview.tsx
index 6e4934d3..5dc27cfc 100644
--- a/frontend/workspace/src/atlas/FilePreview.tsx
+++ b/frontend/workspace/src/atlas/FilePreview.tsx
@@ -19,6 +19,7 @@ import { FONT_MONO, FONT_SANS, FONT_CODE } from "@/styles/tokens"
 import { PdfViewer } from "@/science/renderers/documents/PdfViewer"
 import { ScienceArtifact } from "@/science/ScienceArtifact"
 import { detectScientificFile } from "@/science/files"
+import { NotebookView } from "@/notebook/NotebookView"
 import { toast } from "@/atlas/Toast"
 import { IconFile, IconX, IconCopy, IconDownload, IconBookOpen, IconBraces, IconRefresh } from "@/atlas/shared/Icon"
 
@@ -101,7 +102,7 @@ const LANG: Record<string, string> = {
   log: "text",
 }
 
-type Kind = "markdown" | "pdf" | "image" | "science" | "code" | "binary"
+type Kind = "markdown" | "notebook" | "pdf" | "image" | "science" | "code" | "binary"
 
 type FileData = { content?: string; encoding?: string; mimeType?: string }
 
@@ -163,6 +164,7 @@ export function FileView(props: {
       return "binary"
     }
     if (x === "md" || x === "markdown" || x === "mdx") return "markdown"
+    if (x === "ipynb") return "notebook"
     if (x === "pdf") return "pdf"
     if (scientific()) return "science"
     // .tex / .latex / .sty / .cls are source files → highlighted "code" view
@@ -219,7 +221,7 @@ export function FileView(props: {
     } catch {}
   }
 
-  const toggleable = () => kind() === "markdown" || kind() === "science" || kind() === "code"
+  const toggleable = () => kind() === "markdown" || kind() === "notebook" || kind() === "science" || kind() === "code"
 
   return (
     <div
@@ -409,6 +411,17 @@ export function FileView(props: {
                 </div>
               </Match>
 
+              {/* notebook */}
+              <Match when={kind() === "notebook" && !showSource()}>
+                <NotebookView
+                  path={props.path}
+                  directory={directory()}
+                  text={draft()}
+                  onChange={setDraft}
+                  onRaw={() => setShowSource(true)}
+                />
+              </Match>
+
               {/* pdf */}
               <Match when={kind() === "pdf"}>
                 <div style={{ padding: "14px" }}>
@@ -477,7 +490,7 @@ export function FileView(props: {
               </Match>
 
               {/* code / text — editable source, or highlighted read view */}
-              <Match when={(kind() === "code" || kind() === "science") && showSource()}>
+              <Match when={(kind() === "code" || kind() === "science" || kind() === "notebook") && showSource()}>
                 <textarea
                   value={draft()}
                   spellcheck={false}
@@ -577,6 +590,7 @@ export function FilePreview(props: { path: string; onClose: () => void }): JSX.E
 
 function langFor(k: Kind, x: string): string {
   if (k === "markdown") return "markdown"
+  if (k === "notebook") return "json"
   return LANG[x] ?? "text"
 }
 
diff --git a/frontend/workspace/src/notebook/NotebookView.tsx b/frontend/workspace/src/notebook/NotebookView.tsx
new file mode 100644
index 00000000..c2238538
--- /dev/null
+++ b/frontend/workspace/src/notebook/NotebookView.tsx
@@ -0,0 +1,678 @@
+import { For, Show, createMemo, createSignal, onMount, type JSX } from "solid-js"
+import { Markdown } from "@synsci/ui/markdown"
+import { useSDK } from "@/context/sdk"
+import { usePlatform } from "@/context/platform"
+import { FONT_CODE, FONT_MONO, FONT_SANS } from "@/styles/tokens"
+import {
+  clearOutputs,
+  createCell,
+  insertCell,
+  moveCell,
+  parseNotebook,
+  removeCell,
+  serializeNotebook,
+  sourceText,
+  updateSource,
+  type NotebookCell,
+  type NotebookDocument,
+  type NotebookOutput,
+} from "./model"
+
+type Language = "python" | "r"
+type State = "idle" | "ready" | "running" | "error"
+
+type Execution = {
+  ok: boolean
+  provenance_id: string
+  execution_count: number | null
+  outputs: NotebookOutput[]
+}
+
+const record = (value: unknown): value is Record<string, unknown> =>
+  typeof value === "object" && value !== null && !Array.isArray(value)
+
+const valueText = (value: unknown) => {
+  if (typeof value === "string") return value
+  if (Array.isArray(value)) return value.map((part) => String(part)).join("")
+  if (value === undefined || value === null) return ""
+  return JSON.stringify(value, null, 2)
+}
+
+const languageOf = (notebook: NotebookDocument): Language => {
+  const spec = record(notebook.metadata.kernelspec) ? notebook.metadata.kernelspec : {}
+  const info = record(notebook.metadata.language_info) ? notebook.metadata.language_info : {}
+  const name = String(spec.language ?? spec.name ?? info.name ?? "python").toLowerCase()
+  return name === "r" || name.startsWith("ir") ? "r" : "python"
+}
+
+export function NotebookView(props: {
+  path: string
+  directory: string
+  text: string
+  onChange: (text: string) => void
+  onRaw: () => void
+}): JSX.Element {
+  const sdk = useSDK()
+  const platform = usePlatform()
+  const [state, setState] = createSignal<State>("idle")
+  const [running, setRunning] = createSignal<string[]>([])
+  const [editing, setEditing] = createSignal<string>()
+  const [error, setError] = createSignal("")
+
+  const parsed = createMemo(() => {
+    try {
+      return { notebook: parseNotebook(props.text), error: "" }
+    } catch (cause) {
+      return {
+        notebook: undefined,
+        error: cause instanceof Error ? cause.message : "Invalid notebook JSON",
+      }
+    }
+  })
+  const notebook = () => parsed().notebook
+  const language = () => (notebook() ? languageOf(notebook()!) : "python")
+  const busy = () => running().length > 0
+  const endpoint = (path: string) =>
+    `${sdk.url.replace(/\/$/, "")}/notebook/${path}?directory=${encodeURIComponent(props.directory)}`
+  const send = platform.fetch ?? fetch
+
+  const apply = (next: NotebookDocument) => props.onChange(serializeNotebook(next))
+  const replace = (index: number, next: NotebookCell) => {
+    const current = notebook()
+    if (!current) return
+    apply({
+      ...current,
+      cells: current.cells.map((cell, position) => (position === index ? next : cell)),
+    })
+  }
+
+  const call = async (path: "restart" | "interrupt") => {
+    setError("")
+    const response = await send(endpoint(path), {
+      method: "POST",
+      headers: { "Content-Type": "application/json" },
+      body: JSON.stringify({ id: props.path, language: language() }),
+    })
+    if (!response.ok) throw new Error(`${path} failed (${response.status})`)
+    setState("idle")
+  }
+
+  const runCell = async (index: number) => {
+    const current = notebook()
+    const cell = current?.cells[index]
+    if (!current || !cell || cell.cell_type !== "code" || busy()) return
+
+    setRunning([cell.id])
+    setState("running")
+    setError("")
+    try {
+      const response = await send(endpoint("execute"), {
+        method: "POST",
+        headers: { "Content-Type": "application/json" },
+        body: JSON.stringify({
+          id: props.path,
+          language: language(),
+          code: sourceText(cell),
+        }),
+      })
+      const result = (await response.json()) as Execution | { error?: string; message?: string }
+      if (!response.ok || !("outputs" in result)) {
+        throw new Error(
+          ("message" in result && result.message) || ("error" in result && result.error) || "execution failed",
+        )
+      }
+      replace(index, {
+        ...cell,
+        metadata: {
+          ...cell.metadata,
+          openscience: {
+            ...(record(cell.metadata.openscience) ? cell.metadata.openscience : {}),
+            provenance_id: result.provenance_id,
+            language: language(),
+            executed_at: new Date().toISOString(),
+          },
+        },
+        execution_count: result.execution_count,
+        outputs: result.outputs,
+      })
+      setState(result.ok ? "ready" : "error")
+    } catch (cause) {
+      const message = cause instanceof Error ? cause.message : String(cause)
+      replace(index, {
+        ...cell,
+        execution_count: null,
+        outputs: [{ output_type: "error", ename: "ExecutionError", evalue: message, traceback: [] }],
+      })
+      setError(message)
+      setState("error")
+    } finally {
+      setRunning([])
+    }
+  }
+
+  const runAll = async () => {
+    const cells = notebook()?.cells ?? []
+    for (const cell of cells) {
+      if (cell.cell_type !== "code") continue
+      const index = notebook()?.cells.findIndex((value) => value.id === cell.id) ?? -1
+      await runCell(index)
+    }
+  }
+
+  const setLanguage = (next: Language) => {
+    const current = notebook()
+    if (!current || next === language()) return
+    apply({
+      ...current,
+      metadata: {
+        ...current.metadata,
+        kernelspec:
+          next === "r"
+            ? { display_name: "R", language: "R", name: "ir" }
+            : { display_name: "Python 3", language: "python", name: "python3" },
+        language_info: { name: next },
+      },
+    })
+    void call("restart").catch((cause) => setError(cause instanceof Error ? cause.message : String(cause)))
+  }
+
+  onMount(() => {
+    void send(`${endpoint("status")}&id=${encodeURIComponent(props.path)}&language=${encodeURIComponent(language())}`)
+      .then((response) => response.json())
+      .then((result: { active?: boolean }) => setState(result.active ? "ready" : "idle"))
+      .catch(() => setState("idle"))
+  })
+
+  return (
+    <div
+      data-component="notebook"
+      style={{
+        height: "100%",
+        "min-height": "100%",
+        display: "flex",
+        "flex-direction": "column",
+        background:
+          "radial-gradient(circle at 50% -20%, color-mix(in srgb, var(--color-accent) 8%, transparent), transparent 38%), var(--color-bg-subtle)",
+      }}
+    >
+      <Show
+        when={notebook()}
+        fallback={
+          <div style={empty()}>
+            <div style={{ "font-family": FONT_SANS, "font-size": "15px", "font-weight": 600 }}>
+              This notebook needs repair
+            </div>
+            <div style={{ "font-family": FONT_MONO, "font-size": "11px", color: "var(--color-text-faint)" }}>
+              {parsed().error}
+            </div>
+            <button type="button" style={button(true)} onClick={props.onRaw}>
+              open raw JSON
+            </button>
+          </div>
+        }
+      >
+        {(document) => (
+          <>
+            <div
+              style={{
+                position: "sticky",
+                top: 0,
+                "z-index": 4,
+                display: "flex",
+                "align-items": "center",
+                gap: "8px",
+                padding: "9px max(16px, calc((100% - 920px) / 2))",
+                border: "0",
+                "border-bottom": "1px solid var(--color-border)",
+                background: "color-mix(in srgb, var(--color-bg) 94%, transparent)",
+                "backdrop-filter": "blur(14px)",
+              }}
+            >
+              <select
+                aria-label="Notebook kernel"
+                value={language()}
+                disabled={busy()}
+                onChange={(event) => setLanguage(event.currentTarget.value as Language)}
+                style={select()}
+              >
+                <option value="python">Python 3</option>
+                <option value="r">R</option>
+              </select>
+              <span
+                aria-label={`Kernel ${state()}`}
+                style={{
+                  width: "6px",
+                  height: "6px",
+                  "border-radius": "50%",
+                  background:
+                    state() === "running"
+                      ? "var(--color-warning, #d99b35)"
+                      : state() === "error"
+                        ? "var(--color-danger, #d85b5b)"
+                        : state() === "ready"
+                          ? "var(--color-success, #4a9b71)"
+                          : "var(--color-text-faint)",
+                  "box-shadow":
+                    state() === "running" ? "0 0 0 4px color-mix(in srgb, #d99b35 18%, transparent)" : "none",
+                }}
+              />
+              <span style={{ "font-family": FONT_MONO, "font-size": "10px", color: "var(--color-text-faint)" }}>
+                {state()}
+              </span>
+              <div style={{ flex: 1 }} />
+              <button
+                type="button"
+                data-action="run-all"
+                disabled={busy()}
+                style={button(true)}
+                onClick={() => void runAll()}
+              >
+                {busy() ? "running…" : "run all"}
+              </button>
+              <button
+                type="button"
+                data-action="interrupt-kernel"
+                disabled={!busy()}
+                style={button()}
+                onClick={() => void call("interrupt").catch((cause) => setError(String(cause)))}
+              >
+                interrupt
+              </button>
+              <button
+                type="button"
+                data-action="restart-kernel"
+                style={button()}
+                onClick={() => void call("restart").catch((cause) => setError(String(cause)))}
+              >
+                restart
+              </button>
+              <button type="button" style={button()} onClick={() => apply(clearOutputs(document()))}>
+                clear outputs
+              </button>
+            </div>
+
+            <Show when={error()}>
+              <div
+                role="alert"
+                style={{
+                  margin: "12px auto 0",
+                  width: "min(calc(100% - 32px), 920px)",
+                  padding: "9px 12px",
+                  "box-sizing": "border-box",
+                  border: "1px solid color-mix(in srgb, var(--color-danger, #d85b5b) 40%, var(--color-border))",
+                  "border-radius": "6px",
+                  background: "color-mix(in srgb, var(--color-danger, #d85b5b) 8%, var(--color-bg))",
+                  "font-family": FONT_MONO,
+                  "font-size": "11px",
+                  color: "var(--color-text-muted)",
+                }}
+              >
+                {error()}
+              </div>
+            </Show>
+
+            <div
+              style={{
+                width: "min(calc(100% - 32px), 920px)",
+                margin: "0 auto",
+                padding: "22px 0 80px",
+                display: "flex",
+                "flex-direction": "column",
+                gap: "12px",
+              }}
+            >
+              <For each={document().cells}>
+                {(cell, index) => (
+                  <NotebookCellView
+                    cell={cell}
+                    index={index()}
+                    running={running().includes(cell.id)}
+                    editing={editing() === cell.id}
+                    onEdit={() => setEditing(cell.id)}
+                    onDone={() => setEditing(undefined)}
+                    onSource={(text) => replace(index(), updateSource(cell, text))}
+                    onRun={() => void runCell(index())}
+                    onDelete={() => apply(removeCell(document(), index()))}
+                    onUp={() => apply(moveCell(document(), index(), index() - 1))}
+                    onDown={() => apply(moveCell(document(), index(), index() + 1))}
+                  />
+                )}
+              </For>
+
+              <div style={{ display: "flex", "justify-content": "center", gap: "8px", padding: "10px 0" }}>
+                <button
+                  type="button"
+                  style={button()}
+                  onClick={() => apply(insertCell(document(), document().cells.length, createCell("code")))}
+                >
+                  + code
+                </button>
+                <button
+                  type="button"
+                  style={button()}
+                  onClick={() => apply(insertCell(document(), document().cells.length, createCell("markdown")))}
+                >
+                  + text
+                </button>
+              </div>
+            </div>
+          </>
+        )}
+      </Show>
+    </div>
+  )
+}
+
+function NotebookCellView(props: {
+  cell: NotebookCell
+  index: number
+  running: boolean
+  editing: boolean
+  onEdit: () => void
+  onDone: () => void
+  onSource: (text: string) => void
+  onRun: () => void
+  onDelete: () => void
+  onUp: () => void
+  onDown: () => void
+}): JSX.Element {
+  const code = () => props.cell.cell_type === "code"
+  const outputs = () => (Array.isArray(props.cell.outputs) ? props.cell.outputs : [])
+  const keydown = (event: KeyboardEvent) => {
+    if (!code() || !event.shiftKey || event.key !== "Enter") return
+    event.preventDefault()
+    props.onRun()
+  }
+
+  return (
+    <section
+      data-cell-id={props.cell.id}
+      data-cell-type={props.cell.cell_type}
+      style={{
+        display: "grid",
+        "grid-template-columns": "52px minmax(0, 1fr)",
+        border: "1px solid var(--color-border)",
+        "border-radius": "8px",
+        background: "var(--color-bg)",
+        "box-shadow": "0 1px 0 color-mix(in srgb, var(--color-text) 3%, transparent)",
+        overflow: "hidden",
+      }}
+    >
+      <div
+        style={{
+          display: "flex",
+          "flex-direction": "column",
+          "align-items": "center",
+          gap: "8px",
+          padding: "12px 6px",
+          "border-right": "1px solid var(--color-border)",
+          background: "color-mix(in srgb, var(--color-bg-subtle) 72%, var(--color-bg))",
+        }}
+      >
+        <Show
+          when={code()}
+          fallback={
+            <span style={{ "font-family": FONT_MONO, "font-size": "9px", color: "var(--color-text-faint)" }}>TXT</span>
+          }
+        >
+          <button
+            type="button"
+            data-action="run-cell"
+            title="Run cell (Shift+Enter)"
+            disabled={props.running}
+            onClick={props.onRun}
+            style={runButton(props.running)}
+          >
+            {props.running ? "■" : "▶"}
+          </button>
+          <span style={{ "font-family": FONT_MONO, "font-size": "9px", color: "var(--color-text-faint)" }}>
+            [{props.cell.execution_count ?? " "}]
+          </span>
+        </Show>
+      </div>
+
+      <div style={{ "min-width": 0 }}>
+        <div
+          style={{
+            height: "28px",
+            display: "flex",
+            "align-items": "center",
+            "justify-content": "flex-end",
+            gap: "2px",
+            padding: "0 6px",
+            "border-bottom": code() ? "1px solid var(--color-border)" : "none",
+          }}
+        >
+          <Show when={!code()}>
+            <button type="button" style={mini()} onClick={props.onEdit}>
+              {props.editing ? "editing" : "edit"}
+            </button>
+          </Show>
+          <button type="button" title="Move up" style={mini()} onClick={props.onUp}>
+            ↑
+          </button>
+          <button type="button" title="Move down" style={mini()} onClick={props.onDown}>
+            ↓
+          </button>
+          <button type="button" title="Delete cell" style={mini()} onClick={props.onDelete}>
+            ×
+          </button>
+        </div>
+
+        <Show
+          when={code() || props.editing}
+          fallback={
+            <button
+              type="button"
+              onDblClick={props.onEdit}
+              style={{
+                all: "unset",
+                display: "block",
+                width: "100%",
+                "box-sizing": "border-box",
+                padding: "4px 18px 18px",
+                cursor: "text",
+              }}
+            >
+              <Show
+                when={sourceText(props.cell).trim()}
+                fallback={
+                  <span style={{ "font-family": FONT_SANS, "font-size": "13px", color: "var(--color-text-faint)" }}>
+                    Empty text cell — double-click to edit
+                  </span>
+                }
+              >
+                <Markdown class="atlas-md" text={sourceText(props.cell)} />
+              </Show>
+            </button>
+          }
+        >
+          <textarea
+            aria-label={`${props.cell.cell_type} cell ${props.index + 1}`}
+            value={sourceText(props.cell)}
+            autofocus={props.editing}
+            spellcheck={!code()}
+            onInput={(event) => props.onSource(event.currentTarget.value)}
+            onBlur={() => !code() && props.onDone()}
+            onKeyDown={keydown}
+            style={{
+              all: "unset",
+              display: "block",
+              width: "100%",
+              "min-height": code() ? "84px" : "110px",
+              "box-sizing": "border-box",
+              padding: code() ? "14px 16px 16px" : "12px 18px 18px",
+              "font-family": code() ? FONT_CODE : FONT_SANS,
+              "font-size": code() ? "12px" : "13px",
+              "line-height": code() ? 1.65 : 1.6,
+              color: "var(--color-text)",
+              resize: "vertical",
+              "tab-size": 2,
+            }}
+          />
+        </Show>
+
+        <Show when={code() && outputs().length}>
+          <div
+            data-slot="notebook-output"
+            style={{
+              border: "0",
+              "border-top": "1px solid var(--color-border)",
+              background: "color-mix(in srgb, var(--color-bg-subtle) 50%, var(--color-bg))",
+            }}
+          >
+            <For each={outputs()}>{(output) => <NotebookOutputView output={output} />}</For>
+            <Show when={record(props.cell.metadata.openscience) && props.cell.metadata.openscience.provenance_id}>
+              <div
+                title="Local reproducibility record"
+                style={{
+                  padding: "6px 16px",
+                  "font-family": FONT_MONO,
+                  "font-size": "9px",
+                  color: "var(--color-text-faint)",
+                }}
+              >
+                provenance · {String((props.cell.metadata.openscience as Record<string, unknown>).provenance_id)}
+              </div>
+            </Show>
+          </div>
+        </Show>
+      </div>
+    </section>
+  )
+}
+
+function NotebookOutputView(props: { output: NotebookOutput }): JSX.Element {
+  const data = () => (record(props.output.data) ? props.output.data : {})
+  const png = () => valueText(data()["image/png"])
+  const svg = () => valueText(data()["image/svg+xml"])
+  const html = () => valueText(data()["text/html"])
+  const json = () => data()["application/json"]
+  const plain = () =>
+    props.output.output_type === "stream" ? valueText(props.output.text) : valueText(data()["text/plain"])
+  const traceback = () =>
+    Array.isArray(props.output.traceback)
+      ? props.output.traceback.map((line) => String(line)).join("\n")
+      : `${valueText(props.output.ename)}: ${valueText(props.output.evalue)}`
+
+  return (
+    <div style={{ padding: "12px 16px", "border-bottom": "1px solid var(--color-border)" }}>
+      <Show when={props.output.output_type === "error"}>
+        <pre style={pre("var(--color-danger, #bd4d4d)")}>{traceback()}</pre>
+      </Show>
+      <Show when={props.output.output_type !== "error"}>
+        <Show when={png()}>
+          <img
+            alt="Notebook output"
+            src={`data:image/png;base64,${png()}`}
+            style={{ display: "block", "max-width": "100%", height: "auto", "border-radius": "4px" }}
+          />
+        </Show>
+        <Show when={!png() && svg()}>
+          <img
+            alt="Notebook output"
+            src={`data:image/svg+xml;charset=utf-8,${encodeURIComponent(svg())}`}
+            style={{ display: "block", "max-width": "100%", height: "auto" }}
+          />
+        </Show>
+        <Show when={!png() && !svg() && html()}>
+          <iframe
+            title="Notebook HTML output"
+            sandbox=""
+            srcdoc={`<!doctype html><meta charset="utf-8"><style>body{font:13px system-ui;margin:8px;color:#202124}table{border-collapse:collapse}td,th{padding:5px 8px;border:1px solid #ddd}</style>${html()}`}
+            style={{ width: "100%", height: "220px", border: "0", background: "white", "border-radius": "4px" }}
+          />
+        </Show>
+        <Show when={!png() && !svg() && !html() && json() !== undefined}>
+          <pre style={pre()}>{valueText(json())}</pre>
+        </Show>
+        <Show when={!png() && !svg() && !html() && json() === undefined && plain()}>
+          <pre style={pre(props.output.name === "stderr" ? "var(--color-danger, #bd4d4d)" : undefined)}>{plain()}</pre>
+        </Show>
+      </Show>
+    </div>
+  )
+}
+
+function button(primary = false): JSX.CSSProperties {
+  return {
+    cursor: "pointer",
+    padding: "5px 10px",
+    border: primary ? "1px solid var(--color-text)" : "1px solid var(--color-border)",
+    "border-radius": "5px",
+    background: primary ? "var(--color-text)" : "var(--color-bg)",
+    color: primary ? "var(--color-bg)" : "var(--color-text-muted)",
+    "font-family": FONT_MONO,
+    "font-size": "10px",
+    "font-weight": 600,
+  }
+}
+
+function mini(): JSX.CSSProperties {
+  return {
+    all: "unset",
+    cursor: "pointer",
+    padding: "3px 5px",
+    "border-radius": "3px",
+    "font-family": FONT_MONO,
+    "font-size": "9px",
+    color: "var(--color-text-faint)",
+  }
+}
+
+function runButton(active: boolean): JSX.CSSProperties {
+  return {
+    cursor: active ? "wait" : "pointer",
+    width: "26px",
+    height: "26px",
+    display: "grid",
+    "place-items": "center",
+    padding: 0,
+    border: "1px solid var(--color-border)",
+    "border-radius": "5px",
+    background: active ? "var(--color-text)" : "var(--color-bg)",
+    color: active ? "var(--color-bg)" : "var(--color-text-muted)",
+    "font-size": "9px",
+  }
+}
+
+function select(): JSX.CSSProperties {
+  return {
+    height: "27px",
+    padding: "0 26px 0 9px",
+    border: "1px solid var(--color-border)",
+    "border-radius": "5px",
+    background: "var(--color-bg)",
+    color: "var(--color-text)",
+    "font-family": FONT_MONO,
+    "font-size": "10px",
+  }
+}
+
+function pre(color = "var(--color-text-muted)"): JSX.CSSProperties {
+  return {
+    margin: 0,
+    "white-space": "pre-wrap",
+    "overflow-wrap": "anywhere",
+    "font-family": FONT_CODE,
+    "font-size": "11px",
+    "line-height": 1.55,
+    color,
+  }
+}
+
+function empty(): JSX.CSSProperties {
+  return {
+    flex: 1,
+    display: "flex",
+    "flex-direction": "column",
+    "align-items": "center",
+    "justify-content": "center",
+    gap: "12px",
+    padding: "32px",
+    "text-align": "center",
+    color: "var(--color-text)",
+  }
+}
+
+export default NotebookView
diff --git a/frontend/workspace/src/notebook/model.test.ts b/frontend/workspace/src/notebook/model.test.ts
new file mode 100644
index 00000000..6b5352dc
--- /dev/null
+++ b/frontend/workspace/src/notebook/model.test.ts
@@ -0,0 +1,175 @@
+import { describe, expect, test } from "bun:test"
+import { readFileSync } from "node:fs"
+import { fileURLToPath } from "node:url"
+import {
+  clearOutputs,
+  createCell,
+  insertCell,
+  moveCell,
+  parseNotebook,
+  removeCell,
+  serializeNotebook,
+  sourceText,
+  updateSource,
+} from "./model"
+
+const read = (path: string) => readFileSync(fileURLToPath(new URL(path, import.meta.url)), "utf8")
+
+describe("notebook document model", () => {
+  test("normalizes nbformat cells while preserving unknown fields", () => {
+    const notebook = parseNotebook(
+      JSON.stringify({
+        cells: [
+          {
+            cell_type: "code",
+            execution_count: null,
+            metadata: { tags: ["analysis"] },
+            outputs: [],
+            source: "value = 41\nvalue + 1",
+            vendor: { retained: true },
+          },
+        ],
+        metadata: {
+          kernelspec: { display_name: "Python 3", language: "python", name: "python3" },
+          custom: { retained: true },
+        },
+        nbformat: 4,
+        nbformat_minor: 5,
+        vendor_root: "retained",
+      }),
+    )
+
+    expect(notebook.cells).toHaveLength(1)
+    expect(notebook.cells[0]?.cell_type).toBe("code")
+    expect(notebook.cells[0]?.id).toMatch(/^cell-[a-z0-9]+$/)
+    expect(notebook.cells[0]?.source).toEqual(["value = 41\n", "value + 1"])
+    expect(notebook.cells[0]?.metadata).toEqual({ tags: ["analysis"] })
+    expect(notebook.cells[0]?.vendor).toEqual({ retained: true })
+    expect(notebook.metadata.custom).toEqual({ retained: true })
+    expect(notebook.vendor_root).toBe("retained")
+  })
+
+  test("serializes normalized notebooks as valid nbformat JSON", () => {
+    const notebook = parseNotebook(
+      JSON.stringify({
+        cells: [{ cell_type: "markdown", metadata: {}, source: ["# Result\n", "Useful text"] }],
+        metadata: {},
+        nbformat: 4,
+        nbformat_minor: 5,
+      }),
+    )
+
+    const serialized = serializeNotebook(notebook)
+    const saved = JSON.parse(serialized) as Record<string, unknown>
+
+    expect(serialized.endsWith("\n")).toBe(true)
+    expect(saved.nbformat).toBe(4)
+    expect(saved.nbformat_minor).toBe(5)
+    expect(saved.cells).toEqual(notebook.cells)
+  })
+
+  test("rejects malformed notebook JSON without discarding the source", () => {
+    expect(() => parseNotebook('{"cells": [}')).toThrow("Invalid notebook JSON")
+  })
+
+  test("creates editable code and markdown cells with stable ids", () => {
+    const code = createCell("code", "answer = 42")
+    const markdown = createCell("markdown", "## Notes")
+
+    expect(code).toMatchObject({
+      cell_type: "code",
+      execution_count: null,
+      metadata: {},
+      outputs: [],
+      source: ["answer = 42"],
+    })
+    expect(markdown).toMatchObject({
+      cell_type: "markdown",
+      metadata: {},
+      source: ["## Notes"],
+    })
+    expect(code.id).toMatch(/^cell-[a-z0-9]+$/)
+    expect(markdown.id).toMatch(/^cell-[a-z0-9]+$/)
+    expect(code.id).not.toBe(markdown.id)
+  })
+
+  test("round-trips source text without losing line breaks", () => {
+    const cell = createCell("code", "first()\nsecond()\n")
+    const updated = updateSource(cell, "alpha\n\nomega")
+
+    expect(sourceText(cell)).toBe("first()\nsecond()\n")
+    expect(updated.source).toEqual(["alpha\n", "\n", "omega"])
+    expect(sourceText(updated)).toBe("alpha\n\nomega")
+  })
+
+  test("inserts, moves, and removes cells without mutating the notebook", () => {
+    const notebook = parseNotebook(
+      JSON.stringify({
+        cells: [
+          { cell_type: "markdown", id: "intro", metadata: {}, source: ["Intro"] },
+          { cell_type: "code", id: "analysis", metadata: {}, source: ["run()"], outputs: [], execution_count: null },
+        ],
+        metadata: {},
+        nbformat: 4,
+        nbformat_minor: 5,
+      }),
+    )
+    const inserted = insertCell(notebook, 1, createCell("code", "setup()"))
+    const moved = moveCell(inserted, 2, 0)
+    const removed = removeCell(moved, 1)
+
+    expect(notebook.cells.map((value) => value.id)).toEqual(["intro", "analysis"])
+    expect(inserted.cells.map((value) => value.id)).toEqual(["intro", inserted.cells[1]?.id, "analysis"])
+    expect(moved.cells.map((value) => value.id)).toEqual(["analysis", "intro", inserted.cells[1]?.id])
+    expect(removed.cells.map((value) => value.id)).toEqual(["analysis", inserted.cells[1]?.id])
+  })
+
+  test("clears code outputs and execution counts while retaining other cells", () => {
+    const notebook = parseNotebook(
+      JSON.stringify({
+        cells: [
+          {
+            cell_type: "code",
+            id: "executed",
+            metadata: {},
+            source: ["1 + 1"],
+            execution_count: 7,
+            outputs: [{ output_type: "execute_result", data: { "text/plain": ["2"] }, execution_count: 7 }],
+          },
+          { cell_type: "markdown", id: "notes", metadata: {}, source: ["Result"] },
+        ],
+        metadata: {},
+        nbformat: 4,
+        nbformat_minor: 5,
+      }),
+    )
+
+    const cleared = clearOutputs(notebook)
+
+    expect(cleared.cells[0]?.outputs).toEqual([])
+    expect(cleared.cells[0]?.execution_count).toBeNull()
+    expect(cleared.cells[1]).toEqual(notebook.cells[1])
+    expect(notebook.cells[0]?.outputs).toHaveLength(1)
+  })
+})
+
+describe("notebook file integration", () => {
+  test("routes ipynb files through the native notebook editor", () => {
+    const preview = read("../atlas/FilePreview.tsx")
+
+    expect(preview).toContain('import { NotebookView } from "@/notebook/NotebookView"')
+    expect(preview).toContain('"notebook"')
+    expect(preview).toContain("<NotebookView")
+  })
+
+  test("notebook editor exposes cell and kernel controls", () => {
+    const view = read("./NotebookView.tsx")
+
+    expect(view).toContain('data-component="notebook"')
+    expect(view).toContain('data-action="run-cell"')
+    expect(view).toContain('data-action="run-all"')
+    expect(view).toContain('data-action="restart-kernel"')
+    expect(view).toContain('data-action="interrupt-kernel"')
+    expect(view).toContain('data-slot="notebook-output"')
+  })
+})
diff --git a/frontend/workspace/src/notebook/model.ts b/frontend/workspace/src/notebook/model.ts
new file mode 100644
index 00000000..6dbd4d34
--- /dev/null
+++ b/frontend/workspace/src/notebook/model.ts
@@ -0,0 +1,145 @@
+export type NotebookOutput = Record<string, unknown> & {
+  output_type: string
+}
+
+export type NotebookCell = Record<string, unknown> & {
+  cell_type: "code" | "markdown" | "raw"
+  id: string
+  metadata: Record<string, unknown>
+  source: string[]
+  execution_count?: number | null
+  outputs?: NotebookOutput[]
+}
+
+export type NotebookDocument = Record<string, unknown> & {
+  cells: NotebookCell[]
+  metadata: Record<string, unknown>
+  nbformat: number
+  nbformat_minor: number
+}
+
+const record = (value: unknown): value is Record<string, unknown> =>
+  typeof value === "object" && value !== null && !Array.isArray(value)
+
+const lines = (source: string) => source.match(/[^\n]*\n|[^\n]+$/g) ?? []
+
+const id = () => `cell-${globalThis.crypto.randomUUID().replaceAll("-", "").slice(0, 12)}`
+
+const source = (value: unknown) => {
+  if (typeof value === "string") return lines(value)
+  if (Array.isArray(value) && value.every((part) => typeof part === "string")) return value
+  return []
+}
+
+const cell = (value: unknown): NotebookCell => {
+  if (!record(value)) throw new Error("cells must contain objects")
+  const kind = value.cell_type
+  if (kind !== "code" && kind !== "markdown" && kind !== "raw") {
+    throw new Error("cells must have a supported cell_type")
+  }
+
+  const base: NotebookCell = {
+    ...value,
+    cell_type: kind,
+    id: typeof value.id === "string" && value.id ? value.id : id(),
+    metadata: record(value.metadata) ? value.metadata : {},
+    source: source(value.source),
+  }
+  if (kind !== "code") return base
+
+  return {
+    ...base,
+    execution_count: typeof value.execution_count === "number" ? value.execution_count : null,
+    outputs: Array.isArray(value.outputs)
+      ? value.outputs.filter(
+          (output): output is NotebookOutput => record(output) && typeof output.output_type === "string",
+        )
+      : [],
+  }
+}
+
+export function parseNotebook(text: string): NotebookDocument {
+  try {
+    const value: unknown = JSON.parse(text)
+    if (!record(value) || !Array.isArray(value.cells)) throw new Error("missing cells")
+
+    return {
+      ...value,
+      cells: value.cells.map(cell),
+      metadata: record(value.metadata) ? value.metadata : {},
+      nbformat: typeof value.nbformat === "number" ? value.nbformat : 4,
+      nbformat_minor: typeof value.nbformat_minor === "number" ? value.nbformat_minor : 5,
+    }
+  } catch (error) {
+    const reason = error instanceof Error ? error.message : "unknown error"
+    throw new Error(`Invalid notebook JSON: ${reason}`)
+  }
+}
+
+export function serializeNotebook(notebook: NotebookDocument) {
+  return `${JSON.stringify(notebook, null, 2)}\n`
+}
+
+export function createCell(kind: "code" | "markdown" | "raw", text = ""): NotebookCell {
+  const base: NotebookCell = {
+    cell_type: kind,
+    id: id(),
+    metadata: {},
+    source: lines(text),
+  }
+  if (kind !== "code") return base
+
+  return {
+    ...base,
+    execution_count: null,
+    outputs: [],
+  }
+}
+
+export function sourceText(value: NotebookCell) {
+  return value.source.join("")
+}
+
+export function updateSource(value: NotebookCell, text: string): NotebookCell {
+  return {
+    ...value,
+    source: lines(text),
+  }
+}
+
+export function insertCell(notebook: NotebookDocument, index: number, value: NotebookCell): NotebookDocument {
+  const cells = notebook.cells.slice()
+  cells.splice(Math.max(0, Math.min(index, cells.length)), 0, value)
+  return { ...notebook, cells }
+}
+
+export function removeCell(notebook: NotebookDocument, index: number): NotebookDocument {
+  if (index < 0 || index >= notebook.cells.length) return notebook
+  return {
+    ...notebook,
+    cells: notebook.cells.filter((_, position) => position !== index),
+  }
+}
+
+export function moveCell(notebook: NotebookDocument, from: number, to: number): NotebookDocument {
+  if (from < 0 || from >= notebook.cells.length || from === to) return notebook
+  const cells = notebook.cells.slice()
+  const value = cells.splice(from, 1)[0]
+  if (!value) return notebook
+  cells.splice(Math.max(0, Math.min(to, cells.length)), 0, value)
+  return { ...notebook, cells }
+}
+
+export function clearOutputs(notebook: NotebookDocument): NotebookDocument {
+  return {
+    ...notebook,
+    cells: notebook.cells.map((value) => {
+      if (value.cell_type !== "code") return value
+      return {
+        ...value,
+        execution_count: null,
+        outputs: [],
+      }
+    }),
+  }
+}
diff --git a/frontend/workspace/src/science/files.test.ts b/frontend/workspace/src/science/files.test.ts
index a078aab9..1f024671 100644
--- a/frontend/workspace/src/science/files.test.ts
+++ b/frontend/workspace/src/science/files.test.ts
@@ -91,7 +91,9 @@ describe("scientific file viewer integration", () => {
 
     expect(preview).toContain('import { detectScientificFile } from "@/science/files"')
     expect(preview).toContain('import { ScienceArtifact } from "@/science/ScienceArtifact"')
-    expect(preview).toContain('type Kind = "markdown" | "pdf" | "image" | "science" | "code" | "binary"')
+    expect(preview).toContain(
+      'type Kind = "markdown" | "notebook" | "pdf" | "image" | "science" | "code" | "binary"',
+    )
     expect(preview).toContain("<ScienceArtifact")
   })
 })

From ce012da8d22fabd827e164b8c750ddc15ff8d9a1 Mon Sep 17 00:00:00 2001
From: Aayam Bansal <aayambansal@gmail.com>
Date: Wed, 29 Jul 2026 06:08:11 +0800
Subject: [PATCH 05/40] feat: add notebook diff and exports

---
 frontend/workspace/e2e/notebook.spec.ts       |  11 +-
 frontend/workspace/src/atlas/FilePreview.tsx  |   4 +
 .../workspace/src/notebook/NotebookView.tsx   | 170 +++++++++++++++++-
 frontend/workspace/src/notebook/model.test.ts |  73 ++++++++
 frontend/workspace/src/notebook/model.ts      |  87 +++++++++
 5 files changed, 343 insertions(+), 2 deletions(-)

diff --git a/frontend/workspace/e2e/notebook.spec.ts b/frontend/workspace/e2e/notebook.spec.ts
index 76f6091e..9fdeb229 100644
--- a/frontend/workspace/e2e/notebook.spec.ts
+++ b/frontend/workspace/e2e/notebook.spec.ts
@@ -59,10 +59,19 @@ test("opens, executes, edits, and saves a native Jupyter notebook", async ({ pag
 
     const result = notebook.getByLabel("code cell 3")
     await result.fill("value + 2")
+    await notebook.locator('[data-action="notebook-diff"]').click()
+    await expect(page.getByRole("dialog", { name: "Notebook changes" })).toBeVisible()
+    await page.getByRole("dialog", { name: "Notebook changes" }).getByRole("button", { name: "close" }).click()
+
+    await notebook.locator('[data-action="notebook-export"]').click()
+    const download = page.waitForEvent("download")
+    await page.getByRole("menuitem", { name: "Python script (.py)" }).click()
+    expect((await download).suggestedFilename()).toBe("analysis.py")
+
     await notebook.locator('[data-cell-id="result"] [data-action="run-cell"]').click()
     await expect(notebook.getByText("43", { exact: true })).toBeVisible()
 
-    await page.getByRole("button", { name: "save", exact: true }).click()
+    await page.keyboard.press("Control+s")
     await expect.poll(() => JSON.parse(readFileSync(filepath, "utf8")).cells[2].source).toEqual(["value + 2"])
     await expect
       .poll(() => JSON.parse(readFileSync(filepath, "utf8")).cells[2].outputs[0].data["text/plain"])
diff --git a/frontend/workspace/src/atlas/FilePreview.tsx b/frontend/workspace/src/atlas/FilePreview.tsx
index 5dc27cfc..ff5195f0 100644
--- a/frontend/workspace/src/atlas/FilePreview.tsx
+++ b/frontend/workspace/src/atlas/FilePreview.tsx
@@ -417,7 +417,11 @@ export function FileView(props: {
                   path={props.path}
                   directory={directory()}
                   text={draft()}
+                  savedText={savedText()}
+                  dirty={dirty()}
+                  saving={saving()}
                   onChange={setDraft}
+                  onSave={() => void save()}
                   onRaw={() => setShowSource(true)}
                 />
               </Match>
diff --git a/frontend/workspace/src/notebook/NotebookView.tsx b/frontend/workspace/src/notebook/NotebookView.tsx
index c2238538..dfab9e19 100644
--- a/frontend/workspace/src/notebook/NotebookView.tsx
+++ b/frontend/workspace/src/notebook/NotebookView.tsx
@@ -1,11 +1,15 @@
-import { For, Show, createMemo, createSignal, onMount, type JSX } from "solid-js"
+import { For, Show, createMemo, createSignal, onCleanup, onMount, type JSX } from "solid-js"
 import { Markdown } from "@synsci/ui/markdown"
+import { Diff } from "@synsci/ui/diff"
 import { useSDK } from "@/context/sdk"
 import { usePlatform } from "@/context/platform"
 import { FONT_CODE, FONT_MONO, FONT_SANS } from "@/styles/tokens"
 import {
   clearOutputs,
   createCell,
+  exportHtml,
+  exportMarkdown,
+  exportScript,
   insertCell,
   moveCell,
   parseNotebook,
@@ -49,7 +53,11 @@ export function NotebookView(props: {
   path: string
   directory: string
   text: string
+  savedText: string
+  dirty: boolean
+  saving: boolean
   onChange: (text: string) => void
+  onSave: () => void
   onRaw: () => void
 }): JSX.Element {
   const sdk = useSDK()
@@ -58,6 +66,8 @@ export function NotebookView(props: {
   const [running, setRunning] = createSignal<string[]>([])
   const [editing, setEditing] = createSignal<string>()
   const [error, setError] = createSignal("")
+  const [diff, setDiff] = createSignal(false)
+  const [exports, setExports] = createSignal(false)
 
   const parsed = createMemo(() => {
     try {
@@ -176,7 +186,54 @@ export function NotebookView(props: {
     void call("restart").catch((cause) => setError(cause instanceof Error ? cause.message : String(cause)))
   }
 
+  const snapshot = (text: string) => {
+    try {
+      return exportScript(parseNotebook(text), language())
+    } catch {
+      return text
+    }
+  }
+
+  const download = (format: "script" | "markdown" | "html") => {
+    const current = notebook()
+    if (!current) return
+    const base =
+      props.path
+        .split("/")
+        .pop()
+        ?.replace(/\.ipynb$/i, "") || "notebook"
+    const output =
+      format === "script"
+        ? exportScript(current, language())
+        : format === "markdown"
+          ? exportMarkdown(current, language())
+          : exportHtml(current, base)
+    const extension = format === "script" ? (language() === "r" ? "r" : "py") : format === "markdown" ? "md" : "html"
+    const url = URL.createObjectURL(new Blob([output], { type: "text/plain;charset=utf-8" }))
+    const anchor = document.createElement("a")
+    anchor.href = url
+    anchor.download = `${base}.${extension}`
+    anchor.click()
+    URL.revokeObjectURL(url)
+    setExports(false)
+  }
+
   onMount(() => {
+    const onKey = (event: KeyboardEvent) => {
+      if (!(event.metaKey || event.ctrlKey)) return
+      if (event.key.toLowerCase() === "s") {
+        event.preventDefault()
+        props.onSave()
+        return
+      }
+      if (event.shiftKey && event.key === "Enter") {
+        event.preventDefault()
+        void runAll()
+      }
+    }
+    window.addEventListener("keydown", onKey)
+    onCleanup(() => window.removeEventListener("keydown", onKey))
+
     void send(`${endpoint("status")}&id=${encodeURIComponent(props.path)}&language=${encodeURIComponent(language())}`)
       .then((response) => response.json())
       .then((result: { active?: boolean }) => setState(result.active ? "ready" : "idle"))
@@ -189,6 +246,7 @@ export function NotebookView(props: {
       style={{
         height: "100%",
         "min-height": "100%",
+        position: "relative",
         display: "flex",
         "flex-direction": "column",
         background:
@@ -226,6 +284,7 @@ export function NotebookView(props: {
                 "border-bottom": "1px solid var(--color-border)",
                 background: "color-mix(in srgb, var(--color-bg) 94%, transparent)",
                 "backdrop-filter": "blur(14px)",
+                overflow: "visible",
               }}
             >
               <select
@@ -260,6 +319,56 @@ export function NotebookView(props: {
                 {state()}
               </span>
               <div style={{ flex: 1 }} />
+              <button
+                type="button"
+                data-action="notebook-diff"
+                disabled={!props.dirty}
+                style={button()}
+                onClick={() => setDiff(true)}
+              >
+                diff
+              </button>
+              <div style={{ position: "relative" }}>
+                <button
+                  type="button"
+                  data-action="notebook-export"
+                  style={button()}
+                  onClick={() => setExports((value) => !value)}
+                >
+                  export
+                </button>
+                <Show when={exports()}>
+                  <div
+                    role="menu"
+                    aria-label="Export notebook"
+                    style={{
+                      position: "absolute",
+                      top: "32px",
+                      right: 0,
+                      width: "160px",
+                      padding: "5px",
+                      display: "flex",
+                      "flex-direction": "column",
+                      gap: "2px",
+                      border: "1px solid var(--color-border-strong)",
+                      "border-radius": "7px",
+                      background: "var(--color-bg)",
+                      "box-shadow": "0 12px 32px rgba(0,0,0,0.18)",
+                      "z-index": 8,
+                    }}
+                  >
+                    <button type="button" role="menuitem" style={menu()} onClick={() => download("script")}>
+                      {language() === "r" ? "R script (.r)" : "Python script (.py)"}
+                    </button>
+                    <button type="button" role="menuitem" style={menu()} onClick={() => download("markdown")}>
+                      Markdown report
+                    </button>
+                    <button type="button" role="menuitem" style={menu()} onClick={() => download("html")}>
+                      Standalone HTML
+                    </button>
+                  </div>
+                </Show>
+              </div>
               <button
                 type="button"
                 data-action="run-all"
@@ -289,6 +398,11 @@ export function NotebookView(props: {
               <button type="button" style={button()} onClick={() => apply(clearOutputs(document()))}>
                 clear outputs
               </button>
+              <Show when={props.dirty}>
+                <button type="button" disabled={props.saving} style={button(true)} onClick={props.onSave}>
+                  {props.saving ? "saving…" : "save"}
+                </button>
+              </Show>
             </div>
 
             <Show when={error()}>
@@ -356,6 +470,48 @@ export function NotebookView(props: {
                 </button>
               </div>
             </div>
+
+            <Show when={diff()}>
+              <div
+                role="dialog"
+                aria-label="Notebook changes"
+                style={{
+                  position: "absolute",
+                  inset: 0,
+                  "z-index": 12,
+                  display: "flex",
+                  "flex-direction": "column",
+                  background: "var(--color-bg)",
+                }}
+              >
+                <div
+                  style={{
+                    height: "46px",
+                    display: "flex",
+                    "align-items": "center",
+                    gap: "10px",
+                    padding: "0 14px",
+                    "border-bottom": "1px solid var(--color-border)",
+                  }}
+                >
+                  <strong style={{ "font-family": FONT_SANS, "font-size": "13px" }}>Notebook changes</strong>
+                  <span style={{ "font-family": FONT_MONO, "font-size": "10px", color: "var(--color-text-faint)" }}>
+                    saved checkpoint → working copy
+                  </span>
+                  <div style={{ flex: 1 }} />
+                  <button type="button" style={button()} onClick={() => setDiff(false)}>
+                    close
+                  </button>
+                </div>
+                <div class="atlas-scroll" style={{ flex: 1, "min-height": 0, overflow: "auto" }}>
+                  <Diff
+                    before={{ name: props.path, contents: snapshot(props.savedText) }}
+                    after={{ name: props.path, contents: snapshot(props.text) }}
+                    diffStyle="split"
+                  />
+                </div>
+              </div>
+            </Show>
           </>
         )}
       </Show>
@@ -620,6 +776,18 @@ function mini(): JSX.CSSProperties {
   }
 }
 
+function menu(): JSX.CSSProperties {
+  return {
+    all: "unset",
+    cursor: "pointer",
+    padding: "8px 9px",
+    "border-radius": "4px",
+    "font-family": FONT_SANS,
+    "font-size": "11px",
+    color: "var(--color-text-muted)",
+  }
+}
+
 function runButton(active: boolean): JSX.CSSProperties {
   return {
     cursor: active ? "wait" : "pointer",
diff --git a/frontend/workspace/src/notebook/model.test.ts b/frontend/workspace/src/notebook/model.test.ts
index 6b5352dc..363bef3e 100644
--- a/frontend/workspace/src/notebook/model.test.ts
+++ b/frontend/workspace/src/notebook/model.test.ts
@@ -4,6 +4,9 @@ import { fileURLToPath } from "node:url"
 import {
   clearOutputs,
   createCell,
+  exportHtml,
+  exportMarkdown,
+  exportScript,
   insertCell,
   moveCell,
   parseNotebook,
@@ -151,6 +154,73 @@ describe("notebook document model", () => {
     expect(cleared.cells[1]).toEqual(notebook.cells[1])
     expect(notebook.cells[0]?.outputs).toHaveLength(1)
   })
+
+  test("exports a notebook as an executable percent-format script", () => {
+    const notebook = parseNotebook(
+      JSON.stringify({
+        cells: [
+          { cell_type: "markdown", id: "intro", metadata: {}, source: ["# Analysis\n", "Important context"] },
+          {
+            cell_type: "code",
+            id: "code",
+            metadata: {},
+            source: ["answer = 42\n", "answer"],
+            execution_count: 1,
+            outputs: [],
+          },
+        ],
+        metadata: {},
+        nbformat: 4,
+        nbformat_minor: 5,
+      }),
+    )
+
+    expect(exportScript(notebook, "python")).toBe(
+      "# %% [markdown]\n# # Analysis\n# Important context\n\n# %%\nanswer = 42\nanswer\n",
+    )
+    expect(exportScript(notebook, "r")).toContain("# %%\nanswer = 42")
+  })
+
+  test("exports Markdown with code fences and readable outputs", () => {
+    const notebook = parseNotebook(
+      JSON.stringify({
+        cells: [
+          { cell_type: "markdown", id: "intro", metadata: {}, source: ["# Analysis"] },
+          {
+            cell_type: "code",
+            id: "code",
+            metadata: {},
+            source: ["print(42)"],
+            execution_count: 1,
+            outputs: [{ output_type: "stream", name: "stdout", text: ["42\n"] }],
+          },
+        ],
+        metadata: {},
+        nbformat: 4,
+        nbformat_minor: 5,
+      }),
+    )
+
+    expect(exportMarkdown(notebook, "python")).toBe("# Analysis\n\n```python\nprint(42)\n```\n\n```text\n42\n\n```\n")
+  })
+
+  test("exports a standalone escaped HTML report", () => {
+    const notebook = parseNotebook(
+      JSON.stringify({
+        cells: [{ cell_type: "code", id: "code", metadata: {}, source: ["value < 4"], outputs: [] }],
+        metadata: {},
+        nbformat: 4,
+        nbformat_minor: 5,
+      }),
+    )
+
+    const html = exportHtml(notebook, "Analysis")
+
+    expect(html).toContain("<!doctype html>")
+    expect(html).toContain("<title>Analysis</title>")
+    expect(html).toContain("value &lt; 4")
+    expect(html).not.toContain("value < 4")
+  })
 })
 
 describe("notebook file integration", () => {
@@ -170,6 +240,9 @@ describe("notebook file integration", () => {
     expect(view).toContain('data-action="run-all"')
     expect(view).toContain('data-action="restart-kernel"')
     expect(view).toContain('data-action="interrupt-kernel"')
+    expect(view).toContain('data-action="notebook-diff"')
+    expect(view).toContain('data-action="notebook-export"')
     expect(view).toContain('data-slot="notebook-output"')
+    expect(view).toContain('event.key.toLowerCase() === "s"')
   })
 })
diff --git a/frontend/workspace/src/notebook/model.ts b/frontend/workspace/src/notebook/model.ts
index 6dbd4d34..32639cc9 100644
--- a/frontend/workspace/src/notebook/model.ts
+++ b/frontend/workspace/src/notebook/model.ts
@@ -143,3 +143,90 @@ export function clearOutputs(notebook: NotebookDocument): NotebookDocument {
     }),
   }
 }
+
+const outputText = (value: NotebookOutput) => {
+  if (value.output_type === "stream") {
+    if (Array.isArray(value.text)) return value.text.map(String).join("")
+    return typeof value.text === "string" ? value.text : ""
+  }
+  if (value.output_type === "error") {
+    if (Array.isArray(value.traceback)) return value.traceback.map(String).join("\n")
+    return `${String(value.ename ?? "Error")}: ${String(value.evalue ?? "")}`
+  }
+  if (!record(value.data)) return ""
+  const plain = value.data["text/plain"]
+  if (Array.isArray(plain)) return plain.map(String).join("")
+  return typeof plain === "string" ? plain : ""
+}
+
+export function exportScript(notebook: NotebookDocument, language: "python" | "r") {
+  const comment = language === "r" ? "# " : "# "
+  const cells = notebook.cells.map((value) => {
+    const text = sourceText(value)
+    if (value.cell_type === "code") return `# %%\n${text}`
+    const body = text
+      .split("\n")
+      .map((line) => `${comment}${line}`)
+      .join("\n")
+    return `# %% [${value.cell_type}]\n${body}`
+  })
+  return `${cells.join("\n\n")}\n`
+}
+
+export function exportMarkdown(notebook: NotebookDocument, language: "python" | "r") {
+  const cells = notebook.cells.flatMap((value) => {
+    const text = sourceText(value)
+    if (value.cell_type === "markdown") return [text]
+    if (value.cell_type === "raw") return [`\`\`\`text\n${text}\n\`\`\``]
+
+    const code = `\`\`\`${language}\n${text}\n\`\`\``
+    const outputs = (value.outputs ?? [])
+      .map(outputText)
+      .filter(Boolean)
+      .map((output) => `\`\`\`text\n${output}\n\`\`\``)
+    return [code, ...outputs]
+  })
+  return `${cells.join("\n\n")}\n`
+}
+
+const escapeHtml = (value: string) =>
+  value.replaceAll("&", "&amp;").replaceAll("<", "&lt;").replaceAll(">", "&gt;").replaceAll('"', "&quot;")
+
+export function exportHtml(notebook: NotebookDocument, title: string) {
+  const cells = notebook.cells
+    .map((value) => {
+      const text = escapeHtml(sourceText(value))
+      if (value.cell_type === "markdown") return `<section class="markdown"><pre>${text}</pre></section>`
+      if (value.cell_type === "raw") return `<section class="raw"><pre>${text}</pre></section>`
+      const outputs = (value.outputs ?? [])
+        .map(outputText)
+        .filter(Boolean)
+        .map((output) => `<pre class="output">${escapeHtml(output)}</pre>`)
+        .join("")
+      return `<section class="cell"><pre class="code"><code>${text}</code></pre>${outputs}</section>`
+    })
+    .join("\n")
+
+  return `<!doctype html>
+<html lang="en">
+<head>
+  <meta charset="utf-8">
+  <meta name="viewport" content="width=device-width, initial-scale=1">
+  <title>${escapeHtml(title)}</title>
+  <style>
+    :root { color-scheme: light dark; font: 15px/1.6 ui-sans-serif, system-ui, sans-serif; }
+    body { max-width: 920px; margin: 0 auto; padding: 48px 24px 96px; background: Canvas; color: CanvasText; }
+    section { margin: 0 0 18px; }
+    pre { margin: 0; white-space: pre-wrap; overflow-wrap: anywhere; }
+    .markdown pre { font: inherit; }
+    .code, .output { padding: 16px 18px; border: 1px solid color-mix(in srgb, CanvasText 14%, Canvas); border-radius: 8px; font: 13px/1.6 ui-monospace, monospace; }
+    .code { background: color-mix(in srgb, CanvasText 4%, Canvas); }
+    .output { margin-top: 8px; border-color: color-mix(in srgb, CanvasText 9%, Canvas); }
+  </style>
+</head>
+<body>
+${cells}
+</body>
+</html>
+`
+}

From f3725ac245000572b87654b8553be2870248408f Mon Sep 17 00:00:00 2001
From: Aayam Bansal <aayambansal@gmail.com>
Date: Wed, 29 Jul 2026 06:13:45 +0800
Subject: [PATCH 06/40] feat: add interactive data table workbench

---
 frontend/workspace/e2e/data-table.spec.ts     |  50 ++
 frontend/workspace/src/atlas/FilePreview.tsx  |  29 +-
 frontend/workspace/src/data/DataTableView.tsx | 553 ++++++++++++++++++
 frontend/workspace/src/data/table.test.ts     |  97 +++
 frontend/workspace/src/data/table.ts          | 188 ++++++
 frontend/workspace/src/science/files.test.ts  |   2 +-
 6 files changed, 915 insertions(+), 4 deletions(-)
 create mode 100644 frontend/workspace/e2e/data-table.spec.ts
 create mode 100644 frontend/workspace/src/data/DataTableView.tsx
 create mode 100644 frontend/workspace/src/data/table.test.ts
 create mode 100644 frontend/workspace/src/data/table.ts

diff --git a/frontend/workspace/e2e/data-table.spec.ts b/frontend/workspace/e2e/data-table.spec.ts
new file mode 100644
index 00000000..57d6f44b
--- /dev/null
+++ b/frontend/workspace/e2e/data-table.spec.ts
@@ -0,0 +1,50 @@
+import { mkdtempSync, rmSync, writeFileSync } from "node:fs"
+import { tmpdir } from "node:os"
+import path from "node:path"
+import { test, expect } from "./fixtures"
+
+test("explores, filters, plots, sorts, and exports a scientific CSV", async ({ page, gotoSession }) => {
+  const directory = mkdtempSync(path.join(tmpdir(), "openscience-table-e2e-"))
+  const filename = "expression.csv"
+  writeFileSync(
+    path.join(directory, filename),
+    'gene,count,passed,condition\nTP53,12,true,control\nEGFR,4,false,treated\nBRCA1,,true,control\nMYC,20,true,"treated, high"\n',
+  )
+
+  try {
+    await gotoSession()
+    await page.getByRole("tab", { name: "Files", exact: true }).click()
+    const location = page.getByPlaceholder("/absolute/path")
+    await location.fill(directory)
+    await location.press("Enter")
+    await page.getByPlaceholder("filter this folder…").fill(filename)
+    await page.getByRole("button", { name: new RegExp(`^${filename}\\b`) }).click()
+
+    const table = page.locator('[data-component="data-table"]')
+    await expect(table).toBeVisible()
+    await expect(table.getByText("4 rows", { exact: true })).toBeVisible()
+    await expect(table.getByText("treated, high", { exact: true })).toBeVisible()
+
+    const filter = table.getByLabel("Filter rows")
+    await filter.fill("EGFR")
+    await expect(table.getByText("1 matches", { exact: true })).toBeVisible()
+    await expect(table.getByText("EGFR", { exact: true })).toBeVisible()
+    await expect(table.getByText("TP53", { exact: true })).toHaveCount(0)
+
+    await filter.fill("")
+    await table.locator('[data-action="table-schema"]').click()
+    await expect(table.getByText("1 missing", { exact: true })).toBeVisible()
+    await expect(table.getByText("number", { exact: true })).toBeVisible()
+
+    await table.getByTitle("Sort by count").click()
+    await table.locator('[data-action="table-plot"]').click()
+    await expect(table.getByRole("img", { name: "count histogram" })).toBeVisible()
+    await expect(table.getByText("mean 12", { exact: true })).toBeVisible()
+
+    const download = page.waitForEvent("download")
+    await table.locator('[data-action="table-export"]').click()
+    expect((await download).suggestedFilename()).toBe("expression.filtered.csv")
+  } finally {
+    rmSync(directory, { recursive: true, force: true })
+  }
+})
diff --git a/frontend/workspace/src/atlas/FilePreview.tsx b/frontend/workspace/src/atlas/FilePreview.tsx
index ff5195f0..710942e5 100644
--- a/frontend/workspace/src/atlas/FilePreview.tsx
+++ b/frontend/workspace/src/atlas/FilePreview.tsx
@@ -20,6 +20,8 @@ import { PdfViewer } from "@/science/renderers/documents/PdfViewer"
 import { ScienceArtifact } from "@/science/ScienceArtifact"
 import { detectScientificFile } from "@/science/files"
 import { NotebookView } from "@/notebook/NotebookView"
+import { DataTableView } from "@/data/DataTableView"
+import type { TableFormat } from "@/data/table"
 import { toast } from "@/atlas/Toast"
 import { IconFile, IconX, IconCopy, IconDownload, IconBookOpen, IconBraces, IconRefresh } from "@/atlas/shared/Icon"
 
@@ -102,7 +104,7 @@ const LANG: Record<string, string> = {
   log: "text",
 }
 
-type Kind = "markdown" | "notebook" | "pdf" | "image" | "science" | "code" | "binary"
+type Kind = "markdown" | "notebook" | "table" | "pdf" | "image" | "science" | "code" | "binary"
 
 type FileData = { content?: string; encoding?: string; mimeType?: string }
 
@@ -155,6 +157,11 @@ export function FileView(props: {
   const text = () => (!data() || isBinary() ? "" : (data()!.content ?? ""))
   const dirty = () => draft() !== savedText()
   const scientific = createMemo(() => (isBinary() ? undefined : detectScientificFile(e(), draft())))
+  const tabular = createMemo<TableFormat | undefined>(() => {
+    if (isBinary()) return
+    if (e() === "csv" || e() === "tsv" || e() === "jsonl") return e() as TableFormat
+    if (e() === "json" && draft().trimStart().startsWith("[")) return "json"
+  })
 
   const kind = createMemo<Kind>(() => {
     const x = e()
@@ -165,6 +172,7 @@ export function FileView(props: {
     }
     if (x === "md" || x === "markdown" || x === "mdx") return "markdown"
     if (x === "ipynb") return "notebook"
+    if (tabular()) return "table"
     if (x === "pdf") return "pdf"
     if (scientific()) return "science"
     // .tex / .latex / .sty / .cls are source files → highlighted "code" view
@@ -177,6 +185,7 @@ export function FileView(props: {
     const k = kind()
     if (k === "code") return LANG[e()] ?? e() ?? "text"
     if (k === "science") return scientific()?.format ?? e()
+    if (k === "table") return tabular() ?? e()
     return k
   }
 
@@ -221,7 +230,8 @@ export function FileView(props: {
     } catch {}
   }
 
-  const toggleable = () => kind() === "markdown" || kind() === "notebook" || kind() === "science" || kind() === "code"
+  const toggleable = () =>
+    kind() === "markdown" || kind() === "notebook" || kind() === "table" || kind() === "science" || kind() === "code"
 
   return (
     <div
@@ -426,6 +436,13 @@ export function FileView(props: {
                 />
               </Match>
 
+              {/* tabular data */}
+              <Match when={kind() === "table" && !showSource()}>
+                <Show when={tabular()}>
+                  {(format) => <DataTableView text={draft()} format={format()} name={name()} />}
+                </Show>
+              </Match>
+
               {/* pdf */}
               <Match when={kind() === "pdf"}>
                 <div style={{ padding: "14px" }}>
@@ -494,7 +511,12 @@ export function FileView(props: {
               </Match>
 
               {/* code / text — editable source, or highlighted read view */}
-              <Match when={(kind() === "code" || kind() === "science" || kind() === "notebook") && showSource()}>
+              <Match
+                when={
+                  (kind() === "code" || kind() === "science" || kind() === "notebook" || kind() === "table") &&
+                  showSource()
+                }
+              >
                 <textarea
                   value={draft()}
                   spellcheck={false}
@@ -595,6 +617,7 @@ export function FilePreview(props: { path: string; onClose: () => void }): JSX.E
 function langFor(k: Kind, x: string): string {
   if (k === "markdown") return "markdown"
   if (k === "notebook") return "json"
+  if (k === "table") return x === "jsonl" ? "json" : x
   return LANG[x] ?? "text"
 }
 
diff --git a/frontend/workspace/src/data/DataTableView.tsx b/frontend/workspace/src/data/DataTableView.tsx
new file mode 100644
index 00000000..00ecd3ad
--- /dev/null
+++ b/frontend/workspace/src/data/DataTableView.tsx
@@ -0,0 +1,553 @@
+import { For, Show, createMemo, createSignal, type JSX } from "solid-js"
+import { FONT_CODE, FONT_MONO, FONT_SANS } from "@/styles/tokens"
+import { exportDelimited, parseTable, summarizeColumn, type DataTable, type TableFormat } from "./table"
+
+const PAGE_SIZE = 100
+
+export function DataTableView(props: { text: string; format: TableFormat; name: string }): JSX.Element {
+  const [query, setQuery] = createSignal("")
+  const [sort, setSort] = createSignal<{ index: number; direction: "asc" | "desc" }>()
+  const [page, setPage] = createSignal(0)
+  const [schema, setSchema] = createSignal(false)
+  const [plot, setPlot] = createSignal(false)
+  const [column, setColumn] = createSignal(0)
+
+  const parsed = createMemo(() => {
+    try {
+      return { table: parseTable(props.format, props.text), error: "" }
+    } catch (cause) {
+      return {
+        table: undefined,
+        error: cause instanceof Error ? cause.message : "Could not parse table",
+      }
+    }
+  })
+  const table = () => parsed().table
+  const numeric = createMemo(
+    () =>
+      table()
+        ?.schema.map((value, index) => ({ ...value, index }))
+        .filter((value) => value.type === "number") ?? [],
+  )
+  const plottedColumn = () =>
+    numeric().some((value) => value.index === column()) ? column() : (numeric()[0]?.index ?? 0)
+  const filtered = createMemo(() => {
+    const data = table()
+    if (!data) return []
+    const term = query().trim().toLowerCase()
+    const rows = term ? data.rows.filter((row) => row.some((value) => value.toLowerCase().includes(term))) : data.rows
+    const order = sort()
+    if (!order) return rows
+    const type = data.schema[order.index]?.type ?? "string"
+    return rows
+      .map((row, index) => ({ row, index }))
+      .sort((a, b) => {
+        const left = a.row[order.index] ?? ""
+        const right = b.row[order.index] ?? ""
+        const result = compare(left, right, type)
+        return (result || a.index - b.index) * (order.direction === "asc" ? 1 : -1)
+      })
+      .map((value) => value.row)
+  })
+  const pages = () => Math.max(1, Math.ceil(filtered().length / PAGE_SIZE))
+  const visible = () => filtered().slice(page() * PAGE_SIZE, (page() + 1) * PAGE_SIZE)
+
+  const sortBy = (index: number) => {
+    setPage(0)
+    setSort((current) => {
+      if (!current || current.index !== index) return { index, direction: "asc" }
+      if (current.direction === "asc") return { index, direction: "desc" }
+      return undefined
+    })
+  }
+
+  const download = () => {
+    const data = table()
+    if (!data) return
+    const text = exportDelimited({ columns: data.columns, rows: filtered() })
+    const url = URL.createObjectURL(new Blob([text], { type: "text/csv;charset=utf-8" }))
+    const anchor = document.createElement("a")
+    anchor.href = url
+    anchor.download = `${props.name.replace(/\.[^.]+$/, "")}.filtered.csv`
+    anchor.click()
+    URL.revokeObjectURL(url)
+  }
+
+  return (
+    <div
+      data-component="data-table"
+      style={{
+        height: "100%",
+        "min-height": "100%",
+        display: "flex",
+        "flex-direction": "column",
+        background: "var(--color-bg-subtle)",
+      }}
+    >
+      <Show
+        when={table()}
+        fallback={
+          <div style={empty()}>
+            <strong style={{ "font-family": FONT_SANS, "font-size": "14px" }}>Could not read this table</strong>
+            <span style={{ "font-family": FONT_MONO, "font-size": "11px", color: "var(--color-text-faint)" }}>
+              {parsed().error}
+            </span>
+          </div>
+        }
+      >
+        {(data) => (
+          <>
+            <div
+              style={{
+                display: "flex",
+                "align-items": "center",
+                gap: "8px",
+                padding: "10px 12px",
+                border: "0",
+                "border-bottom": "1px solid var(--color-border)",
+                background: "var(--color-bg)",
+                "flex-wrap": "wrap",
+              }}
+            >
+              <div style={{ display: "flex", "align-items": "baseline", gap: "6px", "margin-right": "4px" }}>
+                <strong style={{ "font-family": FONT_SANS, "font-size": "12px", color: "var(--color-text)" }}>
+                  {data().totalRows.toLocaleString()} rows
+                </strong>
+                <span style={{ "font-family": FONT_MONO, "font-size": "9px", color: "var(--color-text-faint)" }}>
+                  × {data().columns.length} columns
+                </span>
+              </div>
+              <input
+                data-action="table-filter"
+                aria-label="Filter rows"
+                placeholder="filter every column…"
+                value={query()}
+                onInput={(event) => {
+                  setQuery(event.currentTarget.value)
+                  setPage(0)
+                }}
+                style={input()}
+              />
+              <Show when={query()}>
+                <span style={{ "font-family": FONT_MONO, "font-size": "9px", color: "var(--color-text-faint)" }}>
+                  {filtered().length.toLocaleString()} matches
+                </span>
+              </Show>
+              <div style={{ flex: 1 }} />
+              <button
+                type="button"
+                data-action="table-schema"
+                style={button(schema())}
+                onClick={() => setSchema((value) => !value)}
+              >
+                schema
+              </button>
+              <select
+                aria-label="Plot column"
+                value={String(plottedColumn())}
+                disabled={!numeric().length}
+                onChange={(event) => setColumn(Number(event.currentTarget.value))}
+                style={select()}
+              >
+                <For each={numeric()}>{(value) => <option value={value.index}>{value.name}</option>}</For>
+              </select>
+              <button
+                type="button"
+                data-action="table-plot"
+                disabled={!numeric().length}
+                style={button(plot())}
+                onClick={() => setPlot((value) => !value)}
+              >
+                distribution
+              </button>
+              <button type="button" data-action="table-export" style={button()} onClick={download}>
+                export filtered
+              </button>
+            </div>
+
+            <Show when={schema()}>
+              <div
+                class="atlas-scroll"
+                style={{
+                  display: "flex",
+                  gap: "8px",
+                  padding: "10px 12px",
+                  overflow: "auto hidden",
+                  border: "0",
+                  "border-bottom": "1px solid var(--color-border)",
+                  background: "color-mix(in srgb, var(--color-bg-subtle) 70%, var(--color-bg))",
+                }}
+              >
+                <For each={data().schema}>
+                  {(value) => (
+                    <div
+                      style={{
+                        width: "170px",
+                        "flex-shrink": 0,
+                        padding: "9px 10px",
+                        border: "1px solid var(--color-border)",
+                        "border-radius": "6px",
+                        background: "var(--color-bg)",
+                      }}
+                    >
+                      <div
+                        title={value.name}
+                        style={{
+                          "font-family": FONT_CODE,
+                          "font-size": "10px",
+                          color: "var(--color-text)",
+                          overflow: "hidden",
+                          "text-overflow": "ellipsis",
+                          "white-space": "nowrap",
+                        }}
+                      >
+                        {value.name}
+                      </div>
+                      <div
+                        style={{
+                          display: "flex",
+                          gap: "8px",
+                          "margin-top": "5px",
+                          "font-family": FONT_MONO,
+                          "font-size": "9px",
+                          color: "var(--color-text-faint)",
+                        }}
+                      >
+                        <span>{value.type}</span>
+                        <span>{value.unique.toLocaleString()} unique</span>
+                        <span>{value.missing.toLocaleString()} missing</span>
+                      </div>
+                      <div
+                        title={`${value.missing} missing values`}
+                        style={{
+                          height: "3px",
+                          "margin-top": "8px",
+                          "border-radius": "2px",
+                          background: `linear-gradient(90deg, var(--color-warning, #c8923d) ${(value.missing / Math.max(1, data().totalRows)) * 100}%, var(--color-border) 0)`,
+                        }}
+                      />
+                    </div>
+                  )}
+                </For>
+              </div>
+            </Show>
+
+            <Show when={plot() && numeric().length}>
+              <Histogram table={data()} index={plottedColumn()} onClose={() => setPlot(false)} />
+            </Show>
+
+            <div class="atlas-scroll" style={{ flex: 1, "min-height": 0, overflow: "auto" }}>
+              <table
+                style={{
+                  width: "max-content",
+                  "min-width": "100%",
+                  "border-collapse": "separate",
+                  "border-spacing": 0,
+                  "font-family": FONT_CODE,
+                  "font-size": "10px",
+                  "font-variant-numeric": "tabular-nums",
+                }}
+              >
+                <thead>
+                  <tr>
+                    <th style={{ ...head(), left: 0, "z-index": 3, width: "48px", "min-width": "48px" }}>#</th>
+                    <For each={data().columns}>
+                      {(name, index) => (
+                        <th style={head()}>
+                          <button
+                            type="button"
+                            title={`Sort by ${name}`}
+                            onClick={() => sortBy(index())}
+                            style={{
+                              all: "unset",
+                              cursor: "pointer",
+                              width: "100%",
+                              display: "flex",
+                              "align-items": "center",
+                              gap: "6px",
+                            }}
+                          >
+                            <span
+                              style={{
+                                overflow: "hidden",
+                                "text-overflow": "ellipsis",
+                                "white-space": "nowrap",
+                              }}
+                            >
+                              {name}
+                            </span>
+                            <span style={{ color: "var(--color-text-faint)" }}>
+                              {sort()?.index === index() ? (sort()?.direction === "asc" ? "↑" : "↓") : ""}
+                            </span>
+                          </button>
+                        </th>
+                      )}
+                    </For>
+                  </tr>
+                </thead>
+                <tbody>
+                  <For each={visible()}>
+                    {(row, index) => (
+                      <tr>
+                        <td style={{ ...cell(), position: "sticky", left: 0, background: "var(--color-bg-subtle)" }}>
+                          <span style={{ color: "var(--color-text-faint)" }}>
+                            {(page() * PAGE_SIZE + index() + 1).toLocaleString()}
+                          </span>
+                        </td>
+                        <For each={data().columns}>
+                          {(_, column) => (
+                            <td title={row[column()] ?? ""} style={cell()}>
+                              <Show
+                                when={(row[column()] ?? "") !== ""}
+                                fallback={<span style={{ color: "var(--color-text-faint)" }}>—</span>}
+                              >
+                                {row[column()]}
+                              </Show>
+                            </td>
+                          )}
+                        </For>
+                      </tr>
+                    )}
+                  </For>
+                </tbody>
+              </table>
+            </div>
+
+            <div
+              style={{
+                height: "38px",
+                display: "flex",
+                "align-items": "center",
+                "justify-content": "center",
+                gap: "10px",
+                padding: "0 12px",
+                border: "0",
+                "border-top": "1px solid var(--color-border)",
+                background: "var(--color-bg)",
+              }}
+            >
+              <button
+                type="button"
+                disabled={page() === 0}
+                style={pager()}
+                onClick={() => setPage((value) => value - 1)}
+              >
+                ← previous
+              </button>
+              <span style={{ "font-family": FONT_MONO, "font-size": "9px", color: "var(--color-text-faint)" }}>
+                page {page() + 1} / {pages()}
+                {data().truncated ? " · preview capped at 5,000 rows" : ""}
+              </span>
+              <button
+                type="button"
+                disabled={page() + 1 >= pages()}
+                style={pager()}
+                onClick={() => setPage((value) => value + 1)}
+              >
+                next →
+              </button>
+            </div>
+          </>
+        )}
+      </Show>
+    </div>
+  )
+}
+
+function Histogram(props: { table: DataTable; index: number; onClose: () => void }): JSX.Element {
+  const values = () => props.table.rows.map((row) => Number(row[props.index])).filter(Number.isFinite)
+  const stats = () => summarizeColumn(props.table, props.index)
+  const bars = createMemo(() => {
+    const items = values()
+    if (!items.length) return []
+    const min = Math.min(...items)
+    const max = Math.max(...items)
+    const width = max - min || 1
+    const count = Math.min(24, Math.max(6, Math.ceil(Math.sqrt(items.length))))
+    const bins = Array.from({ length: count }, (_, index) => ({ index, count: 0 }))
+    for (const value of items) {
+      const index = Math.min(count - 1, Math.floor(((value - min) / width) * count))
+      const bin = bins[index]
+      if (bin) bin.count += 1
+    }
+    return bins
+  })
+  const peak = () => Math.max(1, ...bars().map((value) => value.count))
+
+  return (
+    <div
+      data-slot="table-plot"
+      style={{
+        padding: "12px 16px 14px",
+        border: "0",
+        "border-bottom": "1px solid var(--color-border)",
+        background: "var(--color-bg)",
+      }}
+    >
+      <div style={{ display: "flex", "align-items": "center", gap: "12px", "margin-bottom": "10px" }}>
+        <strong style={{ "font-family": FONT_SANS, "font-size": "11px" }}>
+          {props.table.columns[props.index]} distribution
+        </strong>
+        <span style={metric()}>n {stats().count.toLocaleString()}</span>
+        <span style={metric()}>min {number(stats().min)}</span>
+        <span style={metric()}>mean {number(stats().mean)}</span>
+        <span style={metric()}>max {number(stats().max)}</span>
+        <div style={{ flex: 1 }} />
+        <button type="button" style={pager()} onClick={props.onClose}>
+          close
+        </button>
+      </div>
+      <svg
+        viewBox="0 0 720 150"
+        role="img"
+        aria-label={`${props.table.columns[props.index]} histogram`}
+        style={{ width: "100%", height: "150px" }}
+      >
+        <line x1="24" y1="132" x2="710" y2="132" stroke="var(--color-border-strong)" />
+        <For each={bars()}>
+          {(bar, index) => {
+            const width = 674 / Math.max(1, bars().length)
+            const height = (bar.count / peak()) * 112
+            return (
+              <rect
+                x={28 + index() * width}
+                y={132 - height}
+                width={Math.max(2, width - 3)}
+                height={height}
+                rx="2"
+                fill="var(--color-text-muted)"
+                opacity="0.82"
+              >
+                <title>{bar.count} rows</title>
+              </rect>
+            )
+          }}
+        </For>
+      </svg>
+    </div>
+  )
+}
+
+function compare(left: string, right: string, type: string) {
+  if (!left && right) return 1
+  if (left && !right) return -1
+  if (type === "number") return Number(left) - Number(right)
+  if (type === "date") return Date.parse(left) - Date.parse(right)
+  if (type === "boolean") return Number(/^true$/i.test(left)) - Number(/^true$/i.test(right))
+  return left.localeCompare(right, undefined, { numeric: true, sensitivity: "base" })
+}
+
+const number = (value: number | undefined) =>
+  value === undefined ? "—" : new Intl.NumberFormat(undefined, { maximumSignificantDigits: 5 }).format(value)
+
+function input(): JSX.CSSProperties {
+  return {
+    width: "min(280px, 32vw)",
+    height: "28px",
+    padding: "0 9px",
+    border: "1px solid var(--color-border)",
+    "border-radius": "5px",
+    outline: "none",
+    background: "var(--color-bg-subtle)",
+    color: "var(--color-text)",
+    "font-family": FONT_SANS,
+    "font-size": "11px",
+  }
+}
+
+function button(active = false): JSX.CSSProperties {
+  return {
+    cursor: "pointer",
+    height: "28px",
+    padding: "0 9px",
+    border: "1px solid var(--color-border)",
+    "border-radius": "5px",
+    background: active ? "var(--color-text)" : "var(--color-bg)",
+    color: active ? "var(--color-bg)" : "var(--color-text-muted)",
+    "font-family": FONT_MONO,
+    "font-size": "9px",
+    "font-weight": 600,
+  }
+}
+
+function select(): JSX.CSSProperties {
+  return {
+    height: "28px",
+    "max-width": "150px",
+    padding: "0 24px 0 8px",
+    border: "1px solid var(--color-border)",
+    "border-radius": "5px",
+    background: "var(--color-bg)",
+    color: "var(--color-text-muted)",
+    "font-family": FONT_MONO,
+    "font-size": "9px",
+  }
+}
+
+function head(): JSX.CSSProperties {
+  return {
+    position: "sticky",
+    top: 0,
+    "z-index": 2,
+    height: "34px",
+    "min-width": "130px",
+    "max-width": "260px",
+    padding: "0 10px",
+    "text-align": "left",
+    "font-weight": 600,
+    color: "var(--color-text-muted)",
+    background: "var(--color-bg)",
+    "border-right": "1px solid var(--color-border)",
+    "border-bottom": "1px solid var(--color-border-strong)",
+  }
+}
+
+function cell(): JSX.CSSProperties {
+  return {
+    height: "31px",
+    "max-width": "320px",
+    padding: "0 10px",
+    overflow: "hidden",
+    "text-overflow": "ellipsis",
+    "white-space": "nowrap",
+    color: "var(--color-text-muted)",
+    background: "var(--color-bg)",
+    "border-right": "1px solid var(--color-border)",
+    "border-bottom": "1px solid var(--color-border)",
+  }
+}
+
+function pager(): JSX.CSSProperties {
+  return {
+    all: "unset",
+    cursor: "pointer",
+    padding: "4px 7px",
+    "border-radius": "4px",
+    "font-family": FONT_MONO,
+    "font-size": "9px",
+    color: "var(--color-text-faint)",
+  }
+}
+
+function metric(): JSX.CSSProperties {
+  return {
+    "font-family": FONT_MONO,
+    "font-size": "9px",
+    color: "var(--color-text-faint)",
+  }
+}
+
+function empty(): JSX.CSSProperties {
+  return {
+    flex: 1,
+    display: "flex",
+    "flex-direction": "column",
+    "align-items": "center",
+    "justify-content": "center",
+    gap: "9px",
+    padding: "32px",
+    color: "var(--color-text)",
+  }
+}
+
+export default DataTableView
diff --git a/frontend/workspace/src/data/table.test.ts b/frontend/workspace/src/data/table.test.ts
new file mode 100644
index 00000000..d530a384
--- /dev/null
+++ b/frontend/workspace/src/data/table.test.ts
@@ -0,0 +1,97 @@
+import { describe, expect, test } from "bun:test"
+import { readFileSync } from "node:fs"
+import { fileURLToPath } from "node:url"
+import { exportDelimited, parseTable, summarizeColumn } from "./table"
+
+const read = (path: string) => readFileSync(fileURLToPath(new URL(path, import.meta.url)), "utf8")
+
+describe("tabular data model", () => {
+  test("parses quoted CSV fields, escaped quotes, and embedded newlines", () => {
+    const table = parseTable("csv", 'sample,value,note\nA,4,"first, row"\nB,,"line 1\nline 2"\nC,8,"said ""yes"""')
+
+    expect(table.columns).toEqual(["sample", "value", "note"])
+    expect(table.rows).toEqual([
+      ["A", "4", "first, row"],
+      ["B", "", "line 1\nline 2"],
+      ["C", "8", 'said "yes"'],
+    ])
+    expect(table.totalRows).toBe(3)
+    expect(table.truncated).toBe(false)
+  })
+
+  test("parses TSV, JSON arrays, and JSON Lines into one table shape", () => {
+    expect(parseTable("tsv", "gene\tcount\nTP53\t12").rows).toEqual([["TP53", "12"]])
+    expect(parseTable("json", '[{"gene":"TP53","count":12},{"gene":"EGFR","active":true}]')).toMatchObject({
+      columns: ["gene", "count", "active"],
+      rows: [
+        ["TP53", "12", ""],
+        ["EGFR", "", "true"],
+      ],
+    })
+    expect(parseTable("jsonl", '{"gene":"TP53","count":12}\n{"gene":"EGFR","count":8}\n')).toMatchObject({
+      columns: ["gene", "count"],
+      rows: [
+        ["TP53", "12"],
+        ["EGFR", "8"],
+      ],
+    })
+  })
+
+  test("infers numeric, boolean, date, and string schemas with missingness", () => {
+    const table = parseTable(
+      "csv",
+      "value,passed,date,label\n1,true,2026-01-01,alpha\n2,false,2026-01-02,beta\n,TRUE,,alpha",
+    )
+
+    expect(table.schema).toEqual([
+      { name: "value", type: "number", missing: 1, unique: 2 },
+      { name: "passed", type: "boolean", missing: 0, unique: 2 },
+      { name: "date", type: "date", missing: 1, unique: 2 },
+      { name: "label", type: "string", missing: 0, unique: 2 },
+    ])
+    expect(summarizeColumn(table, 0)).toMatchObject({ min: 1, max: 2, mean: 1.5, count: 2, missing: 1 })
+  })
+
+  test("caps preview rows while retaining the total count", () => {
+    const body = `value\n${Array.from({ length: 12 }, (_, index) => index).join("\n")}`
+    const table = parseTable("csv", body, 5)
+
+    expect(table.rows).toHaveLength(5)
+    expect(table.totalRows).toBe(12)
+    expect(table.truncated).toBe(true)
+  })
+
+  test("exports selected rows with correct CSV quoting", () => {
+    expect(
+      exportDelimited(
+        {
+          columns: ["name", "note"],
+          rows: [
+            ["A", "plain"],
+            ["B", 'comma, quote " and\nnewline'],
+          ],
+        },
+        ",",
+      ),
+    ).toBe('name,note\nA,plain\nB,"comma, quote "" and\nnewline"\n')
+  })
+
+  test("rejects non-tabular JSON with a useful error", () => {
+    expect(() => parseTable("json", '{"nested":{"value":1}}')).toThrow("array of records")
+  })
+})
+
+describe("data table integration", () => {
+  test("routes table files into the interactive data workbench", () => {
+    const preview = read("../atlas/FilePreview.tsx")
+    const view = read("./DataTableView.tsx")
+
+    expect(preview).toContain('import { DataTableView } from "@/data/DataTableView"')
+    expect(preview).toContain("<DataTableView")
+    expect(view).toContain('data-component="data-table"')
+    expect(view).toContain('data-action="table-filter"')
+    expect(view).toContain('data-action="table-schema"')
+    expect(view).toContain('data-action="table-plot"')
+    expect(view).toContain('data-action="table-export"')
+  })
+})
diff --git a/frontend/workspace/src/data/table.ts b/frontend/workspace/src/data/table.ts
new file mode 100644
index 00000000..4753b079
--- /dev/null
+++ b/frontend/workspace/src/data/table.ts
@@ -0,0 +1,188 @@
+export type TableFormat = "csv" | "tsv" | "json" | "jsonl"
+export type ColumnType = "number" | "boolean" | "date" | "string"
+
+export interface TableSchema {
+  name: string
+  type: ColumnType
+  missing: number
+  unique: number
+}
+
+export interface DataTable {
+  columns: string[]
+  rows: string[][]
+  schema: TableSchema[]
+  totalRows: number
+  truncated: boolean
+}
+
+const record = (value: unknown): value is Record<string, unknown> =>
+  typeof value === "object" && value !== null && !Array.isArray(value)
+
+const scalar = (value: unknown) => {
+  if (value === undefined || value === null) return ""
+  if (typeof value === "string") return value
+  if (typeof value === "number" || typeof value === "boolean" || typeof value === "bigint") return String(value)
+  return JSON.stringify(value)
+}
+
+function delimited(text: string, delimiter: string) {
+  const rows: string[][] = []
+  const state = { index: 0, cell: "", row: [] as string[], quoted: false }
+  const pushCell = () => {
+    state.row.push(state.cell)
+    state.cell = ""
+  }
+  const pushRow = () => {
+    pushCell()
+    rows.push(state.row)
+    state.row = []
+  }
+
+  while (state.index < text.length) {
+    const char = text[state.index] ?? ""
+    const next = text[state.index + 1] ?? ""
+    if (state.quoted && char === '"' && next === '"') {
+      state.cell += '"'
+      state.index += 2
+      continue
+    }
+    if (state.quoted && char === '"') {
+      state.quoted = false
+      state.index += 1
+      continue
+    }
+    if (state.quoted) {
+      state.cell += char
+      state.index += 1
+      continue
+    }
+    if (char === '"' && state.cell === "") {
+      state.quoted = true
+      state.index += 1
+      continue
+    }
+    if (char === delimiter) {
+      pushCell()
+      state.index += 1
+      continue
+    }
+    if (char === "\n" || char === "\r") {
+      pushRow()
+      state.index += char === "\r" && next === "\n" ? 2 : 1
+      continue
+    }
+    state.cell += char
+    state.index += 1
+  }
+  if (state.cell || state.row.length) pushRow()
+  return rows
+}
+
+const headers = (values: string[]) => {
+  const seen = new Map<string, number>()
+  return values.map((value, index) => {
+    const base = value.trim() || `column_${index + 1}`
+    const count = seen.get(base) ?? 0
+    seen.set(base, count + 1)
+    return count ? `${base}_${count + 1}` : base
+  })
+}
+
+const jsonRows = (text: string, format: "json" | "jsonl") => {
+  const values: unknown[] =
+    format === "json"
+      ? (() => {
+          const parsed: unknown = JSON.parse(text)
+          if (!Array.isArray(parsed)) throw new Error("Tabular JSON must be an array of records")
+          return parsed
+        })()
+      : text
+          .split(/\r?\n/)
+          .filter((line) => line.trim())
+          .map((line) => JSON.parse(line) as unknown)
+
+  if (!values.every(record)) throw new Error("Tabular JSON must be an array of records")
+  const columns = [...new Set(values.flatMap((value) => Object.keys(value)))]
+  return {
+    columns,
+    rows: values.map((value) => columns.map((column) => scalar(value[column]))),
+  }
+}
+
+const infer = (values: string[]): ColumnType => {
+  const present = values.map((value) => value.trim()).filter(Boolean)
+  if (!present.length) return "string"
+  if (present.every((value) => /^[-+]?(?:\d+\.?\d*|\.\d+)(?:e[-+]?\d+)?$/i.test(value))) return "number"
+  if (present.every((value) => /^(?:true|false)$/i.test(value))) return "boolean"
+  if (
+    present.every((value) => /^\d{4}-\d{2}-\d{2}(?:[T ][0-9:.+-]+Z?)?$/.test(value) && !Number.isNaN(Date.parse(value)))
+  ) {
+    return "date"
+  }
+  return "string"
+}
+
+const schema = (columns: string[], rows: string[][]): TableSchema[] =>
+  columns.map((name, index) => {
+    const values = rows.map((row) => row[index] ?? "")
+    const present = values.filter((value) => value.trim())
+    const type = infer(values)
+    const normalized = present.map((value) => {
+      if (type === "boolean") return value.toLowerCase()
+      if (type === "number") return String(Number(value))
+      return value
+    })
+    return {
+      name,
+      type,
+      missing: values.length - present.length,
+      unique: new Set(normalized).size,
+    }
+  })
+
+export function parseTable(format: TableFormat, text: string, limit = 5_000): DataTable {
+  const parsed = (() => {
+    if (format === "json" || format === "jsonl") return jsonRows(text, format)
+    const rows = delimited(text, format === "tsv" ? "\t" : ",")
+    const columns = headers(rows[0] ?? [])
+    return {
+      columns,
+      rows: rows.slice(1).map((row) => columns.map((_, index) => row[index] ?? "")),
+    }
+  })()
+
+  return {
+    columns: parsed.columns,
+    rows: parsed.rows.slice(0, limit),
+    schema: schema(parsed.columns, parsed.rows),
+    totalRows: parsed.rows.length,
+    truncated: parsed.rows.length > limit,
+  }
+}
+
+export function summarizeColumn(table: Pick<DataTable, "rows">, index: number) {
+  const values = table.rows
+    .map((row) => row[index] ?? "")
+    .filter((value) => value.trim())
+    .map(Number)
+    .filter(Number.isFinite)
+  const total = values.reduce((sum, value) => sum + value, 0)
+  return {
+    count: values.length,
+    missing: table.rows.length - values.length,
+    min: values.length ? Math.min(...values) : undefined,
+    max: values.length ? Math.max(...values) : undefined,
+    mean: values.length ? total / values.length : undefined,
+  }
+}
+
+const quote = (value: string, delimiter: string) => {
+  if (!value.includes(delimiter) && !value.includes('"') && !value.includes("\n") && !value.includes("\r")) return value
+  return `"${value.replaceAll('"', '""')}"`
+}
+
+export function exportDelimited(table: Pick<DataTable, "columns" | "rows">, delimiter: "," | "\t" = ",") {
+  const rows = [table.columns, ...table.rows]
+  return `${rows.map((row) => row.map((value) => quote(value, delimiter)).join(delimiter)).join("\n")}\n`
+}
diff --git a/frontend/workspace/src/science/files.test.ts b/frontend/workspace/src/science/files.test.ts
index 1f024671..665ec761 100644
--- a/frontend/workspace/src/science/files.test.ts
+++ b/frontend/workspace/src/science/files.test.ts
@@ -92,7 +92,7 @@ describe("scientific file viewer integration", () => {
     expect(preview).toContain('import { detectScientificFile } from "@/science/files"')
     expect(preview).toContain('import { ScienceArtifact } from "@/science/ScienceArtifact"')
     expect(preview).toContain(
-      'type Kind = "markdown" | "notebook" | "pdf" | "image" | "science" | "code" | "binary"',
+      'type Kind = "markdown" | "notebook" | "table" | "pdf" | "image" | "science" | "code" | "binary"',
     )
     expect(preview).toContain("<ScienceArtifact")
   })

From 8a0dbe1db3e0c0d4b19665828f23a73a52f91a64 Mon Sep 17 00:00:00 2001
From: Aayam Bansal <aayambansal@gmail.com>
Date: Wed, 29 Jul 2026 06:19:42 +0800
Subject: [PATCH 07/40] feat: add scientific data workbench

---
 .../workspace/e2e/scientific-data.spec.ts     |  57 ++
 frontend/workspace/src/atlas/FilePreview.tsx  |  27 +-
 frontend/workspace/src/science/files.test.ts  |   4 +-
 .../science/formats/ScientificDataView.tsx    | 809 ++++++++++++++++++
 .../src/science/formats/biological.test.ts    | 194 +++++
 .../src/science/formats/biological.ts         | 458 ++++++++++
 6 files changed, 1543 insertions(+), 6 deletions(-)
 create mode 100644 frontend/workspace/e2e/scientific-data.spec.ts
 create mode 100644 frontend/workspace/src/science/formats/ScientificDataView.tsx
 create mode 100644 frontend/workspace/src/science/formats/biological.test.ts
 create mode 100644 frontend/workspace/src/science/formats/biological.ts

diff --git a/frontend/workspace/e2e/scientific-data.spec.ts b/frontend/workspace/e2e/scientific-data.spec.ts
new file mode 100644
index 00000000..c89f512d
--- /dev/null
+++ b/frontend/workspace/e2e/scientific-data.spec.ts
@@ -0,0 +1,57 @@
+import { mkdtempSync, rmSync, writeFileSync } from "node:fs"
+import { tmpdir } from "node:os"
+import path from "node:path"
+import { test, expect } from "./fixtures"
+
+test("inspects and searches genomics and sequencing files", async ({ page, gotoSession }) => {
+  const directory = mkdtempSync(path.join(tmpdir(), "openscience-bio-e2e-"))
+  writeFileSync(
+    path.join(directory, "cohort.vcf"),
+    [
+      "##fileformat=VCFv4.3",
+      "##reference=GRCh38",
+      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tcase\tcontrol",
+      "chr1\t10\trs1\tA\tG\t60\tPASS\tDP=20\tGT\t0/1\t0/0",
+      "chr1\t20\t.\tA\tAT\t42\tPASS\tDP=12\tGT\t0/1\t0/0",
+      "chr2\t30\t.\tAT\tA\t.\tLowQual\tDP=4\tGT\t1/1\t0/1",
+    ].join("\n"),
+  )
+  writeFileSync(
+    path.join(directory, "reads.fastq"),
+    ["@read_1", "ACGT", "+", "IIII", "@read_2", "GGNN", "+", "!!55", ""].join("\n"),
+  )
+
+  try {
+    await gotoSession()
+    await page.getByRole("tab", { name: "Files", exact: true }).click()
+    const location = page.getByPlaceholder("/absolute/path")
+    await location.fill(directory)
+    await location.press("Enter")
+
+    await page.getByPlaceholder("filter this folder…").fill("cohort.vcf")
+    await page.getByRole("button", { name: /^cohort\.vcf\b/ }).click()
+    const vcf = page.locator('[data-component="scientific-data"][data-format="vcf"]')
+    await expect(vcf).toBeVisible()
+    await expect(vcf.getByText("3 variants", { exact: true })).toBeVisible()
+    await expect(vcf.getByText("Variant classes", { exact: true })).toBeVisible()
+    await expect(vcf.getByText("GRCh38", { exact: true })).toBeVisible()
+
+    await vcf.getByRole("button", { name: "records", exact: true }).click()
+    await expect(vcf.getByText("chr1:10", { exact: true })).toBeVisible()
+    await vcf.getByLabel("Filter scientific records").fill("LowQual")
+    await expect(vcf.getByText("chr2:30", { exact: true })).toBeVisible()
+    await expect(vcf.getByText("chr1:10", { exact: true })).toHaveCount(0)
+
+    await page.getByRole("tab", { name: "Files", exact: true }).click()
+    await page.getByPlaceholder("filter this folder…").fill("reads.fastq")
+    await page.getByRole("button", { name: /^reads\.fastq\b/ }).click()
+    const fastq = page.locator('[data-component="scientific-data"][data-format="fastq"]')
+    await expect(fastq).toBeVisible()
+    await expect(fastq.getByText("2 reads", { exact: true })).toBeVisible()
+    await expect(fastq.getByText("Per-cycle base quality", { exact: true })).toBeVisible()
+    await expect(fastq.getByText("Q25", { exact: true }).first()).toBeVisible()
+    await expect(fastq.getByText("50% bases ≥ Q30", { exact: true })).toBeVisible()
+  } finally {
+    rmSync(directory, { recursive: true, force: true })
+  }
+})
diff --git a/frontend/workspace/src/atlas/FilePreview.tsx b/frontend/workspace/src/atlas/FilePreview.tsx
index 710942e5..13c31dfe 100644
--- a/frontend/workspace/src/atlas/FilePreview.tsx
+++ b/frontend/workspace/src/atlas/FilePreview.tsx
@@ -19,6 +19,8 @@ import { FONT_MONO, FONT_SANS, FONT_CODE } from "@/styles/tokens"
 import { PdfViewer } from "@/science/renderers/documents/PdfViewer"
 import { ScienceArtifact } from "@/science/ScienceArtifact"
 import { detectScientificFile } from "@/science/files"
+import { ScientificDataView } from "@/science/formats/ScientificDataView"
+import { detectBiologicalFormat } from "@/science/formats/biological"
 import { NotebookView } from "@/notebook/NotebookView"
 import { DataTableView } from "@/data/DataTableView"
 import type { TableFormat } from "@/data/table"
@@ -104,7 +106,7 @@ const LANG: Record<string, string> = {
   log: "text",
 }
 
-type Kind = "markdown" | "notebook" | "table" | "pdf" | "image" | "science" | "code" | "binary"
+type Kind = "markdown" | "notebook" | "table" | "scientific-data" | "pdf" | "image" | "science" | "code" | "binary"
 
 type FileData = { content?: string; encoding?: string; mimeType?: string }
 
@@ -157,6 +159,7 @@ export function FileView(props: {
   const text = () => (!data() || isBinary() ? "" : (data()!.content ?? ""))
   const dirty = () => draft() !== savedText()
   const scientific = createMemo(() => (isBinary() ? undefined : detectScientificFile(e(), draft())))
+  const biological = createMemo(() => (isBinary() ? undefined : detectBiologicalFormat(e())))
   const tabular = createMemo<TableFormat | undefined>(() => {
     if (isBinary()) return
     if (e() === "csv" || e() === "tsv" || e() === "jsonl") return e() as TableFormat
@@ -173,6 +176,7 @@ export function FileView(props: {
     if (x === "md" || x === "markdown" || x === "mdx") return "markdown"
     if (x === "ipynb") return "notebook"
     if (tabular()) return "table"
+    if (biological()) return "scientific-data"
     if (x === "pdf") return "pdf"
     if (scientific()) return "science"
     // .tex / .latex / .sty / .cls are source files → highlighted "code" view
@@ -185,6 +189,7 @@ export function FileView(props: {
     const k = kind()
     if (k === "code") return LANG[e()] ?? e() ?? "text"
     if (k === "science") return scientific()?.format ?? e()
+    if (k === "scientific-data") return biological() ?? e()
     if (k === "table") return tabular() ?? e()
     return k
   }
@@ -231,7 +236,12 @@ export function FileView(props: {
   }
 
   const toggleable = () =>
-    kind() === "markdown" || kind() === "notebook" || kind() === "table" || kind() === "science" || kind() === "code"
+    kind() === "markdown" ||
+    kind() === "notebook" ||
+    kind() === "table" ||
+    kind() === "scientific-data" ||
+    kind() === "science" ||
+    kind() === "code"
 
   return (
     <div
@@ -443,6 +453,13 @@ export function FileView(props: {
                 </Show>
               </Match>
 
+              {/* genomic, alignment, and mass-spectrometry data */}
+              <Match when={kind() === "scientific-data" && !showSource()}>
+                <Show when={biological()}>
+                  {(format) => <ScientificDataView text={draft()} format={format()} name={name()} />}
+                </Show>
+              </Match>
+
               {/* pdf */}
               <Match when={kind() === "pdf"}>
                 <div style={{ padding: "14px" }}>
@@ -513,7 +530,11 @@ export function FileView(props: {
               {/* code / text — editable source, or highlighted read view */}
               <Match
                 when={
-                  (kind() === "code" || kind() === "science" || kind() === "notebook" || kind() === "table") &&
+                  (kind() === "code" ||
+                    kind() === "science" ||
+                    kind() === "scientific-data" ||
+                    kind() === "notebook" ||
+                    kind() === "table") &&
                   showSource()
                 }
               >
diff --git a/frontend/workspace/src/science/files.test.ts b/frontend/workspace/src/science/files.test.ts
index 665ec761..d594bc3d 100644
--- a/frontend/workspace/src/science/files.test.ts
+++ b/frontend/workspace/src/science/files.test.ts
@@ -91,9 +91,7 @@ describe("scientific file viewer integration", () => {
 
     expect(preview).toContain('import { detectScientificFile } from "@/science/files"')
     expect(preview).toContain('import { ScienceArtifact } from "@/science/ScienceArtifact"')
-    expect(preview).toContain(
-      'type Kind = "markdown" | "notebook" | "table" | "pdf" | "image" | "science" | "code" | "binary"',
-    )
+    expect(preview).toContain('"scientific-data"')
     expect(preview).toContain("<ScienceArtifact")
   })
 })
diff --git a/frontend/workspace/src/science/formats/ScientificDataView.tsx b/frontend/workspace/src/science/formats/ScientificDataView.tsx
new file mode 100644
index 00000000..7b27a658
--- /dev/null
+++ b/frontend/workspace/src/science/formats/ScientificDataView.tsx
@@ -0,0 +1,809 @@
+import { For, Match, Show, Switch, createMemo, createSignal, type JSX } from "solid-js"
+import { FONT_CODE, FONT_MONO, FONT_SANS } from "@/styles/tokens"
+import {
+  parseBiologicalFile,
+  type BiologicalFile,
+  type BiologicalFormat,
+  type Count,
+  type FastqFile,
+  type IntervalFile,
+  type MzmlFile,
+  type SamFile,
+  type VcfFile,
+} from "./biological"
+
+export function ScientificDataView(props: { text: string; format: BiologicalFormat; name: string }): JSX.Element {
+  const [query, setQuery] = createSignal("")
+  const [view, setView] = createSignal<"overview" | "records">("overview")
+  const parsed = createMemo(() => {
+    try {
+      return { data: parseBiologicalFile(props.format, props.text), error: "" }
+    } catch (cause) {
+      return { data: undefined, error: cause instanceof Error ? cause.message : "Could not inspect scientific file" }
+    }
+  })
+  const data = () => parsed().data
+  const fastq = () => (data()?.format === "fastq" ? (data() as FastqFile) : undefined)
+  const vcf = () => (data()?.format === "vcf" ? (data() as VcfFile) : undefined)
+  const interval = () =>
+    data()?.format === "bed" || data()?.format === "gff" || data()?.format === "gtf"
+      ? (data() as IntervalFile)
+      : undefined
+  const sam = () => (data()?.format === "sam" ? (data() as SamFile) : undefined)
+  const mzml = () => (data()?.format === "mzml" ? (data() as MzmlFile) : undefined)
+  const recordCount = () => {
+    const value = data()
+    if (!value) return 0
+    if (value.format === "fastq") return value.reads
+    if (value.format === "vcf") return value.variants
+    if (value.format === "sam") return value.alignments
+    if (value.format === "mzml") return value.spectra
+    return value.features
+  }
+
+  return (
+    <div
+      data-component="scientific-data"
+      data-format={props.format}
+      style={{
+        height: "100%",
+        "min-height": "100%",
+        display: "flex",
+        "flex-direction": "column",
+        background: "var(--color-bg-subtle)",
+      }}
+    >
+      <Show
+        when={data()}
+        fallback={
+          <div style={empty()}>
+            <strong style={{ "font-family": FONT_SANS, "font-size": "14px" }}>Could not inspect this file</strong>
+            <span style={{ "font-family": FONT_MONO, "font-size": "11px", color: "var(--color-text-faint)" }}>
+              {parsed().error}
+            </span>
+          </div>
+        }
+      >
+        {(value) => (
+          <>
+            <div
+              style={{
+                display: "flex",
+                "align-items": "center",
+                gap: "8px",
+                padding: "10px 12px",
+                border: "0",
+                "border-bottom": "1px solid var(--color-border)",
+                background: "var(--color-bg)",
+                "flex-wrap": "wrap",
+              }}
+            >
+              <span style={formatBadge()}>{props.format.toUpperCase()}</span>
+              <strong style={{ "font-family": FONT_SANS, "font-size": "12px", color: "var(--color-text)" }}>
+                {recordCount().toLocaleString()} {noun(value())}
+              </strong>
+              <Show when={value().truncated}>
+                <span style={warning()}>first 10,000 records inspected</span>
+              </Show>
+              <div style={{ flex: 1 }} />
+              <button type="button" style={button(view() === "overview")} onClick={() => setView("overview")}>
+                overview
+              </button>
+              <Show when={value().format !== "mzml"}>
+                <button type="button" style={button(view() === "records")} onClick={() => setView("records")}>
+                  records
+                </button>
+              </Show>
+            </div>
+
+            <div class="atlas-scroll" style={{ flex: 1, "min-height": 0, overflow: "auto" }}>
+              <Show when={view() === "overview"}>
+                <Switch>
+                  <Match when={fastq()}>{(file) => <FastqOverview file={file()} />}</Match>
+                  <Match when={vcf()}>{(file) => <VcfOverview file={file()} />}</Match>
+                  <Match when={interval()}>{(file) => <IntervalOverview file={file()} />}</Match>
+                  <Match when={sam()}>{(file) => <SamOverview file={file()} />}</Match>
+                  <Match when={mzml()}>{(file) => <MzmlOverview file={file()} />}</Match>
+                </Switch>
+              </Show>
+              <Show when={view() === "records"}>
+                <div
+                  style={{
+                    position: "sticky",
+                    top: 0,
+                    "z-index": 4,
+                    padding: "10px 12px",
+                    background: "var(--color-bg)",
+                    "border-bottom": "1px solid var(--color-border)",
+                  }}
+                >
+                  <input
+                    data-action="scientific-filter"
+                    aria-label="Filter scientific records"
+                    value={query()}
+                    onInput={(event) => setQuery(event.currentTarget.value)}
+                    placeholder="filter records…"
+                    style={input()}
+                  />
+                </div>
+                <Switch>
+                  <Match when={fastq()}>{(file) => <FastqRecords file={file()} query={query()} />}</Match>
+                  <Match when={vcf()}>{(file) => <VcfRecords file={file()} query={query()} />}</Match>
+                  <Match when={interval()}>{(file) => <IntervalRecords file={file()} query={query()} />}</Match>
+                  <Match when={sam()}>{(file) => <SamRecords file={file()} query={query()} />}</Match>
+                </Switch>
+              </Show>
+            </div>
+          </>
+        )}
+      </Show>
+    </div>
+  )
+}
+
+function FastqOverview(props: { file: FastqFile }): JSX.Element {
+  return (
+    <Overview>
+      <Metrics>
+        <Metric label="reads" value={compact(props.file.reads)} detail={`${compact(props.file.bases)} bases`} />
+        <Metric
+          label="mean length"
+          value={`${props.file.meanLength} bp`}
+          detail={`${props.file.minLength}–${props.file.maxLength} bp`}
+        />
+        <Metric label="GC" value={`${props.file.gc}%`} detail={`${props.file.n}% ambiguous N`} />
+        <Metric label="mean quality" value={`Q${props.file.meanQuality}`} detail={`${props.file.q30}% bases ≥ Q30`} />
+      </Metrics>
+      <Panel title="Per-cycle base quality" note={`Phred score · first ${props.file.cycles.length} cycles`}>
+        <Line values={props.file.cycles} floor={0} ceiling={45} />
+      </Panel>
+      <div style={grid()}>
+        <Panel title="Read quality" note="Quick health check">
+          <QualityGauge value={props.file.meanQuality} />
+        </Panel>
+        <Panel title="Parser health" note="FASTQ structural validation">
+          <div style={{ display: "flex", "align-items": "baseline", gap: "8px", padding: "12px 2px" }}>
+            <strong style={large()}>{props.file.invalid}</strong>
+            <span style={muted()}>malformed records</span>
+          </div>
+        </Panel>
+      </div>
+    </Overview>
+  )
+}
+
+function VcfOverview(props: { file: VcfFile }): JSX.Element {
+  return (
+    <Overview>
+      <Metrics>
+        <Metric label="variants" value={compact(props.file.variants)} detail={`${props.file.passed} pass`} />
+        <Metric
+          label="samples"
+          value={String(props.file.samples.length)}
+          detail={props.file.samples.slice(0, 3).join(", ") || "sites only"}
+        />
+        <Metric
+          label="mean QUAL"
+          value={String(props.file.meanQuality || "—")}
+          detail={props.file.fileformat || "VCF"}
+        />
+        <Metric
+          label="reference"
+          value={short(props.file.reference || "unspecified", 18)}
+          detail={`${props.file.chromosomes.length} contigs`}
+        />
+      </Metrics>
+      <div style={grid()}>
+        <Panel title="Variant classes" note="By REF/ALT allele shape">
+          <Bars items={Object.entries(props.file.types).map(([name, count]) => ({ name, count }))} />
+        </Panel>
+        <Panel title="Chromosomes" note="Most populated contigs">
+          <Bars items={props.file.chromosomes.slice(0, 8)} />
+        </Panel>
+      </div>
+      <Panel title="Filter outcomes" note="PASS and caller-specific flags">
+        <Bars items={props.file.filters.slice(0, 10)} />
+      </Panel>
+    </Overview>
+  )
+}
+
+function IntervalOverview(props: { file: IntervalFile }): JSX.Element {
+  return (
+    <Overview>
+      <Metrics>
+        <Metric label="features" value={compact(props.file.features)} detail={props.file.format.toUpperCase()} />
+        <Metric label="total span" value={`${compact(props.file.totalSpan)} bp`} detail="sum of intervals" />
+        <Metric
+          label="mean span"
+          value={`${props.file.meanSpan} bp`}
+          detail={`max ${compact(props.file.maxSpan)} bp`}
+        />
+        <Metric
+          label="contigs"
+          value={String(props.file.chromosomes.length)}
+          detail={`${props.file.types.length} feature types`}
+        />
+      </Metrics>
+      <div style={grid()}>
+        <Panel title="Chromosomes" note="Feature density">
+          <Bars items={props.file.chromosomes.slice(0, 10)} />
+        </Panel>
+        <Panel title="Feature types" note={props.file.format === "bed" ? "BED regions" : "Annotation categories"}>
+          <Bars items={props.file.types.slice(0, 10)} />
+        </Panel>
+      </div>
+    </Overview>
+  )
+}
+
+function SamOverview(props: { file: SamFile }): JSX.Element {
+  const rate = props.file.alignments ? (props.file.mapped / props.file.alignments) * 100 : 0
+  return (
+    <Overview>
+      <Metrics>
+        <Metric
+          label="alignments"
+          value={compact(props.file.alignments)}
+          detail={`${props.file.references.length} references`}
+        />
+        <Metric label="mapped" value={`${round(rate)}%`} detail={`${props.file.unmapped} unmapped`} />
+        <Metric label="mean MAPQ" value={String(props.file.meanMapq)} detail="mapped reads" />
+        <Metric
+          label="sort order"
+          value={props.file.order || "unknown"}
+          detail={props.file.version ? `SAM ${props.file.version}` : "SAM"}
+        />
+      </Metrics>
+      <div style={grid()}>
+        <Panel title="Reference distribution" note="Mapped alignments">
+          <Bars items={props.file.chromosomes.slice(0, 10)} />
+        </Panel>
+        <Panel title="Alignment flags" note="Records may occupy multiple groups">
+          <Bars
+            items={[
+              {
+                name: "primary mapped",
+                count: Math.max(0, props.file.mapped - props.file.secondary - props.file.supplementary),
+              },
+              { name: "secondary", count: props.file.secondary },
+              { name: "supplementary", count: props.file.supplementary },
+              { name: "duplicate", count: props.file.duplicates },
+              { name: "unmapped", count: props.file.unmapped },
+            ]}
+          />
+        </Panel>
+      </div>
+    </Overview>
+  )
+}
+
+function MzmlOverview(props: { file: MzmlFile }): JSX.Element {
+  return (
+    <Overview>
+      <Metrics>
+        <Metric label="spectra" value={compact(props.file.spectra)} detail={props.file.run || "unnamed run"} />
+        <Metric label="chromatograms" value={compact(props.file.chromatograms)} detail="stored traces" />
+        <Metric
+          label="MS levels"
+          value={String(props.file.levels.length)}
+          detail={props.file.levels.map((item) => item.name).join(", ")}
+        />
+        <Metric
+          label="time range"
+          value={props.file.range ? `${round(props.file.range.start)}–${round(props.file.range.end)}` : "—"}
+          detail="scan time in source units"
+        />
+      </Metrics>
+      <div style={grid()}>
+        <Panel title="Spectrum inventory" note="Tandem-MS level distribution">
+          <Bars items={props.file.levels} />
+        </Panel>
+        <Panel title="Acquisition timeline" note={`${props.file.times.length} scans with start time`}>
+          <Rug values={props.file.times} />
+        </Panel>
+      </div>
+      <Panel title="Run readiness" note="What OpenScience found">
+        <div style={{ display: "grid", gap: "8px", padding: "4px 0" }}>
+          <Check ok={props.file.spectra > 0} text="spectrum list detected" />
+          <Check ok={props.file.levels.some((item) => item.name === "MS2")} text="MS/MS spectra detected" />
+          <Check ok={props.file.times.length > 0} text="scan timing metadata detected" />
+        </div>
+      </Panel>
+    </Overview>
+  )
+}
+
+function FastqRecords(props: { file: FastqFile; query: string }): JSX.Element {
+  const rows = () => match(props.file.records, props.query, (record) => `${record.id} ${record.sequence}`)
+  return (
+    <Table columns={["read", "length", "GC", "mean Q", "sequence"]}>
+      <For each={rows()}>
+        {(record) => (
+          <tr>
+            <Cell mono>{record.id}</Cell>
+            <Cell>{record.length}</Cell>
+            <Cell>{record.gc}%</Cell>
+            <Cell>Q{record.quality}</Cell>
+            <Cell mono>{short(record.sequence, 80)}</Cell>
+          </tr>
+        )}
+      </For>
+    </Table>
+  )
+}
+
+function VcfRecords(props: { file: VcfFile; query: string }): JSX.Element {
+  const rows = () =>
+    match(
+      props.file.records,
+      props.query,
+      (record) =>
+        `${record.chrom} ${record.pos} ${record.id} ${record.ref} ${record.alt} ${record.filter} ${record.type}`,
+    )
+  return (
+    <Table columns={["locus", "ID", "REF", "ALT", "type", "QUAL", "filter", "depth"]}>
+      <For each={rows()}>
+        {(record) => (
+          <tr>
+            <Cell mono>
+              {record.chrom}:{record.pos.toLocaleString()}
+            </Cell>
+            <Cell mono>{record.id || "—"}</Cell>
+            <Cell mono>{record.ref}</Cell>
+            <Cell mono>{short(record.alt, 34)}</Cell>
+            <Cell>{record.type}</Cell>
+            <Cell>{record.qual ?? "—"}</Cell>
+            <Cell>{record.filter}</Cell>
+            <Cell>{record.depth ?? "—"}</Cell>
+          </tr>
+        )}
+      </For>
+    </Table>
+  )
+}
+
+function IntervalRecords(props: { file: IntervalFile; query: string }): JSX.Element {
+  const rows = () =>
+    match(
+      props.file.records,
+      props.query,
+      (record) => `${record.chrom} ${record.start} ${record.end} ${record.name} ${record.type} ${record.strand}`,
+    )
+  return (
+    <Table columns={["locus", "name", "type", "span", "score", "strand"]}>
+      <For each={rows()}>
+        {(record) => (
+          <tr>
+            <Cell mono>
+              {record.chrom}:{record.start.toLocaleString()}–{record.end.toLocaleString()}
+            </Cell>
+            <Cell>{record.name || "—"}</Cell>
+            <Cell>{record.type}</Cell>
+            <Cell>{record.span.toLocaleString()} bp</Cell>
+            <Cell>{record.score || "—"}</Cell>
+            <Cell>{record.strand}</Cell>
+          </tr>
+        )}
+      </For>
+    </Table>
+  )
+}
+
+function SamRecords(props: { file: SamFile; query: string }): JSX.Element {
+  const rows = () =>
+    match(
+      props.file.records,
+      props.query,
+      (record) => `${record.name} ${record.reference} ${record.position} ${record.cigar}`,
+    )
+  return (
+    <Table columns={["read", "locus", "flag", "MAPQ", "CIGAR", "length"]}>
+      <For each={rows()}>
+        {(record) => (
+          <tr>
+            <Cell mono>{record.name}</Cell>
+            <Cell mono>
+              {record.reference}:{record.position.toLocaleString()}
+            </Cell>
+            <Cell>{record.flag}</Cell>
+            <Cell>{record.mapq}</Cell>
+            <Cell mono>{record.cigar}</Cell>
+            <Cell>{record.length} bp</Cell>
+          </tr>
+        )}
+      </For>
+    </Table>
+  )
+}
+
+function Overview(props: { children: JSX.Element }): JSX.Element {
+  return <div style={{ display: "grid", gap: "12px", padding: "14px" }}>{props.children}</div>
+}
+
+function Metrics(props: { children: JSX.Element }): JSX.Element {
+  return (
+    <div style={{ display: "grid", "grid-template-columns": "repeat(auto-fit, minmax(150px, 1fr))", gap: "8px" }}>
+      {props.children}
+    </div>
+  )
+}
+
+function Metric(props: { label: string; value: string; detail: string }): JSX.Element {
+  return (
+    <div style={card()}>
+      <span style={{ ...muted(), "text-transform": "uppercase", "letter-spacing": "0.06em" }}>{props.label}</span>
+      <strong style={{ ...large(), "margin-top": "8px" }}>{props.value}</strong>
+      <span
+        title={props.detail}
+        style={{
+          ...muted(),
+          "margin-top": "4px",
+          overflow: "hidden",
+          "text-overflow": "ellipsis",
+          "white-space": "nowrap",
+        }}
+      >
+        {props.detail}
+      </span>
+    </div>
+  )
+}
+
+function Panel(props: { title: string; note: string; children: JSX.Element }): JSX.Element {
+  return (
+    <section style={{ ...card(), padding: "12px 14px" }}>
+      <div style={{ display: "flex", "align-items": "baseline", gap: "8px", "margin-bottom": "12px" }}>
+        <strong style={{ "font-family": FONT_SANS, "font-size": "12px", color: "var(--color-text)" }}>
+          {props.title}
+        </strong>
+        <span style={muted()}>{props.note}</span>
+      </div>
+      {props.children}
+    </section>
+  )
+}
+
+function Bars(props: { items: Count[] }): JSX.Element {
+  const max = () => Math.max(1, ...props.items.map((item) => item.count))
+  return (
+    <div style={{ display: "grid", gap: "7px" }}>
+      <For each={props.items}>
+        {(item) => (
+          <div
+            style={{ display: "grid", "grid-template-columns": "82px 1fr 54px", "align-items": "center", gap: "8px" }}
+          >
+            <span
+              title={item.name}
+              style={{ ...muted(), overflow: "hidden", "text-overflow": "ellipsis", "white-space": "nowrap" }}
+            >
+              {item.name}
+            </span>
+            <div
+              style={{ height: "5px", background: "var(--color-border)", "border-radius": "99px", overflow: "hidden" }}
+            >
+              <div
+                style={{
+                  width: `${(item.count / max()) * 100}%`,
+                  height: "100%",
+                  background: "var(--color-accent)",
+                  "border-radius": "99px",
+                }}
+              />
+            </div>
+            <span style={{ ...muted(), "text-align": "right" }}>{item.count.toLocaleString()}</span>
+          </div>
+        )}
+      </For>
+    </div>
+  )
+}
+
+function Line(props: { values: number[]; floor: number; ceiling: number }): JSX.Element {
+  const width = 720
+  const height = 120
+  const points = () =>
+    props.values
+      .map((value, index) => {
+        const x = props.values.length < 2 ? 0 : (index / (props.values.length - 1)) * width
+        const y =
+          height -
+          ((Math.min(props.ceiling, Math.max(props.floor, value)) - props.floor) / (props.ceiling - props.floor)) *
+            height
+        return `${round(x)},${round(y)}`
+      })
+      .join(" ")
+  return (
+    <div style={{ position: "relative", height: `${height + 24}px` }}>
+      <svg
+        viewBox={`0 0 ${width} ${height}`}
+        preserveAspectRatio="none"
+        style={{ width: "100%", height: `${height}px`, overflow: "visible" }}
+      >
+        <line x1="0" x2={width} y1={height / 3} y2={height / 3} stroke="var(--color-border)" stroke-dasharray="3 4" />
+        <line
+          x1="0"
+          x2={width}
+          y1={(height * 2) / 3}
+          y2={(height * 2) / 3}
+          stroke="var(--color-border)"
+          stroke-dasharray="3 4"
+        />
+        <polyline
+          points={points()}
+          fill="none"
+          stroke="var(--color-accent)"
+          stroke-width="2"
+          vector-effect="non-scaling-stroke"
+        />
+      </svg>
+      <div style={{ display: "flex", "justify-content": "space-between", ...muted() }}>
+        <span>cycle 1</span>
+        <span>cycle {props.values.length}</span>
+      </div>
+    </div>
+  )
+}
+
+function QualityGauge(props: { value: number }): JSX.Element {
+  return (
+    <div style={{ padding: "10px 0" }}>
+      <div style={{ display: "flex", "justify-content": "space-between", "margin-bottom": "8px" }}>
+        <span style={muted()}>low</span>
+        <strong style={{ ...large(), "font-size": "18px" }}>Q{props.value}</strong>
+        <span style={muted()}>excellent</span>
+      </div>
+      <div
+        style={{
+          height: "8px",
+          background: "linear-gradient(90deg, #d65a4a, #d4a72c, #4ca56a)",
+          "border-radius": "99px",
+          position: "relative",
+        }}
+      >
+        <span
+          style={{
+            position: "absolute",
+            left: `${Math.min(100, (props.value / 40) * 100)}%`,
+            top: "50%",
+            width: "12px",
+            height: "12px",
+            background: "var(--color-bg)",
+            border: "2px solid var(--color-text)",
+            "border-radius": "50%",
+            transform: "translate(-50%, -50%)",
+          }}
+        />
+      </div>
+    </div>
+  )
+}
+
+function Rug(props: { values: number[] }): JSX.Element {
+  const min = () => Math.min(0, ...props.values)
+  const max = () => Math.max(1, ...props.values)
+  return (
+    <div
+      style={{ height: "126px", position: "relative", border: "0", "border-bottom": "1px solid var(--color-border)" }}
+    >
+      <For each={props.values.slice(0, 2000)}>
+        {(value, index) => (
+          <span
+            title={`${value}`}
+            style={{
+              position: "absolute",
+              left: `${((value - min()) / Math.max(1, max() - min())) * 100}%`,
+              bottom: 0,
+              width: "1px",
+              height: `${18 + ((index() * 17) % 88)}px`,
+              background: "color-mix(in srgb, var(--color-accent) 62%, transparent)",
+            }}
+          />
+        )}
+      </For>
+    </div>
+  )
+}
+
+function Check(props: { ok: boolean; text: string }): JSX.Element {
+  return (
+    <div
+      style={{
+        display: "flex",
+        gap: "8px",
+        "align-items": "center",
+        "font-family": FONT_SANS,
+        "font-size": "11px",
+        color: "var(--color-text-muted)",
+      }}
+    >
+      <span
+        style={{
+          display: "grid",
+          "place-items": "center",
+          width: "16px",
+          height: "16px",
+          "border-radius": "50%",
+          background: props.ok ? "color-mix(in srgb, #4ca56a 15%, transparent)" : "var(--color-bg-subtle)",
+          color: props.ok ? "#4ca56a" : "var(--color-text-faint)",
+        }}
+      >
+        {props.ok ? "✓" : "·"}
+      </span>
+      {props.text}
+    </div>
+  )
+}
+
+function Table(props: { columns: string[]; children: JSX.Element }): JSX.Element {
+  return (
+    <table style={{ width: "100%", "border-collapse": "collapse", "font-family": FONT_SANS, "font-size": "11px" }}>
+      <thead style={{ position: "sticky", top: "51px", "z-index": 3, background: "var(--color-bg)" }}>
+        <tr>
+          <For each={props.columns}>{(column) => <th style={head()}>{column}</th>}</For>
+        </tr>
+      </thead>
+      <tbody>{props.children}</tbody>
+    </table>
+  )
+}
+
+function Cell(props: { children: JSX.Element; mono?: boolean }): JSX.Element {
+  return (
+    <td
+      style={{
+        padding: "7px 10px",
+        border: "0",
+        "border-bottom": "1px solid var(--color-border)",
+        "font-family": props.mono ? FONT_CODE : FONT_SANS,
+        color: "var(--color-text-muted)",
+        "white-space": "nowrap",
+        "max-width": "320px",
+        overflow: "hidden",
+        "text-overflow": "ellipsis",
+      }}
+    >
+      {props.children}
+    </td>
+  )
+}
+
+function noun(file: BiologicalFile): string {
+  if (file.format === "fastq") return "reads"
+  if (file.format === "vcf") return "variants"
+  if (file.format === "sam") return "alignments"
+  if (file.format === "mzml") return "spectra"
+  return "features"
+}
+
+function match<T>(values: T[], query: string, content: (value: T) => string): T[] {
+  const term = query.trim().toLowerCase()
+  if (!term) return values
+  return values.filter((value) => content(value).toLowerCase().includes(term))
+}
+
+function short(value: string, length: number): string {
+  if (value.length <= length) return value
+  return `${value.slice(0, length - 1)}…`
+}
+
+function compact(value: number): string {
+  return new Intl.NumberFormat("en", {
+    notation: value >= 10_000 ? "compact" : "standard",
+    maximumFractionDigits: 1,
+  }).format(value)
+}
+
+function round(value: number): number {
+  return Math.round(value * 100) / 100
+}
+
+function grid(): JSX.CSSProperties {
+  return { display: "grid", "grid-template-columns": "repeat(auto-fit, minmax(280px, 1fr))", gap: "12px" }
+}
+
+function card(): JSX.CSSProperties {
+  return {
+    padding: "12px",
+    border: "1px solid var(--color-border)",
+    "border-radius": "7px",
+    background: "var(--color-bg)",
+    "min-width": 0,
+  }
+}
+
+function muted(): JSX.CSSProperties {
+  return { "font-family": FONT_MONO, "font-size": "9px", color: "var(--color-text-faint)" }
+}
+
+function large(): JSX.CSSProperties {
+  return {
+    display: "block",
+    "font-family": FONT_SANS,
+    "font-size": "20px",
+    "font-weight": 600,
+    color: "var(--color-text)",
+    "letter-spacing": "-0.02em",
+  }
+}
+
+function formatBadge(): JSX.CSSProperties {
+  return {
+    padding: "2px 7px",
+    "border-radius": "4px",
+    background: "color-mix(in srgb, var(--color-accent) 12%, transparent)",
+    color: "var(--color-accent)",
+    "font-family": FONT_MONO,
+    "font-size": "9px",
+    "font-weight": 600,
+    "letter-spacing": "0.05em",
+  }
+}
+
+function warning(): JSX.CSSProperties {
+  return {
+    padding: "2px 7px",
+    "border-radius": "4px",
+    background: "color-mix(in srgb, #d4a72c 13%, transparent)",
+    color: "#a57500",
+    "font-family": FONT_MONO,
+    "font-size": "9px",
+  }
+}
+
+function button(active = false): JSX.CSSProperties {
+  return {
+    padding: "5px 9px",
+    border: "1px solid var(--color-border)",
+    "border-radius": "5px",
+    background: active ? "var(--color-bg-subtle)" : "transparent",
+    color: active ? "var(--color-text)" : "var(--color-text-muted)",
+    "font-family": FONT_SANS,
+    "font-size": "10px",
+    cursor: "pointer",
+  }
+}
+
+function input(): JSX.CSSProperties {
+  return {
+    width: "min(360px, 100%)",
+    padding: "7px 10px",
+    border: "1px solid var(--color-border)",
+    "border-radius": "5px",
+    outline: "none",
+    background: "var(--color-bg-subtle)",
+    color: "var(--color-text)",
+    "font-family": FONT_SANS,
+    "font-size": "11px",
+  }
+}
+
+function head(): JSX.CSSProperties {
+  return {
+    padding: "7px 10px",
+    border: "0",
+    "border-bottom": "1px solid var(--color-border)",
+    color: "var(--color-text-faint)",
+    "font-family": FONT_MONO,
+    "font-size": "9px",
+    "font-weight": 500,
+    "text-align": "left",
+    "text-transform": "uppercase",
+    "letter-spacing": "0.05em",
+    "white-space": "nowrap",
+  }
+}
+
+function empty(): JSX.CSSProperties {
+  return {
+    display: "grid",
+    "place-items": "center",
+    "align-content": "center",
+    gap: "8px",
+    height: "100%",
+    padding: "36px",
+    "text-align": "center",
+  }
+}
+
+export default ScientificDataView
diff --git a/frontend/workspace/src/science/formats/biological.test.ts b/frontend/workspace/src/science/formats/biological.test.ts
new file mode 100644
index 00000000..31773b9b
--- /dev/null
+++ b/frontend/workspace/src/science/formats/biological.test.ts
@@ -0,0 +1,194 @@
+import { describe, expect, test } from "bun:test"
+import { readFileSync } from "node:fs"
+import { fileURLToPath } from "node:url"
+import { detectBiologicalFormat, parseBiologicalFile } from "./biological"
+
+const read = (path: string) => readFileSync(fileURLToPath(new URL(path, import.meta.url)), "utf8")
+
+describe("biological format detection", () => {
+  test.each([
+    ["FASTQ", "fastq"],
+    ["fq", "fastq"],
+    ["vcf", "vcf"],
+    ["bed", "bed"],
+    ["gff3", "gff"],
+    ["gtf", "gtf"],
+    ["sam", "sam"],
+    ["mzML", "mzml"],
+    ["mzxml", "mzml"],
+  ])("detects %s as %s", (extension, format) => {
+    expect(detectBiologicalFormat(extension)).toBe(format as ReturnType<typeof detectBiologicalFormat>)
+  })
+
+  test("leaves unrelated text files alone", () => {
+    expect(detectBiologicalFormat("txt")).toBeUndefined()
+  })
+})
+
+describe("FASTQ inspection", () => {
+  test("computes read, base, GC, N, and quality summaries", () => {
+    const result = parseBiologicalFile(
+      "fastq",
+      ["@read_1 lane=1", "ACGT", "+", "IIII", "@read_2", "GGNN", "+", "!!55", ""].join("\n"),
+    )
+
+    expect(result.format).toBe("fastq")
+    if (result.format !== "fastq") throw new Error("wrong parser")
+    expect(result.reads).toBe(2)
+    expect(result.bases).toBe(8)
+    expect(result.gc).toBe(50)
+    expect(result.n).toBe(25)
+    expect(result.meanLength).toBe(4)
+    expect(result.meanQuality).toBe(25)
+    expect(result.q30).toBe(50)
+    expect(result.records[0]).toMatchObject({ id: "read_1", length: 4, gc: 50, quality: 40 })
+    expect(result.cycles.slice(0, 4)).toEqual([20, 20, 30, 30])
+  })
+
+  test("reports malformed records without discarding valid reads", () => {
+    const result = parseBiologicalFile("fastq", "@good\nAC\n+\nII\n@broken\nAC\nnot-plus\nII\n")
+    if (result.format !== "fastq") throw new Error("wrong parser")
+    expect(result.reads).toBe(1)
+    expect(result.invalid).toBe(1)
+  })
+})
+
+describe("VCF inspection", () => {
+  test("summarizes samples, filters, chromosomes, and variant classes", () => {
+    const result = parseBiologicalFile(
+      "vcf",
+      [
+        "##fileformat=VCFv4.3",
+        "##reference=GRCh38",
+        "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tcase\tcontrol",
+        "chr1\t10\trs1\tA\tG\t60\tPASS\tDP=20\tGT\t0/1\t0/0",
+        "chr1\t20\t.\tA\tAT\t42\tPASS\tDP=12\tGT\t0/1\t0/0",
+        "chr2\t30\t.\tAT\tA\t.\tLowQual\tDP=4\tGT\t1/1\t0/1",
+        "chr2\t40\t.\tA\t<DEL>\t12\tPASS\tEND=50\tGT\t0/1\t0/0",
+      ].join("\n"),
+    )
+
+    expect(result.format).toBe("vcf")
+    if (result.format !== "vcf") throw new Error("wrong parser")
+    expect(result.fileformat).toBe("VCFv4.3")
+    expect(result.reference).toBe("GRCh38")
+    expect(result.samples).toEqual(["case", "control"])
+    expect(result.variants).toBe(4)
+    expect(result.passed).toBe(3)
+    expect(result.types).toEqual({ snv: 1, insertion: 1, deletion: 1, symbolic: 1, other: 0 })
+    expect(result.chromosomes).toEqual([
+      { name: "chr1", count: 2 },
+      { name: "chr2", count: 2 },
+    ])
+    expect(result.records[0]).toMatchObject({ chrom: "chr1", pos: 10, type: "snv", depth: 20 })
+  })
+})
+
+describe("interval inspection", () => {
+  test("parses BED spans and chromosome coverage", () => {
+    const result = parseBiologicalFile(
+      "bed",
+      ["track name=peaks", "chr1\t10\t20\tpeak-a\t100\t+", "chr1\t30\t45\tpeak-b\t50\t-", "chr2\t5\t8"].join("\n"),
+    )
+
+    expect(result.format).toBe("bed")
+    if (result.format !== "bed") throw new Error("wrong parser")
+    expect(result.features).toBe(3)
+    expect(result.totalSpan).toBe(28)
+    expect(result.meanSpan).toBeCloseTo(9.33, 1)
+    expect(result.chromosomes).toEqual([
+      { name: "chr1", count: 2 },
+      { name: "chr2", count: 1 },
+    ])
+    expect(result.records[0]).toMatchObject({ name: "peak-a", strand: "+", span: 10 })
+  })
+
+  test("parses GFF feature types and attributes", () => {
+    const result = parseBiologicalFile(
+      "gff",
+      [
+        "##gff-version 3",
+        "chr1\tsrc\tgene\t1\t100\t.\t+\t.\tID=gene1;Name=TP53",
+        "chr1\tsrc\texon\t1\t20\t.\t+\t.\tParent=gene1",
+      ].join("\n"),
+    )
+
+    expect(result.format).toBe("gff")
+    if (result.format !== "gff") throw new Error("wrong parser")
+    expect(result.features).toBe(2)
+    expect(result.types).toEqual([
+      { name: "gene", count: 1 },
+      { name: "exon", count: 1 },
+    ])
+    expect(result.records[0]).toMatchObject({ type: "gene", name: "TP53", span: 100 })
+  })
+})
+
+describe("SAM inspection", () => {
+  test("summarizes references, mapping state, flags, and MAPQ", () => {
+    const result = parseBiologicalFile(
+      "sam",
+      [
+        "@HD\tVN:1.6\tSO:coordinate",
+        "@SQ\tSN:chr1\tLN:248956422",
+        "r1\t0\tchr1\t10\t60\t4M\t*\t0\t0\tACGT\tIIII",
+        "r2\t4\t*\t0\t0\t*\t*\t0\t0\tNNNN\t!!!!",
+        "r3\t256\tchr1\t20\t20\t4M\t*\t0\t0\tTGCA\tIIII",
+      ].join("\n"),
+    )
+
+    expect(result.format).toBe("sam")
+    if (result.format !== "sam") throw new Error("wrong parser")
+    expect(result.alignments).toBe(3)
+    expect(result.mapped).toBe(2)
+    expect(result.unmapped).toBe(1)
+    expect(result.secondary).toBe(1)
+    expect(result.meanMapq).toBe(40)
+    expect(result.references).toEqual([{ name: "chr1", length: 248956422 }])
+  })
+})
+
+describe("mzML inspection", () => {
+  test("extracts run metadata and spectrum level inventory", () => {
+    const result = parseBiologicalFile(
+      "mzml",
+      `<?xml version="1.0"?>
+      <mzML>
+        <run id="sample-01">
+          <spectrumList count="3">
+            <spectrum id="scan=1"><cvParam accession="MS:1000511" name="ms level" value="1"/><cvParam accession="MS:1000016" name="scan start time" value="0.5" unitName="minute"/></spectrum>
+            <spectrum id="scan=2"><cvParam accession="MS:1000511" name="ms level" value="2"/><cvParam accession="MS:1000016" name="scan start time" value="0.8" unitName="minute"/></spectrum>
+            <spectrum id="scan=3"><cvParam accession="MS:1000511" name="ms level" value="2"/></spectrum>
+          </spectrumList>
+          <chromatogramList count="2"/>
+        </run>
+      </mzML>`,
+    )
+
+    expect(result.format).toBe("mzml")
+    if (result.format !== "mzml") throw new Error("wrong parser")
+    expect(result.run).toBe("sample-01")
+    expect(result.spectra).toBe(3)
+    expect(result.chromatograms).toBe(2)
+    expect(result.levels).toEqual([
+      { name: "MS1", count: 1 },
+      { name: "MS2", count: 2 },
+    ])
+    expect(result.times).toEqual([0.5, 0.8])
+  })
+})
+
+describe("scientific data workbench integration", () => {
+  test("routes biological formats into the shared file preview", () => {
+    const preview = read("../../atlas/FilePreview.tsx")
+    const view = read("./ScientificDataView.tsx")
+
+    expect(preview).toContain('import { ScientificDataView } from "@/science/formats/ScientificDataView"')
+    expect(preview).toContain('kind() === "scientific-data"')
+    expect(preview).toContain("<ScientificDataView")
+    expect(view).toContain('data-component="scientific-data"')
+    expect(view).toContain("Per-cycle base quality")
+    expect(view).toContain("Variant classes")
+    expect(view).toContain("Spectrum inventory")
+  })
+})
diff --git a/frontend/workspace/src/science/formats/biological.ts b/frontend/workspace/src/science/formats/biological.ts
new file mode 100644
index 00000000..d6941596
--- /dev/null
+++ b/frontend/workspace/src/science/formats/biological.ts
@@ -0,0 +1,458 @@
+export type BiologicalFormat = "fastq" | "vcf" | "bed" | "gff" | "gtf" | "sam" | "mzml"
+
+export interface Count {
+  name: string
+  count: number
+}
+
+export interface FastqRecord {
+  id: string
+  sequence: string
+  length: number
+  gc: number
+  quality: number
+}
+
+export interface FastqFile {
+  format: "fastq"
+  reads: number
+  bases: number
+  gc: number
+  n: number
+  meanLength: number
+  minLength: number
+  maxLength: number
+  meanQuality: number
+  q30: number
+  invalid: number
+  cycles: number[]
+  records: FastqRecord[]
+  truncated: boolean
+}
+
+export interface VcfRecord {
+  chrom: string
+  pos: number
+  id: string
+  ref: string
+  alt: string
+  qual?: number
+  filter: string
+  type: keyof VcfTypes
+  depth?: number
+}
+
+export interface VcfTypes {
+  snv: number
+  insertion: number
+  deletion: number
+  symbolic: number
+  other: number
+}
+
+export interface VcfFile {
+  format: "vcf"
+  fileformat: string
+  reference: string
+  samples: string[]
+  variants: number
+  passed: number
+  meanQuality: number
+  types: VcfTypes
+  chromosomes: Count[]
+  filters: Count[]
+  records: VcfRecord[]
+  truncated: boolean
+}
+
+export interface IntervalRecord {
+  chrom: string
+  start: number
+  end: number
+  name: string
+  type: string
+  strand: string
+  score: string
+  span: number
+}
+
+export interface IntervalFile {
+  format: "bed" | "gff" | "gtf"
+  features: number
+  totalSpan: number
+  meanSpan: number
+  maxSpan: number
+  chromosomes: Count[]
+  types: Count[]
+  records: IntervalRecord[]
+  truncated: boolean
+}
+
+export interface SamRecord {
+  name: string
+  flag: number
+  reference: string
+  position: number
+  mapq: number
+  cigar: string
+  length: number
+}
+
+export interface SamFile {
+  format: "sam"
+  version: string
+  order: string
+  alignments: number
+  mapped: number
+  unmapped: number
+  secondary: number
+  supplementary: number
+  duplicates: number
+  meanMapq: number
+  references: { name: string; length: number }[]
+  chromosomes: Count[]
+  records: SamRecord[]
+  truncated: boolean
+}
+
+export interface MzmlFile {
+  format: "mzml"
+  run: string
+  spectra: number
+  chromatograms: number
+  levels: Count[]
+  times: number[]
+  range?: { start: number; end: number }
+  truncated: boolean
+}
+
+export type BiologicalFile = FastqFile | VcfFile | IntervalFile | SamFile | MzmlFile
+
+const LIMIT = 10_000
+
+const formats: Record<string, BiologicalFormat> = {
+  fastq: "fastq",
+  fq: "fastq",
+  vcf: "vcf",
+  bed: "bed",
+  bedgraph: "bed",
+  gff: "gff",
+  gff3: "gff",
+  gtf: "gtf",
+  sam: "sam",
+  mzml: "mzml",
+  mzxml: "mzml",
+}
+
+export function detectBiologicalFormat(extension: string): BiologicalFormat | undefined {
+  return formats[extension.toLowerCase()]
+}
+
+export function parseBiologicalFile(format: BiologicalFormat, text: string): BiologicalFile {
+  if (format === "fastq") return parseFastq(text)
+  if (format === "vcf") return parseVcf(text)
+  if (format === "sam") return parseSam(text)
+  if (format === "mzml") return parseMzml(text)
+  return parseIntervals(format, text)
+}
+
+function parseFastq(text: string): FastqFile {
+  const lines = text.split(/\r?\n/)
+  const chunks = Array.from({ length: Math.ceil(lines.length / 4) }, (_, index) =>
+    lines.slice(index * 4, index * 4 + 4),
+  )
+  const parsed = chunks.reduce<{ records: FastqRecord[]; qualities: number[][]; invalid: number }>(
+    (all, chunk) => {
+      if (!chunk.some(Boolean)) return all
+      const valid =
+        chunk.length === 4 &&
+        chunk[0]?.startsWith("@") &&
+        chunk[2]?.startsWith("+") &&
+        chunk[1]?.length === chunk[3]?.length
+      if (!valid) return { ...all, invalid: all.invalid + 1 }
+      if (all.records.length >= LIMIT) return all
+      const sequence = chunk[1]!.toUpperCase()
+      const scores = Array.from(chunk[3]!, (value) => Math.max(0, value.charCodeAt(0) - 33))
+      const gc = sequence ? (sequence.match(/[GC]/g)?.length ?? 0) / sequence.length : 0
+      return {
+        records: [
+          ...all.records,
+          {
+            id: chunk[0]!.slice(1).trim().split(/\s+/)[0] || `read_${all.records.length + 1}`,
+            sequence,
+            length: sequence.length,
+            gc: round(gc * 100),
+            quality: round(mean(scores)),
+          },
+        ],
+        qualities: [...all.qualities, scores],
+        invalid: all.invalid,
+      }
+    },
+    { records: [], qualities: [], invalid: 0 },
+  )
+  const sequences = parsed.records.map((record) => record.sequence).join("")
+  const scores = parsed.qualities.flat()
+  const lengths = parsed.records.map((record) => record.length)
+  const max = Math.max(0, ...lengths)
+  const cycles = Array.from({ length: Math.min(max, 250) }, (_, index) =>
+    round(mean(parsed.qualities.map((quality) => quality[index]).filter((value) => value !== undefined))),
+  )
+  return {
+    format: "fastq",
+    reads: parsed.records.length,
+    bases: sequences.length,
+    gc: round(((sequences.match(/[GC]/g)?.length ?? 0) / Math.max(1, sequences.length)) * 100),
+    n: round(((sequences.match(/N/g)?.length ?? 0) / Math.max(1, sequences.length)) * 100),
+    meanLength: round(mean(lengths)),
+    minLength: lengths.length ? Math.min(...lengths) : 0,
+    maxLength: max,
+    meanQuality: round(mean(scores)),
+    q30: round((scores.filter((score) => score >= 30).length / Math.max(1, scores.length)) * 100),
+    invalid: parsed.invalid,
+    cycles,
+    records: parsed.records,
+    truncated: chunks.length - parsed.invalid > LIMIT,
+  }
+}
+
+function parseVcf(text: string): VcfFile {
+  const lines = text.split(/\r?\n/)
+  const meta = Object.fromEntries(
+    lines
+      .filter((line) => line.startsWith("##") && line.includes("="))
+      .map((line) => {
+        const index = line.indexOf("=")
+        return [line.slice(2, index), line.slice(index + 1)]
+      }),
+  )
+  const header = lines.find((line) => line.startsWith("#CHROM"))?.split("\t") ?? []
+  const rows = lines.filter((line) => line && !line.startsWith("#"))
+  const records = rows.slice(0, LIMIT).map((line): VcfRecord => {
+    const fields = line.split("\t")
+    const ref = fields[3] ?? ""
+    const alt = fields[4] ?? ""
+    const info = fields[7] ?? ""
+    return {
+      chrom: fields[0] ?? "",
+      pos: Number(fields[1]) || 0,
+      id: fields[2] === "." ? "" : (fields[2] ?? ""),
+      ref,
+      alt,
+      qual: number(fields[5]),
+      filter: fields[6] || ".",
+      type: variantType(ref, alt),
+      depth: number(info.match(/(?:^|;)DP=(\d+)/)?.[1]),
+    }
+  })
+  const types = records.reduce<VcfTypes>((all, record) => ({ ...all, [record.type]: all[record.type] + 1 }), {
+    snv: 0,
+    insertion: 0,
+    deletion: 0,
+    symbolic: 0,
+    other: 0,
+  })
+  return {
+    format: "vcf",
+    fileformat: meta.fileformat ?? "",
+    reference: meta.reference ?? "",
+    samples: header.slice(9),
+    variants: rows.length,
+    passed: rows.filter((line) => {
+      const filter = line.split("\t")[6]
+      return filter === "PASS" || filter === "."
+    }).length,
+    meanQuality: round(mean(records.map((record) => record.qual).filter((value) => value !== undefined))),
+    types,
+    chromosomes: counts(records.map((record) => record.chrom)),
+    filters: counts(records.map((record) => record.filter)),
+    records,
+    truncated: rows.length > LIMIT,
+  }
+}
+
+function parseIntervals(format: "bed" | "gff" | "gtf", text: string): IntervalFile {
+  const rows = text
+    .split(/\r?\n/)
+    .filter((line) => line && !line.startsWith("#") && !line.startsWith("track") && !line.startsWith("browser"))
+  const records = rows.slice(0, LIMIT).flatMap((line): IntervalRecord[] => {
+    const fields = line.split("\t")
+    if (fields.length < 3) return []
+    if (format === "bed") {
+      const start = Number(fields[1]) || 0
+      const end = Number(fields[2]) || start
+      return [
+        {
+          chrom: fields[0] ?? "",
+          start,
+          end,
+          name: fields[3] ?? "",
+          type: "region",
+          score: fields[4] ?? "",
+          strand: fields[5] ?? ".",
+          span: Math.max(0, end - start),
+        },
+      ]
+    }
+    const start = Number(fields[3]) || 0
+    const end = Number(fields[4]) || start
+    const attributes = attributesOf(fields[8] ?? "")
+    return [
+      {
+        chrom: fields[0] ?? "",
+        start,
+        end,
+        name: attributes.Name ?? attributes.gene_name ?? attributes.ID ?? attributes.gene_id ?? "",
+        type: fields[2] ?? "feature",
+        score: fields[5] ?? "",
+        strand: fields[6] ?? ".",
+        span: Math.max(0, end - start + 1),
+      },
+    ]
+  })
+  const spans = records.map((record) => record.span)
+  return {
+    format,
+    features: rows.length,
+    totalSpan: spans.reduce((total, value) => total + value, 0),
+    meanSpan: round(mean(spans)),
+    maxSpan: spans.length ? Math.max(...spans) : 0,
+    chromosomes: counts(records.map((record) => record.chrom)),
+    types: counts(records.map((record) => record.type)),
+    records,
+    truncated: rows.length > LIMIT,
+  }
+}
+
+function parseSam(text: string): SamFile {
+  const lines = text.split(/\r?\n/).filter(Boolean)
+  const hd =
+    lines
+      .find((line) => line.startsWith("@HD"))
+      ?.split("\t")
+      .slice(1) ?? []
+  const header = Object.fromEntries(hd.map((entry) => entry.split(":", 2)))
+  const references = lines
+    .filter((line) => line.startsWith("@SQ"))
+    .map((line) =>
+      Object.fromEntries(
+        line
+          .split("\t")
+          .slice(1)
+          .map((entry) => entry.split(":", 2)),
+      ),
+    )
+    .map((record) => ({ name: record.SN ?? "", length: Number(record.LN) || 0 }))
+  const rows = lines.filter((line) => !line.startsWith("@"))
+  const records = rows.slice(0, LIMIT).flatMap((line): SamRecord[] => {
+    const fields = line.split("\t")
+    if (fields.length < 11) return []
+    return [
+      {
+        name: fields[0] ?? "",
+        flag: Number(fields[1]) || 0,
+        reference: fields[2] ?? "*",
+        position: Number(fields[3]) || 0,
+        mapq: Number(fields[4]) || 0,
+        cigar: fields[5] ?? "*",
+        length: fields[9]?.length ?? 0,
+      },
+    ]
+  })
+  const mapped = records.filter((record) => !(record.flag & 4))
+  return {
+    format: "sam",
+    version: header.VN ?? "",
+    order: header.SO ?? "",
+    alignments: rows.length,
+    mapped: mapped.length,
+    unmapped: records.filter((record) => record.flag & 4).length,
+    secondary: records.filter((record) => record.flag & 256).length,
+    supplementary: records.filter((record) => record.flag & 2048).length,
+    duplicates: records.filter((record) => record.flag & 1024).length,
+    meanMapq: round(mean(mapped.map((record) => record.mapq))),
+    references,
+    chromosomes: counts(mapped.map((record) => record.reference)),
+    records,
+    truncated: rows.length > LIMIT,
+  }
+}
+
+function parseMzml(text: string): MzmlFile {
+  const spectra =
+    Number(text.match(/<spectrumList\b[^>]*\bcount="(\d+)"/i)?.[1]) || (text.match(/<spectrum\b/gi) ?? []).length
+  const chromatograms =
+    Number(text.match(/<chromatogramList\b[^>]*\bcount="(\d+)"/i)?.[1]) ||
+    (text.match(/<chromatogram\b/gi) ?? []).length
+  const blocks = text.match(/<spectrum\b[\s\S]*?<\/spectrum>/gi) ?? []
+  const levels = counts(
+    blocks.map(
+      (block) =>
+        `MS${block.match(/accession="MS:1000511"[^>]*\bvalue="(\d+)"/i)?.[1] ?? block.match(/name="ms level"[^>]*\bvalue="(\d+)"/i)?.[1] ?? "?"}`,
+    ),
+  ).sort((a, b) => a.name.localeCompare(b.name, undefined, { numeric: true }))
+  const times = Array.from(
+    text.matchAll(/(?:accession="MS:1000016"|name="scan start time")[^>]*\bvalue="([\d.]+)"/gi),
+    (match) => Number(match[1]),
+  ).filter(Number.isFinite)
+  return {
+    format: "mzml",
+    run: text.match(/<run\b[^>]*\bid="([^"]+)"/i)?.[1] ?? "",
+    spectra,
+    chromatograms,
+    levels,
+    times: times.slice(0, LIMIT),
+    range: times.length ? { start: Math.min(...times), end: Math.max(...times) } : undefined,
+    truncated: times.length > LIMIT,
+  }
+}
+
+function variantType(ref: string, alt: string): keyof VcfTypes {
+  if (alt.startsWith("<") || alt.includes("[") || alt.includes("]")) return "symbolic"
+  const alternatives = alt.split(",")
+  if (ref.length === 1 && alternatives.every((value) => value.length === 1)) return "snv"
+  if (alternatives.every((value) => value.length > ref.length)) return "insertion"
+  if (alternatives.every((value) => value.length < ref.length)) return "deletion"
+  return "other"
+}
+
+function attributesOf(value: string): Record<string, string> {
+  return Object.fromEntries(
+    value
+      .split(";")
+      .map((item) => item.trim())
+      .filter(Boolean)
+      .map((item) => {
+        const equal = item.indexOf("=")
+        if (equal >= 0) return [item.slice(0, equal), item.slice(equal + 1).replace(/^"|"$/g, "")]
+        const space = item.indexOf(" ")
+        if (space >= 0) return [item.slice(0, space), item.slice(space + 1).replace(/^"|"$/g, "")]
+        return [item, ""]
+      }),
+  )
+}
+
+function counts(values: string[]): Count[] {
+  const map = values.reduce<Record<string, number>>((all, value) => {
+    if (!value) return all
+    return { ...all, [value]: (all[value] ?? 0) + 1 }
+  }, {})
+  return Object.entries(map)
+    .map(([name, count]) => ({ name, count }))
+    .sort((a, b) => b.count - a.count)
+}
+
+function number(value?: string): number | undefined {
+  if (!value || value === ".") return
+  const result = Number(value)
+  return Number.isFinite(result) ? result : undefined
+}
+
+function mean(values: number[]): number {
+  if (!values.length) return 0
+  return values.reduce((total, value) => total + value, 0) / values.length
+}
+
+function round(value: number): number {
+  return Math.round(value * 100) / 100
+}

From b2b1e2f769ec9d80c1c130d9116f975e09909d9e Mon Sep 17 00:00:00 2001
From: Aayam Bansal <aayambansal@gmail.com>
Date: Wed, 29 Jul 2026 06:27:16 +0800
Subject: [PATCH 08/40] feat: inspect scientific binary files

---
 backend/cli/src/file/index.ts                 |  35 +-
 backend/cli/src/file/science.ts               | 254 +++++++
 backend/cli/src/server/routes/file.ts         |  59 ++
 backend/cli/test/file/science-inspect.test.ts | 117 ++++
 frontend/workspace/e2e/binary-science.spec.ts |  44 ++
 frontend/workspace/src/atlas/FilePreview.tsx  |  47 +-
 .../src/science/formats/BinaryScienceView.tsx | 643 ++++++++++++++++++
 .../src/science/formats/binary.test.ts        |  53 ++
 .../workspace/src/science/formats/binary.ts   |  71 ++
 tooling/sdk/js/src/v2/gen/sdk.gen.ts          | 216 ++++++
 tooling/sdk/js/src/v2/gen/types.gen.ts        | 130 ++++
 tooling/sdk/openapi.json                      | 362 ++++++++++
 12 files changed, 2025 insertions(+), 6 deletions(-)
 create mode 100644 backend/cli/src/file/science.ts
 create mode 100644 backend/cli/test/file/science-inspect.test.ts
 create mode 100644 frontend/workspace/e2e/binary-science.spec.ts
 create mode 100644 frontend/workspace/src/science/formats/BinaryScienceView.tsx
 create mode 100644 frontend/workspace/src/science/formats/binary.test.ts
 create mode 100644 frontend/workspace/src/science/formats/binary.ts

diff --git a/backend/cli/src/file/index.ts b/backend/cli/src/file/index.ts
index 5db6e9b3..2c02a9c0 100644
--- a/backend/cli/src/file/index.ts
+++ b/backend/cli/src/file/index.ts
@@ -15,6 +15,7 @@ import fuzzysort from "fuzzysort"
 import { Global } from "../global"
 import { FileWatcher } from "./watcher"
 import { createSearchCache } from "./search-cache"
+import { ScienceFile } from "./science"
 
 export namespace File {
   const log = Log.create({ service: "file" })
@@ -73,6 +74,8 @@ export namespace File {
         .optional(),
       encoding: z.literal("base64").optional(),
       mimeType: z.string().optional(),
+      size: z.number().optional(),
+      truncated: z.boolean().optional(),
     })
     .meta({
       ref: "FileContent",
@@ -303,13 +306,23 @@ export namespace File {
       return { type: "text", content: "" }
     }
 
-    const encode = await shouldEncode(bunFile)
+    const encode = ScienceFile.binary(file) || (await shouldEncode(bunFile))
 
     if (encode) {
+      if (bunFile.size > 16 * 1024 * 1024) {
+        return {
+          type: "text",
+          content: "",
+          mimeType: bunFile.type || "application/octet-stream",
+          encoding: "base64",
+          size: bunFile.size,
+          truncated: true,
+        }
+      }
       const buffer = await bunFile.arrayBuffer().catch(() => new ArrayBuffer(0))
       const content = Buffer.from(buffer).toString("base64")
       const mimeType = bunFile.type || "application/octet-stream"
-      return { type: "text", content, mimeType, encoding: "base64" }
+      return { type: "text", content, mimeType, encoding: "base64", size: bunFile.size }
     }
 
     // Return the file content verbatim — callers like the web editor write
@@ -333,6 +346,24 @@ export namespace File {
     return { type: "text", content }
   }
 
+  export async function inspect(file: string): Promise<ScienceFile.Inspection> {
+    const full = path.join(Instance.directory, file)
+    if (!Instance.containsPath(full)) {
+      throw new Error(`Access denied: path escapes project directory`)
+    }
+    return ScienceFile.inspect(full, file)
+  }
+
+  export async function raw(file: string): Promise<BunFile> {
+    const full = path.join(Instance.directory, file)
+    if (!Instance.containsPath(full)) {
+      throw new Error(`Access denied: path escapes project directory`)
+    }
+    const content = Bun.file(full)
+    if (!(await content.exists())) throw new HTTPException(404, { message: `File not found: ${file}` })
+    return content
+  }
+
   export async function write(file: string, content: string): Promise<Content> {
     using _ = log.time("write", { file })
     const full = path.join(Instance.directory, file)
diff --git a/backend/cli/src/file/science.ts b/backend/cli/src/file/science.ts
new file mode 100644
index 00000000..2c2febdb
--- /dev/null
+++ b/backend/cli/src/file/science.ts
@@ -0,0 +1,254 @@
+import path from "node:path"
+import z from "zod"
+
+export namespace ScienceFile {
+  export const Format = z.enum(["bam", "cram", "h5ad", "loom"])
+  export type Format = z.infer<typeof Format>
+
+  export const Inspection = z.object({
+    format: Format,
+    name: z.string(),
+    size: z.number(),
+    modified: z.number(),
+    signature: z.boolean(),
+    index: z.string().optional(),
+    tool: z.object({
+      name: z.string(),
+      available: z.boolean(),
+      detail: z.string().optional(),
+    }),
+    details: z.record(z.string(), z.unknown()),
+  })
+  export type Inspection = z.infer<typeof Inspection>
+
+  const python = String.raw`
+import json, sys
+try:
+    import h5py
+except Exception as exc:
+    print(json.dumps({"error": "h5py is not available", "detail": str(exc)}))
+    raise SystemExit(2)
+
+target = sys.argv[1]
+result = {"groups": [], "datasets": [], "attributes": {}, "summary": {}}
+
+def clean(value):
+    if hasattr(value, "tolist"):
+        value = value.tolist()
+    if isinstance(value, bytes):
+        return value.decode("utf-8", "replace")
+    if isinstance(value, (str, int, float, bool)) or value is None:
+        return value
+    if isinstance(value, (list, tuple)):
+        return [clean(item) for item in value[:50]]
+    return str(value)
+
+with h5py.File(target, "r") as handle:
+    result["attributes"] = {str(key): clean(value) for key, value in list(handle.attrs.items())[:50]}
+
+    def visit(name, value):
+        if len(result["groups"]) + len(result["datasets"]) >= 500:
+            return
+        if isinstance(value, h5py.Group):
+            result["groups"].append(name)
+            return
+        result["datasets"].append({
+            "path": name,
+            "shape": list(value.shape),
+            "dtype": str(value.dtype),
+            "bytes": int(value.size * value.dtype.itemsize),
+        })
+
+    handle.visititems(visit)
+    matrix = handle.get("X")
+    if matrix is None:
+        matrix = handle.get("matrix")
+    if matrix is not None and hasattr(matrix, "shape"):
+        result["summary"]["matrix"] = list(matrix.shape)
+    if "obs" in handle:
+        obs_index = handle["obs"].get("_index")
+        if obs_index is not None:
+            result["summary"]["observations"] = len(obs_index)
+    if "var" in handle:
+        var_index = handle["var"].get("_index")
+        if var_index is not None:
+            result["summary"]["variables"] = len(var_index)
+    if matrix is not None and hasattr(matrix, "shape") and len(matrix.shape) >= 2:
+        result["summary"].setdefault("observations", int(matrix.shape[0]))
+        result["summary"].setdefault("variables", int(matrix.shape[1]))
+    if "obsm" in handle:
+        result["summary"]["embeddings"] = list(handle["obsm"].keys())[:100]
+    if "layers" in handle:
+        result["summary"]["layers"] = list(handle["layers"].keys())[:100]
+    if "row_attrs" in handle:
+        result["summary"]["row_attributes"] = list(handle["row_attrs"].keys())[:100]
+    if "col_attrs" in handle:
+        result["summary"]["column_attributes"] = list(handle["col_attrs"].keys())[:100]
+
+print(json.dumps(result))
+`
+
+  export function format(file: string): Format | undefined {
+    const extension = path.extname(file).slice(1).toLowerCase()
+    return Format.options.find((value) => value === extension)
+  }
+
+  export function binary(file: string): boolean {
+    return format(file) !== undefined
+  }
+
+  export async function inspect(full: string, relative: string): Promise<Inspection> {
+    const kind = format(relative)
+    if (!kind) throw new Error(`Unsupported scientific binary format`)
+    const file = Bun.file(full)
+    if (!(await file.exists())) throw new Error(`File not found: ${relative}`)
+    const stat = await file.stat()
+    const bytes = new Uint8Array(await file.slice(0, 16).arrayBuffer())
+    const base = {
+      format: kind,
+      name: path.basename(relative),
+      size: stat.size,
+      modified: stat.mtimeMs,
+    }
+    if (kind === "h5ad" || kind === "loom") return inspectHdf5(full, base, bytes)
+    return inspectAlignment(full, relative, base, bytes)
+  }
+
+  async function inspectHdf5(
+    full: string,
+    base: Pick<Inspection, "format" | "name" | "size" | "modified">,
+    bytes: Uint8Array,
+  ): Promise<Inspection> {
+    const bin = Bun.which("python3") ?? Bun.which("python")
+    const signature = [0x89, 0x48, 0x44, 0x46, 0x0d, 0x0a, 0x1a, 0x0a].every((value, index) => bytes[index] === value)
+    if (!bin) {
+      return {
+        ...base,
+        signature,
+        tool: { name: "h5py", available: false, detail: "Python is not available on PATH" },
+        details: {},
+      }
+    }
+    const result = await command([bin, "-c", python, full], 20_000)
+    const data = result.code === 0 ? json(result.stdout) : undefined
+    return {
+      ...base,
+      signature,
+      tool: {
+        name: "h5py",
+        available: result.code === 0,
+        detail:
+          result.code === 0
+            ? `inspected with ${path.basename(bin)}`
+            : detail(result.stdout, result.stderr) ||
+              "Install h5py in the Python environment used to launch OpenScience",
+      },
+      details: data ?? {},
+    }
+  }
+
+  async function inspectAlignment(
+    full: string,
+    relative: string,
+    base: Pick<Inspection, "format" | "name" | "size" | "modified">,
+    bytes: Uint8Array,
+  ): Promise<Inspection> {
+    const bin = Bun.which("samtools")
+    const cram = base.format === "cram"
+    const signature = cram
+      ? bytes[0] === 0x43 && bytes[1] === 0x52 && bytes[2] === 0x41 && bytes[3] === 0x4d
+      : bytes[0] === 0x1f && bytes[1] === 0x8b
+    const index = await findIndex(full, relative, cram)
+    const version = cram && signature ? `${bytes[4] ?? 0}.${bytes[5] ?? 0}` : undefined
+    if (!bin) {
+      return {
+        ...base,
+        signature,
+        index,
+        tool: { name: "samtools", available: false, detail: "Install samtools to inspect headers and references" },
+        details: version ? { version } : {},
+      }
+    }
+    const header = await command([bin, "view", "-H", full], 20_000)
+    const refs = header.stdout
+      .split(/\r?\n/)
+      .filter((line) => line.startsWith("@SQ"))
+      .map((line) =>
+        Object.fromEntries(
+          line
+            .split("\t")
+            .slice(1)
+            .map((part) => part.split(":", 2)),
+        ),
+      )
+      .map((record) => ({ name: record.SN ?? "", length: Number(record.LN) || 0 }))
+    const hd = header.stdout
+      .split(/\r?\n/)
+      .find((line) => line.startsWith("@HD"))
+      ?.split("\t")
+      .slice(1)
+      .map((part) => part.split(":", 2))
+    const stats = index ? await command([bin, "idxstats", full], 20_000) : undefined
+    const chromosomes =
+      stats?.code === 0
+        ? stats.stdout
+            .split(/\r?\n/)
+            .filter(Boolean)
+            .map((line) => line.split("\t"))
+            .filter((row) => row[0] !== "*")
+            .map((row) => ({
+              name: row[0] ?? "",
+              length: Number(row[1]) || 0,
+              mapped: Number(row[2]) || 0,
+              unmapped: Number(row[3]) || 0,
+            }))
+        : []
+    return {
+      ...base,
+      signature,
+      index,
+      tool: {
+        name: "samtools",
+        available: header.code === 0,
+        detail: header.code === 0 ? "header inspected locally" : detail(header.stdout, header.stderr),
+      },
+      details: {
+        ...(version ? { version } : {}),
+        header: hd ? Object.fromEntries(hd) : {},
+        references: refs,
+        chromosomes,
+      },
+    }
+  }
+
+  async function findIndex(full: string, relative: string, cram: boolean): Promise<string | undefined> {
+    const extension = cram ? ".crai" : ".bai"
+    const candidates = [full + extension, full.replace(/\.[^.]+$/, extension)]
+    const found = await Promise.all(
+      candidates.map(async (candidate) => ((await Bun.file(candidate).exists()) ? candidate : undefined)),
+    )
+    const value = found.find(Boolean)
+    if (!value) return
+    return path.join(path.dirname(relative), path.basename(value)).replace(/^\.\//, "")
+  }
+
+  async function command(args: string[], timeout: number): Promise<{ code: number; stdout: string; stderr: string }> {
+    const process = Bun.spawn(args, { stdout: "pipe", stderr: "pipe" })
+    const timer = setTimeout(() => process.kill(), timeout)
+    const code = await process.exited
+    clearTimeout(timer)
+    const [stdout, stderr] = await Promise.all([
+      new Response(process.stdout).text(),
+      new Response(process.stderr).text(),
+    ])
+    return { code, stdout, stderr }
+  }
+
+  function json(value: string): Record<string, unknown> | undefined {
+    return JSON.parse(value) as Record<string, unknown>
+  }
+
+  function detail(stdout: string, stderr: string): string {
+    return (stderr.trim() || stdout.trim()).slice(0, 500)
+  }
+}
diff --git a/backend/cli/src/server/routes/file.ts b/backend/cli/src/server/routes/file.ts
index 961ebcdf..53af25f5 100644
--- a/backend/cli/src/server/routes/file.ts
+++ b/backend/cli/src/server/routes/file.ts
@@ -6,6 +6,7 @@ import { Ripgrep } from "../../file/ripgrep"
 import { LSP } from "../../lsp"
 import { Instance } from "../../project/instance"
 import { lazy } from "../../util/lazy"
+import { ScienceFile } from "../../file/science"
 
 export const FileRoutes = lazy(() =>
   new Hono()
@@ -202,6 +203,64 @@ export const FileRoutes = lazy(() =>
         return c.json(content)
       },
     )
+    .get(
+      "/file/inspect",
+      describeRoute({
+        summary: "Inspect a scientific binary file",
+        description: "Inspect BAM, CRAM, H5AD, or LOOM metadata with locally available scientific tools.",
+        operationId: "file.inspect",
+        responses: {
+          200: {
+            description: "Scientific file inspection",
+            content: {
+              "application/json": {
+                schema: resolver(ScienceFile.Inspection),
+              },
+            },
+          },
+        },
+      }),
+      validator(
+        "query",
+        z.object({
+          path: z.string(),
+        }),
+      ),
+      async (c) => {
+        const result = await File.inspect(c.req.valid("query").path)
+        return c.json(result)
+      },
+    )
+    .get(
+      "/file/raw",
+      describeRoute({
+        summary: "Download a file",
+        description: "Stream a project file without loading it into the JSON API as base64.",
+        operationId: "file.raw",
+        responses: {
+          200: {
+            description: "Raw file contents",
+          },
+        },
+      }),
+      validator(
+        "query",
+        z.object({
+          path: z.string(),
+        }),
+      ),
+      async (c) => {
+        const path = c.req.valid("query").path
+        const content = await File.raw(path)
+        return new Response(content, {
+          headers: {
+            "Content-Type": content.type || "application/octet-stream",
+            "Content-Length": String(content.size),
+            "Content-Disposition": `attachment; filename*=UTF-8''${encodeURIComponent(path.split("/").pop() || "download")}`,
+          },
+        })
+      },
+    )
     .get(
       "/file/status",
       describeRoute({
diff --git a/backend/cli/test/file/science-inspect.test.ts b/backend/cli/test/file/science-inspect.test.ts
new file mode 100644
index 00000000..ad9cedc2
--- /dev/null
+++ b/backend/cli/test/file/science-inspect.test.ts
@@ -0,0 +1,117 @@
+import { describe, expect, test } from "bun:test"
+import path from "node:path"
+import { File } from "../../src/file"
+import { Instance } from "../../src/project/instance"
+import { tmpdir } from "../fixture/fixture"
+
+describe("File.inspect", () => {
+  test("recognizes H5AD containers and reports local inspection capabilities", async () => {
+    await using tmp = await tmpdir({
+      init: async (directory) => {
+        const signature = Uint8Array.from([0x89, 0x48, 0x44, 0x46, 0x0d, 0x0a, 0x1a, 0x0a, 0, 0, 0, 0])
+        await Bun.write(path.join(directory, "cells.h5ad"), signature)
+      },
+    })
+
+    await Instance.provide({
+      directory: tmp.path,
+      fn: async () => {
+        const result = await File.inspect("cells.h5ad")
+        expect(result).toMatchObject({
+          format: "h5ad",
+          name: "cells.h5ad",
+          size: 12,
+          signature: true,
+          tool: { name: "h5py" },
+        })
+        expect(typeof result.tool.available).toBe("boolean")
+      },
+    })
+  })
+
+  test("recognizes CRAM version bytes and adjacent indexes", async () => {
+    await using tmp = await tmpdir({
+      init: async (directory) => {
+        await Bun.write(path.join(directory, "sample.cram"), Uint8Array.from([0x43, 0x52, 0x41, 0x4d, 3, 1, 0, 0]))
+        await Bun.write(path.join(directory, "sample.cram.crai"), "index")
+      },
+    })
+
+    await Instance.provide({
+      directory: tmp.path,
+      fn: async () => {
+        const result = await File.inspect("sample.cram")
+        expect(result).toMatchObject({
+          format: "cram",
+          signature: true,
+          index: "sample.cram.crai",
+          details: { version: "3.1" },
+          tool: { name: "samtools" },
+        })
+      },
+    })
+  })
+
+  test("recognizes BAM and conventional index names", async () => {
+    await using tmp = await tmpdir({
+      init: async (directory) => {
+        await Bun.write(path.join(directory, "sample.bam"), Uint8Array.from([0x1f, 0x8b, 8, 4, 0, 0, 0, 0]))
+        await Bun.write(path.join(directory, "sample.bai"), "index")
+      },
+    })
+
+    await Instance.provide({
+      directory: tmp.path,
+      fn: async () => {
+        const result = await File.inspect("sample.bam")
+        expect(result).toMatchObject({
+          format: "bam",
+          signature: true,
+          index: "sample.bai",
+          tool: { name: "samtools" },
+        })
+      },
+    })
+  })
+
+  test("rejects unsupported extensions and paths outside the project", async () => {
+    await using tmp = await tmpdir({
+      init: async (directory) => {
+        await Bun.write(path.join(directory, "notes.bin"), "content")
+      },
+    })
+
+    await Instance.provide({
+      directory: tmp.path,
+      fn: async () => {
+        await expect(File.inspect("notes.bin")).rejects.toThrow("Unsupported scientific binary format")
+        await expect(File.inspect("../../outside.h5ad")).rejects.toThrow("Access denied")
+      },
+    })
+  })
+})
+
+describe("large binary reads", () => {
+  test("returns metadata instead of base64-loading files above the preview limit", async () => {
+    await using tmp = await tmpdir({
+      init: async (directory) => {
+        const file = Bun.file(path.join(directory, "large.bam"))
+        const writer = file.writer()
+        writer.write(Uint8Array.from([0x1f, 0x8b, 8, 4]))
+        writer.write(new Uint8Array(16 * 1024 * 1024))
+        await writer.end()
+      },
+    })
+
+    await Instance.provide({
+      directory: tmp.path,
+      fn: async () => {
+        const result = await File.read("large.bam")
+        expect(result.encoding).toBe("base64")
+        expect(result.content).toBe("")
+        expect(result.truncated).toBe(true)
+        expect(result.size).toBeGreaterThan(16 * 1024 * 1024)
+      },
+    })
+  })
+})
diff --git a/frontend/workspace/e2e/binary-science.spec.ts b/frontend/workspace/e2e/binary-science.spec.ts
new file mode 100644
index 00000000..4c2d15d9
--- /dev/null
+++ b/frontend/workspace/e2e/binary-science.spec.ts
@@ -0,0 +1,44 @@
+import { mkdtempSync, rmSync, writeFileSync } from "node:fs"
+import { tmpdir } from "node:os"
+import path from "node:path"
+import { test, expect } from "./fixtures"
+
+test("inspects and streams scientific binary containers", async ({ page, gotoSession }) => {
+  const directory = mkdtempSync(path.join(tmpdir(), "openscience-binary-e2e-"))
+  writeFileSync(
+    path.join(directory, "cells.h5ad"),
+    Uint8Array.from([0x89, 0x48, 0x44, 0x46, 0x0d, 0x0a, 0x1a, 0x0a, 0, 0, 0, 0]),
+  )
+  writeFileSync(path.join(directory, "sample.cram"), Uint8Array.from([0x43, 0x52, 0x41, 0x4d, 3, 1, 0, 0]))
+  writeFileSync(path.join(directory, "sample.cram.crai"), "index")
+
+  try {
+    await gotoSession()
+    await page.getByRole("tab", { name: "Files", exact: true }).click()
+    const location = page.getByPlaceholder("/absolute/path")
+    await location.fill(directory)
+    await location.press("Enter")
+
+    await page.getByPlaceholder("filter this folder…").fill("cells.h5ad")
+    await page.getByRole("button", { name: /^cells\.h5ad\b/ }).click()
+    const h5ad = page.locator('[data-component="binary-science"][data-format="h5ad"]')
+    await expect(h5ad).toBeVisible()
+    await expect(h5ad.getByText("signature valid", { exact: true })).toBeVisible()
+    await expect(h5ad.getByText("H5AD container detected", { exact: true })).toBeVisible()
+    await expect(h5ad.getByText("python -m pip install h5py anndata", { exact: true })).toBeVisible()
+
+    const download = page.waitForEvent("download")
+    await page.getByRole("button", { name: "download", exact: true }).click()
+    expect((await download).suggestedFilename()).toBe("cells.h5ad")
+
+    await page.getByRole("tab", { name: "Files", exact: true }).click()
+    await page.getByPlaceholder("filter this folder…").fill("sample.cram")
+    await page.locator('button[title$="/sample.cram"]').click()
+    const cram = page.locator('[data-component="binary-science"][data-format="cram"]')
+    await expect(cram).toBeVisible()
+    await expect(cram.getByText("sample.cram.crai", { exact: true })).toBeVisible()
+    await expect(cram.getByText("CRAM container detected", { exact: true })).toBeVisible()
+  } finally {
+    rmSync(directory, { recursive: true, force: true })
+  }
+})
diff --git a/frontend/workspace/src/atlas/FilePreview.tsx b/frontend/workspace/src/atlas/FilePreview.tsx
index 13c31dfe..51c4ee49 100644
--- a/frontend/workspace/src/atlas/FilePreview.tsx
+++ b/frontend/workspace/src/atlas/FilePreview.tsx
@@ -21,6 +21,8 @@ import { ScienceArtifact } from "@/science/ScienceArtifact"
 import { detectScientificFile } from "@/science/files"
 import { ScientificDataView } from "@/science/formats/ScientificDataView"
 import { detectBiologicalFormat } from "@/science/formats/biological"
+import { BinaryScienceView } from "@/science/formats/BinaryScienceView"
+import { detectBinaryScienceFormat } from "@/science/formats/binary"
 import { NotebookView } from "@/notebook/NotebookView"
 import { DataTableView } from "@/data/DataTableView"
 import type { TableFormat } from "@/data/table"
@@ -106,9 +108,19 @@ const LANG: Record<string, string> = {
   log: "text",
 }
 
-type Kind = "markdown" | "notebook" | "table" | "scientific-data" | "pdf" | "image" | "science" | "code" | "binary"
+type Kind =
+  | "markdown"
+  | "notebook"
+  | "table"
+  | "scientific-data"
+  | "scientific-binary"
+  | "pdf"
+  | "image"
+  | "science"
+  | "code"
+  | "binary"
 
-type FileData = { content?: string; encoding?: string; mimeType?: string }
+type FileData = { content?: string; encoding?: string; mimeType?: string; size?: number; truncated?: boolean }
 
 /**
  * Inline file view — header (icon + name + subtitle + controls) over the
@@ -160,6 +172,7 @@ export function FileView(props: {
   const dirty = () => draft() !== savedText()
   const scientific = createMemo(() => (isBinary() ? undefined : detectScientificFile(e(), draft())))
   const biological = createMemo(() => (isBinary() ? undefined : detectBiologicalFormat(e())))
+  const binaryScience = createMemo(() => detectBinaryScienceFormat(e()))
   const tabular = createMemo<TableFormat | undefined>(() => {
     if (isBinary()) return
     if (e() === "csv" || e() === "tsv" || e() === "jsonl") return e() as TableFormat
@@ -171,6 +184,7 @@ export function FileView(props: {
     if (isBinary()) {
       if (mime().startsWith("image/") || ["png", "jpg", "jpeg", "gif", "webp", "bmp", "svg"].includes(x)) return "image"
       if (mime() === "application/pdf" || x === "pdf") return "pdf"
+      if (binaryScience()) return "scientific-binary"
       return "binary"
     }
     if (x === "md" || x === "markdown" || x === "mdx") return "markdown"
@@ -190,6 +204,7 @@ export function FileView(props: {
     if (k === "code") return LANG[e()] ?? e() ?? "text"
     if (k === "science") return scientific()?.format ?? e()
     if (k === "scientific-data") return biological() ?? e()
+    if (k === "scientific-binary") return binaryScience() ?? e()
     if (k === "table") return tabular() ?? e()
     return k
   }
@@ -235,6 +250,23 @@ export function FileView(props: {
     } catch {}
   }
 
+  const download = async () => {
+    try {
+      const doFetch = platform.fetch ?? fetch
+      const url = `${sdk.url.replace(/\/$/, "")}/file/raw?directory=${encodeURIComponent(directory())}&path=${encodeURIComponent(props.path)}`
+      const response = await doFetch(url)
+      if (!response.ok) throw new Error(`download failed (${response.status})`)
+      const object = URL.createObjectURL(await response.blob())
+      const anchor = document.createElement("a")
+      anchor.href = object
+      anchor.download = name()
+      anchor.click()
+      URL.revokeObjectURL(object)
+    } catch (error) {
+      toast.error("download failed", error instanceof Error ? error.message : String(error))
+    }
+  }
+
   const toggleable = () =>
     kind() === "markdown" ||
     kind() === "notebook" ||
@@ -342,9 +374,9 @@ export function FileView(props: {
           </button>
         </Show>
         <Show when={isBinary()}>
-          <a href={dataUrl()} download={name()} title="download" style={{ ...iconBtn(), "text-decoration": "none" }}>
+          <button type="button" onClick={() => void download()} title="download" style={iconBtn()}>
             <IconDownload size={13} strokeWidth={1.6} />
-          </a>
+          </button>
         </Show>
 
         <button type="button" onClick={() => setRefreshKey((k) => k + 1)} title="refresh" style={iconBtn()}>
@@ -460,6 +492,13 @@ export function FileView(props: {
                 </Show>
               </Match>
 
+              {/* large scientific containers */}
+              <Match when={kind() === "scientific-binary"}>
+                <Show when={binaryScience()}>
+                  {(format) => <BinaryScienceView path={props.path} directory={directory()} format={format()} />}
+                </Show>
+              </Match>
+
               {/* pdf */}
               <Match when={kind() === "pdf"}>
                 <div style={{ padding: "14px" }}>
diff --git a/frontend/workspace/src/science/formats/BinaryScienceView.tsx b/frontend/workspace/src/science/formats/BinaryScienceView.tsx
new file mode 100644
index 00000000..80b7db64
--- /dev/null
+++ b/frontend/workspace/src/science/formats/BinaryScienceView.tsx
@@ -0,0 +1,643 @@
+import { For, Match, Show, Switch, createResource, type JSX } from "solid-js"
+import { usePlatform } from "@/context/platform"
+import { useSDK } from "@/context/sdk"
+import { FONT_CODE, FONT_MONO, FONT_SANS } from "@/styles/tokens"
+import {
+  formatBytes,
+  normalizeInspection,
+  numbers,
+  object,
+  objects,
+  strings,
+  type BinaryInspection,
+  type BinaryScienceFormat,
+} from "./binary"
+
+export function BinaryScienceView(props: {
+  path: string
+  directory: string
+  format: BinaryScienceFormat
+}): JSX.Element {
+  const sdk = useSDK()
+  const platform = usePlatform()
+  const [inspection, { refetch }] = createResource(
+    () => [props.directory, props.path] as const,
+    async ([directory, path]) => {
+      const request = platform.fetch ?? fetch
+      const url = `${sdk.url.replace(/\/$/, "")}/file/inspect?directory=${encodeURIComponent(directory)}&path=${encodeURIComponent(path)}`
+      const response = await request(url)
+      if (!response.ok) throw new Error(`inspection failed (${response.status})`)
+      return normalizeInspection(await response.json())
+    },
+  )
+
+  return (
+    <div
+      data-component="binary-science"
+      data-format={props.format}
+      style={{
+        height: "100%",
+        "min-height": "100%",
+        display: "flex",
+        "flex-direction": "column",
+        background: "var(--color-bg-subtle)",
+      }}
+    >
+      <Show
+        when={!inspection.loading}
+        fallback={
+          <div style={empty()}>
+            <Pulse />
+            <strong style={title()}>Inspecting {props.format.toUpperCase()}</strong>
+            <span style={muted()}>Reading local metadata without uploading the file</span>
+          </div>
+        }
+      >
+        <Show
+          when={!inspection.error && inspection()}
+          fallback={
+            <div style={empty()}>
+              <strong style={title()}>Could not inspect this file</strong>
+              <span style={muted()}>
+                {inspection.error instanceof Error ? inspection.error.message : String(inspection.error)}
+              </span>
+              <button type="button" style={button()} onClick={() => void refetch()}>
+                retry
+              </button>
+            </div>
+          }
+        >
+          {(file) => (
+            <div class="atlas-scroll" style={{ flex: 1, overflow: "auto", padding: "14px" }}>
+              <div style={{ display: "grid", gap: "12px", "max-width": "1100px", margin: "0 auto" }}>
+                <Header file={file()} />
+                <Show when={!file().tool.available}>
+                  <Capability file={file()} />
+                </Show>
+                <Switch>
+                  <Match when={file().format === "h5ad" || file().format === "loom"}>
+                    <Hdf5 file={file()} />
+                  </Match>
+                  <Match when={file().format === "bam" || file().format === "cram"}>
+                    <Alignment file={file()} />
+                  </Match>
+                </Switch>
+              </div>
+            </div>
+          )}
+        </Show>
+      </Show>
+    </div>
+  )
+}
+
+function Header(props: { file: BinaryInspection }): JSX.Element {
+  return (
+    <>
+      <div
+        style={{
+          display: "flex",
+          "align-items": "center",
+          gap: "10px",
+          padding: "13px 14px",
+          border: "1px solid var(--color-border)",
+          "border-radius": "8px",
+          background: "var(--color-bg)",
+        }}
+      >
+        <div
+          style={{
+            width: "34px",
+            height: "34px",
+            display: "grid",
+            "place-items": "center",
+            "border-radius": "7px",
+            background: "color-mix(in srgb, var(--color-accent) 11%, transparent)",
+            color: "var(--color-accent)",
+            "font-family": FONT_MONO,
+            "font-size": "10px",
+            "font-weight": 700,
+          }}
+        >
+          {props.file.format.toUpperCase()}
+        </div>
+        <div style={{ flex: 1, "min-width": 0 }}>
+          <strong
+            style={{
+              display: "block",
+              "font-family": FONT_SANS,
+              "font-size": "13px",
+              color: "var(--color-text)",
+              overflow: "hidden",
+              "text-overflow": "ellipsis",
+              "white-space": "nowrap",
+            }}
+          >
+            {props.file.name}
+          </strong>
+          <span style={muted()}>local · never uploaded</span>
+        </div>
+        <Status ok={props.file.signature} label={props.file.signature ? "signature valid" : "signature unverified"} />
+        <Status
+          ok={props.file.tool.available}
+          label={props.file.tool.available ? `${props.file.tool.name} ready` : `${props.file.tool.name} missing`}
+        />
+      </div>
+      <div
+        style={{
+          display: "grid",
+          "grid-template-columns": "repeat(auto-fit, minmax(150px, 1fr))",
+          gap: "8px",
+        }}
+      >
+        <Metric label="file size" value={formatBytes(props.file.size)} detail="streamed on download" />
+        <Metric
+          label="format"
+          value={props.file.format.toUpperCase()}
+          detail={props.file.signature ? "recognized container" : "extension match"}
+        />
+        <Metric
+          label="index"
+          value={props.file.index ? "ready" : "none"}
+          detail={props.file.index ?? indexHint(props.file.format)}
+        />
+        <Metric
+          label="inspector"
+          value={props.file.tool.available ? "available" : "limited"}
+          detail={props.file.tool.detail ?? props.file.tool.name}
+        />
+      </div>
+    </>
+  )
+}
+
+function Capability(props: { file: BinaryInspection }): JSX.Element {
+  const hdf = props.file.format === "h5ad" || props.file.format === "loom"
+  return (
+    <section
+      data-slot="binary-capability"
+      style={{
+        padding: "13px 14px",
+        border: "1px solid color-mix(in srgb, #d4a72c 45%, var(--color-border))",
+        "border-radius": "8px",
+        background: "color-mix(in srgb, #d4a72c 7%, var(--color-bg))",
+      }}
+    >
+      <div style={{ display: "flex", gap: "10px", "align-items": "flex-start" }}>
+        <span style={{ color: "#b07a00", "font-size": "14px" }}>◇</span>
+        <div style={{ display: "grid", gap: "5px" }}>
+          <strong style={{ "font-family": FONT_SANS, "font-size": "11px", color: "var(--color-text)" }}>
+            Add {props.file.tool.name} for full schema inspection
+          </strong>
+          <span style={{ ...muted(), "line-height": 1.55 }}>
+            {props.file.tool.detail ||
+              "The file was identified safely, but its scientific metadata needs a local reader."}
+          </span>
+          <code
+            style={{
+              width: "fit-content",
+              padding: "5px 7px",
+              "border-radius": "4px",
+              background: "var(--color-bg-subtle)",
+              "font-family": FONT_CODE,
+              "font-size": "10px",
+              color: "var(--color-text-muted)",
+              "user-select": "all",
+            }}
+          >
+            {hdf ? "python -m pip install h5py anndata" : "conda install -c bioconda samtools"}
+          </code>
+        </div>
+      </div>
+    </section>
+  )
+}
+
+function Hdf5(props: { file: BinaryInspection }): JSX.Element {
+  const summary = () => object(props.file.details.summary)
+  const matrix = () => numbers(summary().matrix)
+  const datasets = () => objects(props.file.details.datasets)
+  const groups = () => strings(props.file.details.groups)
+  const embeddings = () => strings(summary().embeddings)
+  const layers = () => strings(summary().layers)
+  const row = () => strings(summary().row_attributes)
+  const column = () => strings(summary().column_attributes)
+  return (
+    <>
+      <Show when={props.file.tool.available}>
+        <div style={{ display: "grid", "grid-template-columns": "repeat(auto-fit, minmax(150px, 1fr))", gap: "8px" }}>
+          <Metric
+            label="matrix"
+            value={
+              matrix().length
+                ? matrix()
+                    .map((value) => value.toLocaleString())
+                    .join(" × ")
+                : "—"
+            }
+            detail={props.file.format === "h5ad" ? "observations × variables" : "rows × columns"}
+          />
+          <Metric
+            label="observations"
+            value={scalar(summary().observations)}
+            detail={`${row().length} row attributes`}
+          />
+          <Metric
+            label="variables"
+            value={scalar(summary().variables)}
+            detail={`${column().length} column attributes`}
+          />
+          <Metric label="datasets" value={String(datasets().length)} detail={`${groups().length} groups`} />
+        </div>
+        <Show when={embeddings().length || layers().length || row().length || column().length}>
+          <Panel title="Scientific schema" note="Analysis-ready structures">
+            <div style={{ display: "grid", gap: "10px" }}>
+              <Tags label="embeddings" values={embeddings()} />
+              <Tags label="layers" values={layers()} />
+              <Tags label="row attributes" values={row()} />
+              <Tags label="column attributes" values={column()} />
+            </div>
+          </Panel>
+        </Show>
+        <Panel title="Dataset inventory" note={`First ${datasets().length} datasets`}>
+          <div style={{ overflow: "auto" }}>
+            <table style={table()}>
+              <thead>
+                <tr>
+                  <th style={head()}>path</th>
+                  <th style={head()}>shape</th>
+                  <th style={head()}>dtype</th>
+                  <th style={head()}>storage</th>
+                </tr>
+              </thead>
+              <tbody>
+                <For each={datasets()}>
+                  {(dataset) => (
+                    <tr>
+                      <td style={cell(true)}>{String(dataset.path ?? "")}</td>
+                      <td style={cell(true)}>{numbers(dataset.shape).join(" × ") || "scalar"}</td>
+                      <td style={cell()}>{String(dataset.dtype ?? "")}</td>
+                      <td style={cell()}>{formatBytes(typeof dataset.bytes === "number" ? dataset.bytes : 0)}</td>
+                    </tr>
+                  )}
+                </For>
+              </tbody>
+            </table>
+          </div>
+        </Panel>
+      </Show>
+      <Show when={!props.file.tool.available}>
+        <Fallback
+          title={`${props.file.format.toUpperCase()} container detected`}
+          body="OpenScience verified the HDF5 signature and preserved the file locally. Install the optional reader above to reveal observations, variables, embeddings, layers, and every dataset."
+        />
+      </Show>
+    </>
+  )
+}
+
+function Alignment(props: { file: BinaryInspection }): JSX.Element {
+  const header = () => object(props.file.details.header)
+  const references = () => objects(props.file.details.references)
+  const chromosomes = () => objects(props.file.details.chromosomes)
+  const max = () => Math.max(1, ...chromosomes().map((item) => (typeof item.mapped === "number" ? item.mapped : 0)))
+  return (
+    <>
+      <Show when={props.file.tool.available}>
+        <div style={{ display: "grid", "grid-template-columns": "repeat(auto-fit, minmax(150px, 1fr))", gap: "8px" }}>
+          <Metric label="references" value={String(references().length)} detail="header sequences" />
+          <Metric
+            label="version"
+            value={String(header().VN ?? props.file.details.version ?? "—")}
+            detail={props.file.format.toUpperCase()}
+          />
+          <Metric label="sort order" value={String(header().SO ?? "unknown")} detail="alignment header" />
+          <Metric
+            label="mapped reads"
+            value={compact(
+              chromosomes().reduce((total, item) => total + (typeof item.mapped === "number" ? item.mapped : 0), 0),
+            )}
+            detail={props.file.index ? "from index" : "index required"}
+          />
+        </div>
+        <Panel
+          title="Reference coverage"
+          note={props.file.index ? "Mapped reads from the adjacent index" : "Add an index for counts"}
+        >
+          <Show
+            when={chromosomes().length}
+            fallback={
+              <span style={muted()}>
+                Header loaded. Place a BAI/CRAI beside the file to calculate per-reference counts.
+              </span>
+            }
+          >
+            <div style={{ display: "grid", gap: "7px" }}>
+              <For each={chromosomes().slice(0, 40)}>
+                {(item) => {
+                  const mapped = typeof item.mapped === "number" ? item.mapped : 0
+                  return (
+                    <div
+                      style={{
+                        display: "grid",
+                        "grid-template-columns": "90px 1fr 70px",
+                        gap: "8px",
+                        "align-items": "center",
+                      }}
+                    >
+                      <span style={{ ...muted(), overflow: "hidden", "text-overflow": "ellipsis" }}>
+                        {String(item.name ?? "")}
+                      </span>
+                      <div
+                        style={{
+                          height: "5px",
+                          "border-radius": "99px",
+                          background: "var(--color-border)",
+                          overflow: "hidden",
+                        }}
+                      >
+                        <div
+                          style={{
+                            width: `${(mapped / max()) * 100}%`,
+                            height: "100%",
+                            background: "var(--color-accent)",
+                          }}
+                        />
+                      </div>
+                      <span style={{ ...muted(), "text-align": "right" }}>{mapped.toLocaleString()}</span>
+                    </div>
+                  )
+                }}
+              </For>
+            </div>
+          </Show>
+        </Panel>
+        <Panel title="Reference dictionary" note="Sequences declared in the alignment header">
+          <div style={{ overflow: "auto" }}>
+            <table style={table()}>
+              <thead>
+                <tr>
+                  <th style={head()}>reference</th>
+                  <th style={head()}>length</th>
+                </tr>
+              </thead>
+              <tbody>
+                <For each={references()}>
+                  {(reference) => (
+                    <tr>
+                      <td style={cell(true)}>{String(reference.name ?? "")}</td>
+                      <td style={cell()}>
+                        {typeof reference.length === "number" ? reference.length.toLocaleString() : "—"} bp
+                      </td>
+                    </tr>
+                  )}
+                </For>
+              </tbody>
+            </table>
+          </div>
+        </Panel>
+      </Show>
+      <Show when={!props.file.tool.available}>
+        <Fallback
+          title={`${props.file.format.toUpperCase()} container detected`}
+          body={`OpenScience verified the container${props.file.index ? " and found its index" : ""}. Install samtools above to reveal the header, reference dictionary, sort order, and indexed read counts.`}
+        />
+      </Show>
+    </>
+  )
+}
+
+function Metric(props: { label: string; value: string; detail: string }): JSX.Element {
+  return (
+    <div style={card()}>
+      <span style={{ ...muted(), "text-transform": "uppercase", "letter-spacing": "0.06em" }}>{props.label}</span>
+      <strong
+        style={{
+          display: "block",
+          "margin-top": "7px",
+          "font-family": FONT_SANS,
+          "font-size": "18px",
+          "font-weight": 600,
+          color: "var(--color-text)",
+          "letter-spacing": "-0.02em",
+        }}
+      >
+        {props.value}
+      </strong>
+      <span
+        title={props.detail}
+        style={{
+          ...muted(),
+          display: "block",
+          "margin-top": "4px",
+          overflow: "hidden",
+          "text-overflow": "ellipsis",
+          "white-space": "nowrap",
+        }}
+      >
+        {props.detail}
+      </span>
+    </div>
+  )
+}
+
+function Panel(props: { title: string; note: string; children: JSX.Element }): JSX.Element {
+  return (
+    <section style={card()}>
+      <div style={{ display: "flex", "align-items": "baseline", gap: "8px", "margin-bottom": "12px" }}>
+        <strong style={{ "font-family": FONT_SANS, "font-size": "12px", color: "var(--color-text)" }}>
+          {props.title}
+        </strong>
+        <span style={muted()}>{props.note}</span>
+      </div>
+      {props.children}
+    </section>
+  )
+}
+
+function Tags(props: { label: string; values: string[] }): JSX.Element {
+  return (
+    <Show when={props.values.length}>
+      <div style={{ display: "grid", "grid-template-columns": "100px 1fr", gap: "8px" }}>
+        <span style={muted()}>{props.label}</span>
+        <div style={{ display: "flex", gap: "5px", "flex-wrap": "wrap" }}>
+          <For each={props.values.slice(0, 30)}>
+            {(value) => (
+              <code
+                style={{
+                  padding: "2px 6px",
+                  "border-radius": "4px",
+                  background: "var(--color-bg-subtle)",
+                  "font-family": FONT_CODE,
+                  "font-size": "9px",
+                  color: "var(--color-text-muted)",
+                }}
+              >
+                {value}
+              </code>
+            )}
+          </For>
+        </div>
+      </div>
+    </Show>
+  )
+}
+
+function Fallback(props: { title: string; body: string }): JSX.Element {
+  return (
+    <div
+      style={{
+        ...card(),
+        padding: "28px",
+        display: "grid",
+        "place-items": "center",
+        gap: "8px",
+        "text-align": "center",
+      }}
+    >
+      <div
+        style={{
+          width: "42px",
+          height: "42px",
+          display: "grid",
+          "place-items": "center",
+          "border-radius": "50%",
+          background: "var(--color-bg-subtle)",
+          color: "var(--color-text-faint)",
+          "font-family": FONT_MONO,
+        }}
+      >
+        01
+      </div>
+      <strong style={title()}>{props.title}</strong>
+      <span style={{ ...muted(), "max-width": "580px", "line-height": 1.65 }}>{props.body}</span>
+    </div>
+  )
+}
+
+function Status(props: { ok: boolean; label: string }): JSX.Element {
+  return (
+    <span
+      style={{
+        padding: "3px 7px",
+        "border-radius": "99px",
+        border: `1px solid ${props.ok ? "color-mix(in srgb, #4ca56a 45%, var(--color-border))" : "var(--color-border)"}`,
+        background: props.ok ? "color-mix(in srgb, #4ca56a 9%, transparent)" : "var(--color-bg-subtle)",
+        color: props.ok ? "#418c59" : "var(--color-text-faint)",
+        "font-family": FONT_MONO,
+        "font-size": "9px",
+        "white-space": "nowrap",
+      }}
+    >
+      {props.label}
+    </span>
+  )
+}
+
+function Pulse(): JSX.Element {
+  return (
+    <span
+      style={{
+        width: "18px",
+        height: "18px",
+        border: "2px solid var(--color-border)",
+        "border-top-color": "var(--color-accent)",
+        "border-radius": "50%",
+        animation: "spin 0.8s linear infinite",
+      }}
+    />
+  )
+}
+
+function scalar(value: unknown): string {
+  return typeof value === "number" ? value.toLocaleString() : "—"
+}
+
+function compact(value: number): string {
+  return new Intl.NumberFormat("en", {
+    notation: value >= 10_000 ? "compact" : "standard",
+    maximumFractionDigits: 1,
+  }).format(value)
+}
+
+function indexHint(format: BinaryScienceFormat): string {
+  if (format === "bam") return "BAI recommended"
+  if (format === "cram") return "CRAI recommended"
+  return "not required"
+}
+
+function table(): JSX.CSSProperties {
+  return { width: "100%", "border-collapse": "collapse", "font-family": FONT_SANS, "font-size": "10px" }
+}
+
+function head(): JSX.CSSProperties {
+  return {
+    padding: "6px 8px",
+    border: "0",
+    "border-bottom": "1px solid var(--color-border)",
+    color: "var(--color-text-faint)",
+    "font-family": FONT_MONO,
+    "font-size": "9px",
+    "font-weight": 500,
+    "text-align": "left",
+    "text-transform": "uppercase",
+    "letter-spacing": "0.04em",
+  }
+}
+
+function cell(mono = false): JSX.CSSProperties {
+  return {
+    padding: "7px 8px",
+    border: "0",
+    "border-bottom": "1px solid var(--color-border)",
+    color: "var(--color-text-muted)",
+    "font-family": mono ? FONT_CODE : FONT_SANS,
+    "font-size": "10px",
+    "white-space": "nowrap",
+  }
+}
+
+function card(): JSX.CSSProperties {
+  return {
+    padding: "12px 14px",
+    border: "1px solid var(--color-border)",
+    "border-radius": "8px",
+    background: "var(--color-bg)",
+    "min-width": 0,
+  }
+}
+
+function muted(): JSX.CSSProperties {
+  return { "font-family": FONT_MONO, "font-size": "9px", color: "var(--color-text-faint)" }
+}
+
+function title(): JSX.CSSProperties {
+  return { "font-family": FONT_SANS, "font-size": "13px", color: "var(--color-text)" }
+}
+
+function empty(): JSX.CSSProperties {
+  return {
+    display: "grid",
+    "place-items": "center",
+    "align-content": "center",
+    gap: "9px",
+    height: "100%",
+    padding: "36px",
+    "text-align": "center",
+  }
+}
+
+function button(): JSX.CSSProperties {
+  return {
+    padding: "6px 10px",
+    border: "1px solid var(--color-border)",
+    "border-radius": "5px",
+    background: "var(--color-bg)",
+    color: "var(--color-text)",
+    "font-family": FONT_SANS,
+    "font-size": "10px",
+    cursor: "pointer",
+  }
+}
+
+export default BinaryScienceView
diff --git a/frontend/workspace/src/science/formats/binary.test.ts b/frontend/workspace/src/science/formats/binary.test.ts
new file mode 100644
index 00000000..d68da263
--- /dev/null
+++ b/frontend/workspace/src/science/formats/binary.test.ts
@@ -0,0 +1,53 @@
+import { describe, expect, test } from "bun:test"
+import { readFileSync } from "node:fs"
+import { fileURLToPath } from "node:url"
+import { detectBinaryScienceFormat, formatBytes, normalizeInspection } from "./binary"
+
+const read = (path: string) => readFileSync(fileURLToPath(new URL(path, import.meta.url)), "utf8")
+
+describe("binary scientific format helpers", () => {
+  test.each([
+    ["bam", "bam"],
+    ["CRAM", "cram"],
+    ["h5ad", "h5ad"],
+    ["loom", "loom"],
+  ])("detects %s", (extension, format) => {
+    expect(detectBinaryScienceFormat(extension)).toBe(format as ReturnType<typeof detectBinaryScienceFormat>)
+  })
+
+  test("does not claim generic binaries", () => {
+    expect(detectBinaryScienceFormat("bin")).toBeUndefined()
+  })
+
+  test("formats scientific file sizes compactly", () => {
+    expect(formatBytes(1024)).toBe("1 KB")
+    expect(formatBytes(2.5 * 1024 * 1024)).toBe("2.5 MB")
+    expect(formatBytes(3 * 1024 * 1024 * 1024)).toBe("3 GB")
+  })
+
+  test("normalizes malformed API data into a safe inspection", () => {
+    expect(
+      normalizeInspection({ format: "bam", size: 12, tool: { name: "samtools", available: false } }),
+    ).toMatchObject({
+      format: "bam",
+      size: 12,
+      signature: false,
+      details: {},
+      tool: { name: "samtools", available: false },
+    })
+  })
+})
+
+describe("binary scientific workbench integration", () => {
+  test("routes supported containers through local inspection and raw downloads", () => {
+    const preview = read("../../atlas/FilePreview.tsx")
+    const view = read("./BinaryScienceView.tsx")
+
+    expect(preview).toContain('import { BinaryScienceView } from "@/science/formats/BinaryScienceView"')
+    expect(preview).toContain('return "scientific-binary"')
+    expect(preview).toContain("/file/raw?")
+    expect(view).toContain("/file/inspect?")
+    expect(view).toContain("Dataset inventory")
+    expect(view).toContain("Reference coverage")
+  })
+})
diff --git a/frontend/workspace/src/science/formats/binary.ts b/frontend/workspace/src/science/formats/binary.ts
new file mode 100644
index 00000000..1295bba9
--- /dev/null
+++ b/frontend/workspace/src/science/formats/binary.ts
@@ -0,0 +1,71 @@
+export type BinaryScienceFormat = "bam" | "cram" | "h5ad" | "loom"
+
+export interface BinaryInspection {
+  format: BinaryScienceFormat
+  name: string
+  size: number
+  modified: number
+  signature: boolean
+  index?: string
+  tool: {
+    name: string
+    available: boolean
+    detail?: string
+  }
+  details: Record<string, unknown>
+}
+
+const formats = new Set<BinaryScienceFormat>(["bam", "cram", "h5ad", "loom"])
+
+export function detectBinaryScienceFormat(extension: string): BinaryScienceFormat | undefined {
+  const value = extension.toLowerCase() as BinaryScienceFormat
+  return formats.has(value) ? value : undefined
+}
+
+export function formatBytes(bytes: number): string {
+  if (bytes < 1024) return `${bytes} B`
+  const units = ["KB", "MB", "GB", "TB"]
+  const order = Math.min(units.length - 1, Math.floor(Math.log(bytes) / Math.log(1024)) - 1)
+  const value = bytes / 1024 ** (order + 1)
+  return `${Math.round(value * 10) / 10} ${units[order]}`
+}
+
+export function normalizeInspection(value: unknown): BinaryInspection {
+  const data = object(value)
+  const tool = object(data.tool)
+  const candidate = typeof data.format === "string" ? detectBinaryScienceFormat(data.format) : undefined
+  return {
+    format: candidate ?? "bam",
+    name: typeof data.name === "string" ? data.name : "",
+    size: typeof data.size === "number" ? data.size : 0,
+    modified: typeof data.modified === "number" ? data.modified : 0,
+    signature: data.signature === true,
+    index: typeof data.index === "string" ? data.index : undefined,
+    tool: {
+      name: typeof tool.name === "string" ? tool.name : "local inspector",
+      available: tool.available === true,
+      detail: typeof tool.detail === "string" ? tool.detail : undefined,
+    },
+    details: object(data.details),
+  }
+}
+
+export function objects(value: unknown): Record<string, unknown>[] {
+  if (!Array.isArray(value)) return []
+  return value.filter((item): item is Record<string, unknown> => Boolean(item) && typeof item === "object")
+}
+
+export function strings(value: unknown): string[] {
+  if (!Array.isArray(value)) return []
+  return value.filter((item): item is string => typeof item === "string")
+}
+
+export function numbers(value: unknown): number[] {
+  if (!Array.isArray(value)) return []
+  return value.filter((item): item is number => typeof item === "number")
+}
+
+export function object(value: unknown): Record<string, unknown> {
+  if (!value || typeof value !== "object" || Array.isArray(value)) return {}
+  return value as Record<string, unknown>
+}
diff --git a/tooling/sdk/js/src/v2/gen/sdk.gen.ts b/tooling/sdk/js/src/v2/gen/sdk.gen.ts
index 5e2c72c0..d22f41af 100644
--- a/tooling/sdk/js/src/v2/gen/sdk.gen.ts
+++ b/tooling/sdk/js/src/v2/gen/sdk.gen.ts
@@ -32,9 +32,11 @@ import type {
   ConfigUpdateResponses,
   EventSubscribeResponses,
   ExperimentalResourceListResponses,
+  FileInspectResponses,
   FileListResponses,
   FilePartInput,
   FilePartSource,
+  FileRawResponses,
   FileReadResponses,
   FileStatusResponses,
   FileWriteResponses,
@@ -75,6 +77,10 @@ import type {
   McpLocalConfig,
   McpRemoteConfig,
   McpStatusResponses,
+  NotebookExecuteResponses,
+  NotebookInterruptResponses,
+  NotebookRestartResponses,
+  NotebookStatusResponses,
   Part as Part2,
   PartDeleteErrors,
   PartDeleteResponses,
@@ -3310,6 +3316,66 @@ export class File extends HeyApiClient {
     })
   }
 
+  /**
+   * Inspect a scientific binary file
+   *
+   * Inspect BAM, CRAM, H5AD, or LOOM metadata with locally available scientific tools.
+   */
+  public inspect<ThrowOnError extends boolean = false>(
+    parameters: {
+      directory?: string
+      path: string
+    },
+    options?: Options<never, ThrowOnError>,
+  ) {
+    const params = buildClientParams(
+      [parameters],
+      [
+        {
+          args: [
+            { in: "query", key: "directory" },
+            { in: "query", key: "path" },
+          ],
+        },
+      ],
+    )
+    return (options?.client ?? this.client).get<FileInspectResponses, unknown, ThrowOnError>({
+      url: "/file/inspect",
+      ...options,
+      ...params,
+    })
+  }
+
+  /**
+   * Download a file
+   *
+   * Stream a project file without loading it into the JSON API as base64.
+   */
+  public raw<ThrowOnError extends boolean = false>(
+    parameters: {
+      directory?: string
+      path: string
+    },
+    options?: Options<never, ThrowOnError>,
+  ) {
+    const params = buildClientParams(
+      [parameters],
+      [
+        {
+          args: [
+            { in: "query", key: "directory" },
+            { in: "query", key: "path" },
+          ],
+        },
+      ],
+    )
+    return (options?.client ?? this.client).get<FileRawResponses, unknown, ThrowOnError>({
+      url: "/file/raw",
+      ...options,
+      ...params,
+    })
+  }
+
   /**
    * Get file status
    *
@@ -3330,6 +3396,151 @@ export class File extends HeyApiClient {
   }
 }
 
+export class Notebook extends HeyApiClient {
+  /**
+   * Execute a notebook cell
+   *
+   * Execute code in a persistent project-scoped Python or R kernel.
+   */
+  public execute<ThrowOnError extends boolean = false>(
+    parameters?: {
+      directory?: string
+      id?: string
+      language?: "python" | "r"
+      code?: string
+      timeout?: number
+    },
+    options?: Options<never, ThrowOnError>,
+  ) {
+    const params = buildClientParams(
+      [parameters],
+      [
+        {
+          args: [
+            { in: "query", key: "directory" },
+            { in: "body", key: "id" },
+            { in: "body", key: "language" },
+            { in: "body", key: "code" },
+            { in: "body", key: "timeout" },
+          ],
+        },
+      ],
+    )
+    return (options?.client ?? this.client).post<NotebookExecuteResponses, unknown, ThrowOnError>({
+      url: "/notebook/execute",
+      ...options,
+      ...params,
+      headers: {
+        "Content-Type": "application/json",
+        ...options?.headers,
+        ...params.headers,
+      },
+    })
+  }
+
+  /**
+   * Get notebook kernel status
+   */
+  public status<ThrowOnError extends boolean = false>(
+    parameters: {
+      directory?: string
+      id: string
+      language: "python" | "r"
+    },
+    options?: Options<never, ThrowOnError>,
+  ) {
+    const params = buildClientParams(
+      [parameters],
+      [
+        {
+          args: [
+            { in: "query", key: "directory" },
+            { in: "query", key: "id" },
+            { in: "query", key: "language" },
+          ],
+        },
+      ],
+    )
+    return (options?.client ?? this.client).get<NotebookStatusResponses, unknown, ThrowOnError>({
+      url: "/notebook/status",
+      ...options,
+      ...params,
+    })
+  }
+
+  /**
+   * Restart a notebook kernel
+   */
+  public restart<ThrowOnError extends boolean = false>(
+    parameters?: {
+      directory?: string
+      id?: string
+      language?: "python" | "r"
+    },
+    options?: Options<never, ThrowOnError>,
+  ) {
+    const params = buildClientParams(
+      [parameters],
+      [
+        {
+          args: [
+            { in: "query", key: "directory" },
+            { in: "body", key: "id" },
+            { in: "body", key: "language" },
+          ],
+        },
+      ],
+    )
+    return (options?.client ?? this.client).post<NotebookRestartResponses, unknown, ThrowOnError>({
+      url: "/notebook/restart",
+      ...options,
+      ...params,
+      headers: {
+        "Content-Type": "application/json",
+        ...options?.headers,
+        ...params.headers,
+      },
+    })
+  }
+
+  /**
+   * Interrupt a notebook kernel
+   *
+   * Stop the running cell and release its kernel. The next execution starts a fresh kernel.
+   */
+  public interrupt<ThrowOnError extends boolean = false>(
+    parameters?: {
+      directory?: string
+      id?: string
+      language?: "python" | "r"
+    },
+    options?: Options<never, ThrowOnError>,
+  ) {
+    const params = buildClientParams(
+      [parameters],
+      [
+        {
+          args: [
+            { in: "query", key: "directory" },
+            { in: "body", key: "id" },
+            { in: "body", key: "language" },
+          ],
+        },
+      ],
+    )
+    return (options?.client ?? this.client).post<NotebookInterruptResponses, unknown, ThrowOnError>({
+      url: "/notebook/interrupt",
+      ...options,
+      ...params,
+      headers: {
+        "Content-Type": "application/json",
+        ...options?.headers,
+        ...params.headers,
+      },
+    })
+  }
+}
+
 export class Config3 extends HeyApiClient {
   /**
    * Remove MCP server
@@ -4176,6 +4387,11 @@ export class OpenScienceClient extends HeyApiClient {
     return (this._file ??= new File({ client: this.client }))
   }
 
+  private _notebook?: Notebook
+  get notebook(): Notebook {
+    return (this._notebook ??= new Notebook({ client: this.client }))
+  }
+
   private _mcp?: Mcp
   get mcp(): Mcp {
     return (this._mcp ??= new Mcp({ client: this.client }))
diff --git a/tooling/sdk/js/src/v2/gen/types.gen.ts b/tooling/sdk/js/src/v2/gen/types.gen.ts
index f4947f19..9e89d242 100644
--- a/tooling/sdk/js/src/v2/gen/types.gen.ts
+++ b/tooling/sdk/js/src/v2/gen/types.gen.ts
@@ -2162,6 +2162,8 @@ export type FileContent = {
   }
   encoding?: "base64"
   mimeType?: string
+  size?: number
+  truncated?: boolean
 }
 
 export type File = {
@@ -5289,6 +5291,57 @@ export type FileWriteResponses = {
 
 export type FileWriteResponse = FileWriteResponses[keyof FileWriteResponses]
 
+export type FileInspectData = {
+  body?: never
+  path?: never
+  query: {
+    directory?: string
+    path: string
+  }
+  url: "/file/inspect"
+}
+
+export type FileInspectResponses = {
+  /**
+   * Scientific file inspection
+   */
+  200: {
+    format: "bam" | "cram" | "h5ad" | "loom"
+    name: string
+    size: number
+    modified: number
+    signature: boolean
+    index?: string
+    tool: {
+      name: string
+      available: boolean
+      detail?: string
+    }
+    details: {
+      [key: string]: unknown
+    }
+  }
+}
+
+export type FileInspectResponse = FileInspectResponses[keyof FileInspectResponses]
+
+export type FileRawData = {
+  body?: never
+  path?: never
+  query: {
+    directory?: string
+    path: string
+  }
+  url: "/file/raw"
+}
+
+export type FileRawResponses = {
+  /**
+   * Raw file contents
+   */
+  200: unknown
+}
+
 export type FileStatusData = {
   body?: never
   path?: never
@@ -5307,6 +5360,83 @@ export type FileStatusResponses = {
 
 export type FileStatusResponse = FileStatusResponses[keyof FileStatusResponses]
 
+export type NotebookExecuteData = {
+  body?: {
+    id: string
+    language: "python" | "r"
+    code: string
+    timeout?: number
+  }
+  path?: never
+  query?: {
+    directory?: string
+  }
+  url: "/notebook/execute"
+}
+
+export type NotebookExecuteResponses = {
+  /**
+   * Jupyter-compatible cell outputs
+   */
+  200: unknown
+}
+
+export type NotebookStatusData = {
+  body?: never
+  path?: never
+  query: {
+    directory?: string
+    id: string
+    language: "python" | "r"
+  }
+  url: "/notebook/status"
+}
+
+export type NotebookStatusResponses = {
+  /**
+   * Kernel state
+   */
+  200: unknown
+}
+
+export type NotebookRestartData = {
+  body?: {
+    id: string
+    language: "python" | "r"
+  }
+  path?: never
+  query?: {
+    directory?: string
+  }
+  url: "/notebook/restart"
+}
+
+export type NotebookRestartResponses = {
+  /**
+   * Kernel state
+   */
+  200: unknown
+}
+
+export type NotebookInterruptData = {
+  body?: {
+    id: string
+    language: "python" | "r"
+  }
+  path?: never
+  query?: {
+    directory?: string
+  }
+  url: "/notebook/interrupt"
+}
+
+export type NotebookInterruptResponses = {
+  /**
+   * Kernel state
+   */
+  200: unknown
+}
+
 export type McpStatusData = {
   body?: never
   path?: never
diff --git a/tooling/sdk/openapi.json b/tooling/sdk/openapi.json
index 967ea700..5f6d6ee2 100644
--- a/tooling/sdk/openapi.json
+++ b/tooling/sdk/openapi.json
@@ -7281,6 +7281,143 @@
         ]
       }
     },
+    "/file/inspect": {
+      "get": {
+        "operationId": "file.inspect",
+        "parameters": [
+          {
+            "in": "query",
+            "name": "directory",
+            "schema": {
+              "type": "string"
+            }
+          },
+          {
+            "in": "query",
+            "name": "path",
+            "schema": {
+              "type": "string"
+            },
+            "required": true
+          }
+        ],
+        "summary": "Inspect a scientific binary file",
+        "description": "Inspect BAM, CRAM, H5AD, or LOOM metadata with locally available scientific tools.",
+        "responses": {
+          "200": {
+            "description": "Scientific file inspection",
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "object",
+                  "properties": {
+                    "format": {
+                      "type": "string",
+                      "enum": [
+                        "bam",
+                        "cram",
+                        "h5ad",
+                        "loom"
+                      ]
+                    },
+                    "name": {
+                      "type": "string"
+                    },
+                    "size": {
+                      "type": "number"
+                    },
+                    "modified": {
+                      "type": "number"
+                    },
+                    "signature": {
+                      "type": "boolean"
+                    },
+                    "index": {
+                      "type": "string"
+                    },
+                    "tool": {
+                      "type": "object",
+                      "properties": {
+                        "name": {
+                          "type": "string"
+                        },
+                        "available": {
+                          "type": "boolean"
+                        },
+                        "detail": {
+                          "type": "string"
+                        }
+                      },
+                      "required": [
+                        "name",
+                        "available"
+                      ]
+                    },
+                    "details": {
+                      "type": "object",
+                      "propertyNames": {
+                        "type": "string"
+                      },
+                      "additionalProperties": {}
+                    }
+                  },
+                  "required": [
+                    "format",
+                    "name",
+                    "size",
+                    "modified",
+                    "signature",
+                    "tool",
+                    "details"
+                  ]
+                }
+              }
+            }
+          }
+        },
+        "x-codeSamples": [
+          {
+            "lang": "js",
+            "source": "import { createOpenScienceClient } from \"@synsci/sdk\"\n\nconst client = createOpenScienceClient()\nawait client.file.inspect({\n  ...\n})"
+          }
+        ]
+      }
+    },
+    "/file/raw": {
+      "get": {
+        "operationId": "file.raw",
+        "parameters": [
+          {
+            "in": "query",
+            "name": "directory",
+            "schema": {
+              "type": "string"
+            }
+          },
+          {
+            "in": "query",
+            "name": "path",
+            "schema": {
+              "type": "string"
+            },
+            "required": true
+          }
+        ],
+        "summary": "Download a file",
+        "description": "Stream a project file without loading it into the JSON API as base64.",
+        "responses": {
+          "200": {
+            "description": "Raw file contents"
+          }
+        },
+        "x-codeSamples": [
+          {
+            "lang": "js",
+            "source": "import { createOpenScienceClient } from \"@synsci/sdk\"\n\nconst client = createOpenScienceClient()\nawait client.file.raw({\n  ...\n})"
+          }
+        ]
+      }
+    },
     "/file/status": {
       "get": {
         "operationId": "file.status",
@@ -7318,6 +7455,225 @@
         ]
       }
     },
+    "/notebook/execute": {
+      "post": {
+        "operationId": "notebook.execute",
+        "parameters": [
+          {
+            "in": "query",
+            "name": "directory",
+            "schema": {
+              "type": "string"
+            }
+          }
+        ],
+        "summary": "Execute a notebook cell",
+        "description": "Execute code in a persistent project-scoped Python or R kernel.",
+        "responses": {
+          "200": {
+            "description": "Jupyter-compatible cell outputs"
+          }
+        },
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "type": "object",
+                "properties": {
+                  "id": {
+                    "type": "string",
+                    "minLength": 1,
+                    "maxLength": 1024
+                  },
+                  "language": {
+                    "type": "string",
+                    "enum": [
+                      "python",
+                      "r"
+                    ]
+                  },
+                  "code": {
+                    "type": "string",
+                    "maxLength": 2000000
+                  },
+                  "timeout": {
+                    "type": "integer",
+                    "minimum": 5000,
+                    "maximum": 600000
+                  }
+                },
+                "required": [
+                  "id",
+                  "language",
+                  "code"
+                ]
+              }
+            }
+          }
+        },
+        "x-codeSamples": [
+          {
+            "lang": "js",
+            "source": "import { createOpenScienceClient } from \"@synsci/sdk\"\n\nconst client = createOpenScienceClient()\nawait client.notebook.execute({\n  ...\n})"
+          }
+        ]
+      }
+    },
+    "/notebook/status": {
+      "get": {
+        "operationId": "notebook.status",
+        "parameters": [
+          {
+            "in": "query",
+            "name": "directory",
+            "schema": {
+              "type": "string"
+            }
+          },
+          {
+            "in": "query",
+            "name": "id",
+            "schema": {
+              "type": "string",
+              "minLength": 1,
+              "maxLength": 1024
+            },
+            "required": true
+          },
+          {
+            "in": "query",
+            "name": "language",
+            "schema": {
+              "type": "string",
+              "enum": [
+                "python",
+                "r"
+              ]
+            },
+            "required": true
+          }
+        ],
+        "summary": "Get notebook kernel status",
+        "responses": {
+          "200": {
+            "description": "Kernel state"
+          }
+        },
+        "x-codeSamples": [
+          {
+            "lang": "js",
+            "source": "import { createOpenScienceClient } from \"@synsci/sdk\"\n\nconst client = createOpenScienceClient()\nawait client.notebook.status({\n  ...\n})"
+          }
+        ]
+      }
+    },
+    "/notebook/restart": {
+      "post": {
+        "operationId": "notebook.restart",
+        "parameters": [
+          {
+            "in": "query",
+            "name": "directory",
+            "schema": {
+              "type": "string"
+            }
+          }
+        ],
+        "summary": "Restart a notebook kernel",
+        "responses": {
+          "200": {
+            "description": "Kernel state"
+          }
+        },
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "type": "object",
+                "properties": {
+                  "id": {
+                    "type": "string",
+                    "minLength": 1,
+                    "maxLength": 1024
+                  },
+                  "language": {
+                    "type": "string",
+                    "enum": [
+                      "python",
+                      "r"
+                    ]
+                  }
+                },
+                "required": [
+                  "id",
+                  "language"
+                ]
+              }
+            }
+          }
+        },
+        "x-codeSamples": [
+          {
+            "lang": "js",
+            "source": "import { createOpenScienceClient } from \"@synsci/sdk\"\n\nconst client = createOpenScienceClient()\nawait client.notebook.restart({\n  ...\n})"
+          }
+        ]
+      }
+    },
+    "/notebook/interrupt": {
+      "post": {
+        "operationId": "notebook.interrupt",
+        "parameters": [
+          {
+            "in": "query",
+            "name": "directory",
+            "schema": {
+              "type": "string"
+            }
+          }
+        ],
+        "summary": "Interrupt a notebook kernel",
+        "description": "Stop the running cell and release its kernel. The next execution starts a fresh kernel.",
+        "responses": {
+          "200": {
+            "description": "Kernel state"
+          }
+        },
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "type": "object",
+                "properties": {
+                  "id": {
+                    "type": "string",
+                    "minLength": 1,
+                    "maxLength": 1024
+                  },
+                  "language": {
+                    "type": "string",
+                    "enum": [
+                      "python",
+                      "r"
+                    ]
+                  }
+                },
+                "required": [
+                  "id",
+                  "language"
+                ]
+              }
+            }
+          }
+        },
+        "x-codeSamples": [
+          {
+            "lang": "js",
+            "source": "import { createOpenScienceClient } from \"@synsci/sdk\"\n\nconst client = createOpenScienceClient()\nawait client.notebook.interrupt({\n  ...\n})"
+          }
+        ]
+      }
+    },
     "/mcp": {
       "get": {
         "operationId": "mcp.status",
@@ -15164,6 +15520,12 @@
           },
           "mimeType": {
             "type": "string"
+          },
+          "size": {
+            "type": "number"
+          },
+          "truncated": {
+            "type": "boolean"
           }
         },
         "required": [

From 943dd6ca2f1512bcdc900fe5facbd4e67f24de0f Mon Sep 17 00:00:00 2001
From: Aayam Bansal <aayambansal@gmail.com>
Date: Wed, 29 Jul 2026 06:34:43 +0800
Subject: [PATCH 09/40] feat: add local artifact gallery

---
 backend/cli/src/file/artifacts.ts             | 163 ++++
 backend/cli/src/file/index.ts                 |  13 +
 backend/cli/src/server/routes/file.ts         |  45 +
 backend/cli/test/file/artifacts.test.ts       | 120 +++
 .../workspace/e2e/artifact-gallery.spec.ts    |  59 ++
 .../src/artifacts/ArtifactGallery.tsx         | 790 ++++++++++++++++++
 .../workspace/src/artifacts/model.test.ts     |  35 +
 frontend/workspace/src/artifacts/model.ts     |  87 ++
 frontend/workspace/src/atlas/FileExplorer.tsx | 135 +--
 tooling/sdk/js/src/v2/gen/sdk.gen.ts          |  51 ++
 tooling/sdk/js/src/v2/gen/types.gen.ts        |  67 ++
 tooling/sdk/openapi.json                      | 177 ++++
 12 files changed, 1612 insertions(+), 130 deletions(-)
 create mode 100644 backend/cli/src/file/artifacts.ts
 create mode 100644 backend/cli/test/file/artifacts.test.ts
 create mode 100644 frontend/workspace/e2e/artifact-gallery.spec.ts
 create mode 100644 frontend/workspace/src/artifacts/ArtifactGallery.tsx
 create mode 100644 frontend/workspace/src/artifacts/model.test.ts
 create mode 100644 frontend/workspace/src/artifacts/model.ts

diff --git a/backend/cli/src/file/artifacts.ts b/backend/cli/src/file/artifacts.ts
new file mode 100644
index 00000000..beb4ad96
--- /dev/null
+++ b/backend/cli/src/file/artifacts.ts
@@ -0,0 +1,163 @@
+import { $ } from "bun"
+import fs from "node:fs"
+import path from "node:path"
+import z from "zod"
+
+export namespace ArtifactFile {
+  export const Kind = z.enum([
+    "notebook",
+    "dataset",
+    "figure",
+    "report",
+    "structure",
+    "sequence",
+    "genomics",
+    "spectrum",
+    "model",
+    "archive",
+  ])
+  export type Kind = z.infer<typeof Kind>
+
+  export const Info = z.object({
+    name: z.string(),
+    path: z.string(),
+    kind: Kind,
+    format: z.string(),
+    size: z.number(),
+    modified: z.number(),
+  })
+  export type Info = z.infer<typeof Info>
+
+  export const Provenance = z.object({
+    path: z.string(),
+    tracked: z.boolean(),
+    dirty: z.boolean(),
+    status: z.enum(["clean", "modified", "added", "deleted", "untracked", "local"]),
+    branch: z.string().optional(),
+    commit: z
+      .object({
+        sha: z.string(),
+        author: z.string(),
+        email: z.string(),
+        date: z.string(),
+        message: z.string(),
+      })
+      .optional(),
+  })
+  export type Provenance = z.infer<typeof Provenance>
+
+  const kinds: Record<Kind, string[]> = {
+    notebook: ["ipynb"],
+    dataset: ["csv", "tsv", "jsonl", "parquet", "feather", "arrow", "xls", "xlsx", "h5", "hdf5", "h5ad", "loom"],
+    figure: ["png", "jpg", "jpeg", "svg", "webp", "tif", "tiff", "gif"],
+    report: ["pdf", "html", "htm", "md", "markdown", "docx", "tex", "latex"],
+    structure: ["pdb", "ent", "cif", "mmcif", "pdbqt", "gro", "xyz", "sdf", "mol", "mol2", "smi", "smiles"],
+    sequence: ["fa", "fasta", "faa", "fna", "ffn", "frn", "fastq", "fq"],
+    genomics: ["vcf", "bcf", "bam", "cram", "bed", "bedgraph", "gff", "gff3", "gtf", "bigwig", "bw"],
+    spectrum: ["mzml", "mzxml", "mgf", "cdf"],
+    model: ["pkl", "pickle", "joblib", "pt", "pth", "ckpt", "safetensors", "onnx", "pb"],
+    archive: ["zip", "tar", "gz", "bz2", "xz", "7z"],
+  }
+  const extensions = Object.fromEntries(
+    Object.entries(kinds).flatMap(([kind, values]) => values.map((value) => [value, kind])),
+  ) as Record<string, Kind>
+  const excluded = new Set([
+    ".git",
+    ".hg",
+    ".svn",
+    ".cache",
+    ".next",
+    ".turbo",
+    ".venv",
+    "node_modules",
+    "dist",
+    "build",
+    "target",
+    "vendor",
+    "__pycache__",
+  ])
+  const LIMIT = 5_000
+  const DEPTH = 16
+
+  export function classify(file: string): { kind: Kind; format: string } | undefined {
+    const format = path.extname(file).slice(1).toLowerCase()
+    const kind = extensions[format]
+    if (!kind) return
+    return { kind, format }
+  }
+
+  export async function scan(root: string): Promise<Info[]> {
+    const artifacts: Info[] = []
+    const walk = async (directory: string, relative: string, depth: number): Promise<void> => {
+      if (depth > DEPTH || artifacts.length >= LIMIT) return
+      const entries = await fs.promises.readdir(directory, { withFileTypes: true }).catch(() => [] as fs.Dirent[])
+      for (const entry of entries) {
+        if (artifacts.length >= LIMIT) return
+        if (entry.isDirectory()) {
+          if (excluded.has(entry.name) || entry.name.startsWith(".")) continue
+          await walk(path.join(directory, entry.name), path.join(relative, entry.name), depth + 1)
+          continue
+        }
+        if (!entry.isFile()) continue
+        const classified = classify(entry.name)
+        if (!classified) continue
+        const full = path.join(directory, entry.name)
+        const stat = await fs.promises.stat(full).catch(() => undefined)
+        if (!stat) continue
+        artifacts.push({
+          name: entry.name,
+          path: path.join(relative, entry.name).replaceAll(path.sep, "/").replace(/^\.\//, ""),
+          kind: classified.kind,
+          format: classified.format,
+          size: stat.size,
+          modified: stat.mtimeMs,
+        })
+      }
+    }
+    await walk(root, ".", 0)
+    return artifacts.toSorted((a, b) => b.modified - a.modified || a.path.localeCompare(b.path))
+  }
+
+  export async function provenance(root: string, file: string): Promise<Provenance> {
+    const inside = await $`git rev-parse --is-inside-work-tree`.cwd(root).quiet().nothrow()
+    if (inside.exitCode !== 0) {
+      return { path: file, tracked: false, dirty: false, status: "local" }
+    }
+    const [branchResult, trackedResult, statusResult, logResult] = await Promise.all([
+      $`git branch --show-current`.cwd(root).quiet().nothrow().text(),
+      $`git ls-files --error-unmatch -- ${file}`.cwd(root).quiet().nothrow(),
+      $`git status --porcelain=v1 -- ${file}`.cwd(root).quiet().nothrow().text(),
+      $`git log -1 --format=%H%x00%an%x00%ae%x00%aI%x00%s -- ${file}`.cwd(root).quiet().nothrow().text(),
+    ])
+    const tracked = trackedResult.exitCode === 0
+    const code = statusResult.trim().slice(0, 2)
+    const status = statusOf(code, tracked)
+    const parts = logResult.trim().split("\0")
+    const commit =
+      parts.length >= 5
+        ? {
+            sha: parts[0]!,
+            author: parts[1]!,
+            email: parts[2]!,
+            date: parts[3]!,
+            message: parts.slice(4).join("\0"),
+          }
+        : undefined
+    return {
+      path: file,
+      tracked,
+      dirty: status !== "clean",
+      status,
+      branch: branchResult.trim() || undefined,
+      commit,
+    }
+  }
+
+  function statusOf(code: string, tracked: boolean): Provenance["status"] {
+    if (code === "??") return "untracked"
+    if (code.includes("D")) return "deleted"
+    if (code.includes("A")) return "added"
+    if (code) return "modified"
+    return tracked ? "clean" : "local"
+  }
+}
diff --git a/backend/cli/src/file/index.ts b/backend/cli/src/file/index.ts
index 2c02a9c0..40f266bf 100644
--- a/backend/cli/src/file/index.ts
+++ b/backend/cli/src/file/index.ts
@@ -16,6 +16,7 @@ import { Global } from "../global"
 import { FileWatcher } from "./watcher"
 import { createSearchCache } from "./search-cache"
 import { ScienceFile } from "./science"
+import { ArtifactFile } from "./artifacts"
 
 export namespace File {
   const log = Log.create({ service: "file" })
@@ -364,6 +365,18 @@ export namespace File {
     return content
   }
 
+  export async function artifacts(): Promise<ArtifactFile.Info[]> {
+    return ArtifactFile.scan(Instance.directory)
+  }
+
+  export async function provenance(file: string): Promise<ArtifactFile.Provenance> {
+    const full = path.join(Instance.directory, file)
+    if (!Instance.containsPath(full)) {
+      throw new Error(`Access denied: path escapes project directory`)
+    }
+    return ArtifactFile.provenance(Instance.directory, file)
+  }
+
   export async function write(file: string, content: string): Promise<Content> {
     using _ = log.time("write", { file })
     const full = path.join(Instance.directory, file)
diff --git a/backend/cli/src/server/routes/file.ts b/backend/cli/src/server/routes/file.ts
index 53af25f5..8a15b774 100644
--- a/backend/cli/src/server/routes/file.ts
+++ b/backend/cli/src/server/routes/file.ts
@@ -7,6 +7,7 @@ import { LSP } from "../../lsp"
 import { Instance } from "../../project/instance"
 import { lazy } from "../../util/lazy"
 import { ScienceFile } from "../../file/science"
+import { ArtifactFile } from "../../file/artifacts"
 
 export const FileRoutes = lazy(() =>
   new Hono()
@@ -261,6 +262,50 @@ export const FileRoutes = lazy(() =>
         })
       },
     )
+    .get(
+      "/file/artifacts",
+      describeRoute({
+        summary: "List local research artifacts",
+        description: "Discover notebooks, datasets, figures, reports, models, and scientific files in the project.",
+        operationId: "file.artifacts",
+        responses: {
+          200: {
+            description: "Research artifacts",
+            content: {
+              "application/json": {
+                schema: resolver(ArtifactFile.Info.array()),
+              },
+            },
+          },
+        },
+      }),
+      async (c) => c.json(await File.artifacts()),
+    )
+    .get(
+      "/file/provenance",
+      describeRoute({
+        summary: "Get local file provenance",
+        description: "Read Git branch, dirty state, and latest commit metadata for a project file.",
+        operationId: "file.provenance",
+        responses: {
+          200: {
+            description: "Local provenance",
+            content: {
+              "application/json": {
+                schema: resolver(ArtifactFile.Provenance),
+              },
+            },
+          },
+        },
+      }),
+      validator(
+        "query",
+        z.object({
+          path: z.string(),
+        }),
+      ),
+      async (c) => c.json(await File.provenance(c.req.valid("query").path)),
+    )
     .get(
       "/file/status",
       describeRoute({
diff --git a/backend/cli/test/file/artifacts.test.ts b/backend/cli/test/file/artifacts.test.ts
new file mode 100644
index 00000000..d9a924c4
--- /dev/null
+++ b/backend/cli/test/file/artifacts.test.ts
@@ -0,0 +1,120 @@
+import { describe, expect, test } from "bun:test"
+import { $ } from "bun"
+import path from "node:path"
+import { ArtifactFile } from "../../src/file/artifacts"
+import { File } from "../../src/file"
+import { Instance } from "../../src/project/instance"
+import { tmpdir } from "../fixture/fixture"
+
+describe("ArtifactFile.classify", () => {
+  test.each([
+    ["analysis.ipynb", "notebook"],
+    ["cells.h5ad", "dataset"],
+    ["counts.parquet", "dataset"],
+    ["figure.svg", "figure"],
+    ["manuscript.pdf", "report"],
+    ["protein.cif", "structure"],
+    ["reads.fastq", "sequence"],
+    ["cohort.vcf", "genomics"],
+    ["run.mzML", "spectrum"],
+    ["weights.safetensors", "model"],
+    ["bundle.zip", "archive"],
+  ])("classifies %s as %s", (file, kind) => {
+    expect(ArtifactFile.classify(file)?.kind).toBe(ArtifactFile.Kind.parse(kind))
+  })
+
+  test("does not treat source code as a research artifact", () => {
+    expect(ArtifactFile.classify("pipeline.py")).toBeUndefined()
+  })
+})
+
+describe("File.artifacts", () => {
+  test("discovers local artifacts recursively with metadata and skips dependency trees", async () => {
+    await using tmp = await tmpdir({
+      init: async (directory) => {
+        await Bun.write(path.join(directory, "analysis.ipynb"), "{}")
+        await Bun.write(path.join(directory, "results", "figure.png"), Uint8Array.from([1, 2, 3]))
+        await Bun.write(path.join(directory, "results", "table.csv"), "x,y\n1,2\n")
+        await Bun.write(path.join(directory, "src", "pipeline.py"), "print('not an artifact')")
+        await Bun.write(path.join(directory, "node_modules", "package", "paper.pdf"), "skip")
+      },
+    })
+
+    await Instance.provide({
+      directory: tmp.path,
+      fn: async () => {
+        const result = await File.artifacts()
+        expect(result.map((item) => item.path).toSorted()).toEqual([
+          "analysis.ipynb",
+          "results/figure.png",
+          "results/table.csv",
+        ])
+        expect(result.find((item) => item.path === "analysis.ipynb")).toMatchObject({
+          kind: "notebook",
+          format: "ipynb",
+          size: 2,
+        })
+        expect(result.find((item) => item.path === "results/figure.png")).toMatchObject({
+          kind: "figure",
+          format: "png",
+          size: 3,
+        })
+      },
+    })
+  })
+})
+
+describe("File.provenance", () => {
+  test("reports branch, latest commit, and dirty state for a tracked artifact", async () => {
+    await using tmp = await tmpdir({
+      git: true,
+      init: async (directory) => {
+        await Bun.write(path.join(directory, "results.csv"), "metric,value\naccuracy,0.9\n")
+        await $`git add results.csv`.cwd(directory).quiet()
+        await $`git -c user.name=OpenScience -c user.email=test@openscience.local commit -m "record baseline"`
+          .cwd(directory)
+          .quiet()
+        await Bun.write(path.join(directory, "results.csv"), "metric,value\naccuracy,0.95\n")
+      },
+    })
+
+    await Instance.provide({
+      directory: tmp.path,
+      fn: async () => {
+        const result = await File.provenance("results.csv")
+        expect(result).toMatchObject({
+          path: "results.csv",
+          tracked: true,
+          dirty: true,
+          status: "modified",
+          branch: "master",
+          commit: {
+            author: "OpenScience",
+            email: "test@openscience.local",
+            message: "record baseline",
+          },
+        })
+        expect(result.commit?.sha).toHaveLength(40)
+      },
+    })
+  })
+
+  test("reports a clean local-only state outside git", async () => {
+    await using tmp = await tmpdir({
+      init: async (directory) => {
+        await Bun.write(path.join(directory, "report.pdf"), "pdf")
+      },
+    })
+
+    await Instance.provide({
+      directory: tmp.path,
+      fn: async () => {
+        expect(await File.provenance("report.pdf")).toMatchObject({
+          tracked: false,
+          dirty: false,
+          status: "local",
+        })
+      },
+    })
+  })
+})
diff --git a/frontend/workspace/e2e/artifact-gallery.spec.ts b/frontend/workspace/e2e/artifact-gallery.spec.ts
new file mode 100644
index 00000000..8ce933ea
--- /dev/null
+++ b/frontend/workspace/e2e/artifact-gallery.spec.ts
@@ -0,0 +1,59 @@
+import { mkdirSync, mkdtempSync, rmSync, writeFileSync } from "node:fs"
+import { tmpdir } from "node:os"
+import path from "node:path"
+import { test, expect } from "./fixtures"
+
+test("discovers, filters, opens, downloads, and contextualizes local research artifacts", async ({
+  page,
+  gotoSession,
+}) => {
+  const directory = mkdtempSync(path.join(tmpdir(), "openscience-artifacts-e2e-"))
+  mkdirSync(path.join(directory, "results"))
+  writeFileSync(path.join(directory, "analysis.ipynb"), '{"cells":[],"metadata":{},"nbformat":4,"nbformat_minor":5}')
+  writeFileSync(path.join(directory, "results", "counts.csv"), "gene,count\nTP53,12\nEGFR,4\n")
+  writeFileSync(
+    path.join(directory, "results", "plot.svg"),
+    '<svg xmlns="http://www.w3.org/2000/svg" width="10" height="10"><circle cx="5" cy="5" r="4"/></svg>',
+  )
+  writeFileSync(path.join(directory, "pipeline.py"), "print('source, not artifact')")
+
+  try {
+    await gotoSession()
+    await page.getByRole("tab", { name: "Files", exact: true }).click()
+    const location = page.getByPlaceholder("/absolute/path")
+    await location.fill(directory)
+    await location.press("Enter")
+    await page.getByRole("button", { name: "artifacts", exact: true }).click()
+
+    const gallery = page.locator('[data-component="artifact-gallery"]')
+    await expect(gallery).toBeVisible()
+    await expect(gallery.getByText("3 discovered locally", { exact: true })).toBeVisible()
+    await expect(gallery.locator("[data-artifact]")).toHaveCount(3)
+    await expect(gallery.getByText("pipeline.py", { exact: true })).toHaveCount(0)
+
+    await gallery.getByRole("button", { name: /^figure 1$/ }).click()
+    await expect(gallery.locator("[data-artifact]")).toHaveCount(1)
+    await expect(gallery.locator('[data-artifact="results/plot.svg"]')).toBeVisible()
+
+    await gallery.getByRole("button", { name: /^dataset 1$/ }).click()
+    await gallery.locator('[data-artifact="results/counts.csv"]').click()
+    const detail = gallery.locator('[data-component="artifact-detail"]')
+    await expect(detail).toBeVisible()
+    await expect(detail.getByText("results/counts.csv", { exact: true })).toBeVisible()
+    await expect(detail.getByText("local file · no Git provenance", { exact: true })).toBeVisible()
+
+    await detail.getByRole("button", { name: "add to context", exact: true }).click()
+    await expect(page.getByRole("tab", { name: "Chat", exact: true })).toHaveAttribute("aria-selected", "true")
+    await expect(page.locator("form").getByText("counts.csv", { exact: true })).toBeVisible()
+
+    await page.getByRole("tab", { name: "Files", exact: true }).click()
+    await page.getByRole("button", { name: "artifacts", exact: true }).click()
+    await gallery.getByRole("button", { name: /^dataset 1$/ }).click()
+    await gallery.locator('[data-artifact="results/counts.csv"]').click()
+    await detail.getByRole("button", { name: "open", exact: true }).click()
+    await expect(page.locator('[data-component="data-table"]')).toBeVisible()
+    await expect(page.getByText("2 rows", { exact: true })).toBeVisible()
+  } finally {
+    rmSync(directory, { recursive: true, force: true })
+  }
+})
diff --git a/frontend/workspace/src/artifacts/ArtifactGallery.tsx b/frontend/workspace/src/artifacts/ArtifactGallery.tsx
new file mode 100644
index 00000000..efe32d46
--- /dev/null
+++ b/frontend/workspace/src/artifacts/ArtifactGallery.tsx
@@ -0,0 +1,790 @@
+import { For, Show, createMemo, createResource, createSignal, type JSX } from "solid-js"
+import { usePlatform } from "@/context/platform"
+import { usePrompt } from "@/context/prompt"
+import { useSDK } from "@/context/sdk"
+import { centerTabs } from "@/atlas/store/centerTabs"
+import { toast } from "@/atlas/Toast"
+import {
+  IconArchive,
+  IconBookOpen,
+  IconCopy,
+  IconDownload,
+  IconFile,
+  IconFlask,
+  IconRefresh,
+  IconSearch,
+  IconX,
+} from "@/atlas/shared/Icon"
+import { FONT_CODE, FONT_MONO, FONT_SANS } from "@/styles/tokens"
+import {
+  artifactKinds,
+  filterArtifacts,
+  formatArtifactKind,
+  groupArtifacts,
+  normalizeArtifacts,
+  sortArtifacts,
+  type ArtifactInfo,
+  type ArtifactKind,
+  type ArtifactSort,
+} from "./model"
+
+interface Provenance {
+  path: string
+  tracked: boolean
+  dirty: boolean
+  status: string
+  branch?: string
+  commit?: {
+    sha: string
+    author: string
+    email: string
+    date: string
+    message: string
+  }
+}
+
+export function ArtifactGallery(props: { directory: string; onOpen: (path: string) => void }): JSX.Element {
+  const sdk = useSDK()
+  const platform = usePlatform()
+  const prompt = usePrompt()
+  const [query, setQuery] = createSignal("")
+  const [kind, setKind] = createSignal<ArtifactKind | "all">("all")
+  const [sort, setSort] = createSignal<ArtifactSort>("recent")
+  const [selected, setSelected] = createSignal<string>()
+  const [refresh, setRefresh] = createSignal(0)
+  const request = () => platform.fetch ?? fetch
+  const url = (route: string, path?: string) =>
+    `${sdk.url.replace(/\/$/, "")}${route}?directory=${encodeURIComponent(props.directory)}${path ? `&path=${encodeURIComponent(path)}` : ""}`
+
+  const [data] = createResource(
+    () => [props.directory, refresh()] as const,
+    async () => {
+      const response = await request()(url("/file/artifacts"))
+      if (!response.ok) throw new Error(`artifact scan failed (${response.status})`)
+      return normalizeArtifacts(await response.json())
+    },
+  )
+  const rows = () => data.latest ?? []
+  const groups = createMemo(() => groupArtifacts(rows()))
+  const filtered = createMemo(() => sortArtifacts(filterArtifacts(rows(), kind(), query()), sort()))
+  const artifact = createMemo(() => rows().find((item) => item.path === selected()))
+  const totalSize = createMemo(() => rows().reduce((total, item) => total + item.size, 0))
+
+  const download = async (item: ArtifactInfo) => {
+    const response = await request()(url("/file/raw", item.path))
+    if (!response.ok) {
+      toast.error("download failed", `${response.status}`)
+      return
+    }
+    const object = URL.createObjectURL(await response.blob())
+    const anchor = document.createElement("a")
+    anchor.href = object
+    anchor.download = item.name
+    anchor.click()
+    URL.revokeObjectURL(object)
+  }
+
+  const copy = async (value: string, label: string) => {
+    await navigator.clipboard?.writeText(value)
+    toast.success("copied", label)
+  }
+
+  const attach = (item: ArtifactInfo) => {
+    prompt.context.add({ type: "file", path: item.path })
+    centerTabs.showChat()
+    toast.success("added to context", item.name)
+  }
+
+  return (
+    <div
+      data-component="artifact-gallery"
+      style={{
+        flex: 1,
+        "min-height": 0,
+        display: "flex",
+        "flex-direction": "column",
+        background: "var(--color-bg-subtle)",
+        overflow: "hidden",
+      }}
+    >
+      <div
+        style={{
+          padding: "14px 16px 12px",
+          border: "0",
+          "border-bottom": "1px solid var(--color-border)",
+          background: "var(--color-bg)",
+          display: "grid",
+          gap: "12px",
+        }}
+      >
+        <div style={{ display: "flex", "align-items": "center", gap: "10px" }}>
+          <div style={{ flex: 1, "min-width": 0 }}>
+            <div style={{ display: "flex", "align-items": "baseline", gap: "8px" }}>
+              <strong style={{ "font-family": FONT_SANS, "font-size": "14px", color: "var(--color-text)" }}>
+                Research artifacts
+              </strong>
+              <span style={muted()}>{rows().length.toLocaleString()} discovered locally</span>
+            </div>
+            <Show when={rows().length}>
+              <div style={{ ...muted(), "margin-top": "3px" }}>
+                {groups().length} categories · {formatBytes(totalSize())} · nothing uploaded
+              </div>
+            </Show>
+          </div>
+          <div style={search()}>
+            <IconSearch size={11} strokeWidth={1.5} />
+            <input
+              value={query()}
+              onInput={(event) => setQuery(event.currentTarget.value)}
+              placeholder="find an artifact…"
+              aria-label="Find an artifact"
+              style={{
+                all: "unset",
+                width: "180px",
+                "font-family": FONT_SANS,
+                "font-size": "10px",
+                color: "var(--color-text)",
+              }}
+            />
+          </div>
+          <select
+            aria-label="Sort artifacts"
+            value={sort()}
+            onChange={(event) => setSort(event.currentTarget.value as ArtifactSort)}
+            style={select()}
+          >
+            <option value="recent">recent first</option>
+            <option value="name">name</option>
+            <option value="size">largest first</option>
+          </select>
+          <button
+            type="button"
+            title="refresh artifacts"
+            style={iconButton()}
+            onClick={() => setRefresh((value) => value + 1)}
+          >
+            <IconRefresh size={12} strokeWidth={1.5} />
+          </button>
+        </div>
+        <div class="atlas-scroll" style={{ display: "flex", gap: "5px", overflow: "auto hidden" }}>
+          <button type="button" style={filterButton(kind() === "all")} onClick={() => setKind("all")}>
+            all <span>{rows().length}</span>
+          </button>
+          <For each={groups()}>
+            {(group) => (
+              <button type="button" style={filterButton(kind() === group.kind)} onClick={() => setKind(group.kind)}>
+                {formatArtifactKind(group.kind)} <span>{group.count}</span>
+              </button>
+            )}
+          </For>
+        </div>
+      </div>
+
+      <Show
+        when={!data.loading || data.latest}
+        fallback={
+          <div style={empty()}>
+            <span style={{ "font-family": FONT_MONO, "font-size": "11px", color: "var(--color-text-faint)" }}>
+              indexing project artifacts…
+            </span>
+          </div>
+        }
+      >
+        <Show
+          when={!data.error}
+          fallback={
+            <div style={empty()}>
+              <IconArchive size={22} strokeWidth={1.3} />
+              <strong style={emptyTitle()}>Artifact scan unavailable</strong>
+              <span style={muted()}>{data.error instanceof Error ? data.error.message : String(data.error)}</span>
+              <button type="button" style={actionButton()} onClick={() => setRefresh((value) => value + 1)}>
+                retry
+              </button>
+            </div>
+          }
+        >
+          <Show
+            when={filtered().length}
+            fallback={
+              <div style={empty()}>
+                <IconArchive size={24} strokeWidth={1.2} />
+                <strong style={emptyTitle()}>
+                  {rows().length ? "No matching artifacts" : "No research artifacts yet"}
+                </strong>
+                <span style={{ ...muted(), "max-width": "430px", "line-height": 1.6 }}>
+                  {rows().length
+                    ? "Try another search or category."
+                    : "Notebooks, datasets, figures, reports, structures, sequences, spectra, and model files appear here automatically."}
+                </span>
+              </div>
+            }
+          >
+            <div style={{ flex: 1, "min-height": 0, display: "flex", overflow: "hidden" }}>
+              <div
+                class="atlas-scroll"
+                style={{
+                  flex: 1,
+                  "min-width": 0,
+                  overflow: "auto",
+                  padding: "14px",
+                }}
+              >
+                <div
+                  style={{
+                    display: "grid",
+                    "grid-template-columns": "repeat(auto-fill, minmax(185px, 1fr))",
+                    gap: "9px",
+                    "align-content": "start",
+                  }}
+                >
+                  <For each={filtered()}>
+                    {(item) => (
+                      <ArtifactCard
+                        item={item}
+                        active={selected() === item.path}
+                        onSelect={() => setSelected(item.path)}
+                        onOpen={() => props.onOpen(item.path)}
+                      />
+                    )}
+                  </For>
+                </div>
+              </div>
+              <Show when={artifact()}>
+                {(item) => (
+                  <ArtifactDetail
+                    item={item()}
+                    directory={props.directory}
+                    url={url}
+                    request={request()}
+                    onClose={() => setSelected(undefined)}
+                    onOpen={() => props.onOpen(item().path)}
+                    onDownload={() => void download(item())}
+                    onCopy={() => void copy(item().path, item().path)}
+                    onAttach={() => attach(item())}
+                  />
+                )}
+              </Show>
+            </div>
+          </Show>
+        </Show>
+      </Show>
+    </div>
+  )
+}
+
+function ArtifactCard(props: {
+  item: ArtifactInfo
+  active: boolean
+  onSelect: () => void
+  onOpen: () => void
+}): JSX.Element {
+  return (
+    <button
+      type="button"
+      data-artifact={props.item.path}
+      aria-label={`${props.item.name} artifact`}
+      onClick={props.onSelect}
+      onDblClick={props.onOpen}
+      onKeyDown={(event) => {
+        if (event.key === "Enter") props.onOpen()
+      }}
+      style={{
+        all: "unset",
+        cursor: "pointer",
+        display: "grid",
+        "grid-template-rows": "86px auto",
+        border: `1px solid ${props.active ? "var(--color-accent)" : "var(--color-border)"}`,
+        "border-radius": "8px",
+        background: "var(--color-bg)",
+        overflow: "hidden",
+        "box-shadow": props.active ? "0 0 0 1px color-mix(in srgb, var(--color-accent) 20%, transparent)" : "none",
+        transition: "border-color 120ms ease, transform 120ms ease, box-shadow 120ms ease",
+      }}
+    >
+      <ArtifactVisual item={props.item} />
+      <div style={{ display: "grid", gap: "7px", padding: "10px 11px" }}>
+        <div style={{ display: "flex", gap: "7px", "align-items": "center", "min-width": 0 }}>
+          <span style={{ color: accent(props.item.kind), display: "inline-flex" }}>
+            <KindIcon kind={props.item.kind} size={12} />
+          </span>
+          <strong
+            title={props.item.path}
+            style={{
+              flex: 1,
+              "min-width": 0,
+              overflow: "hidden",
+              "text-overflow": "ellipsis",
+              "white-space": "nowrap",
+              "font-family": FONT_SANS,
+              "font-size": "11px",
+              "font-weight": 550,
+              color: "var(--color-text)",
+            }}
+          >
+            {props.item.name}
+          </strong>
+        </div>
+        <div style={{ display: "flex", gap: "5px", "align-items": "center" }}>
+          <span style={badge(accent(props.item.kind))}>{props.item.format.toUpperCase()}</span>
+          <span style={{ ...muted(), flex: 1 }}>{formatArtifactKind(props.item.kind)}</span>
+          <span style={muted()}>{formatBytes(props.item.size)}</span>
+        </div>
+      </div>
+    </button>
+  )
+}
+
+function ArtifactVisual(props: { item: ArtifactInfo }): JSX.Element {
+  const seed = () => Array.from(props.item.path).reduce((total, value) => total + value.charCodeAt(0), 0)
+  return (
+    <div
+      style={{
+        position: "relative",
+        overflow: "hidden",
+        background: `color-mix(in srgb, ${accent(props.item.kind)} 8%, var(--color-bg-subtle))`,
+        border: "0",
+        "border-bottom": "1px solid var(--color-border)",
+      }}
+    >
+      <div style={{ position: "absolute", inset: "12px", display: "flex", "align-items": "flex-end", gap: "4px" }}>
+        <For each={Array.from({ length: 13 })}>
+          {(_, index) => (
+            <span
+              style={{
+                flex: 1,
+                height: `${18 + ((seed() + index() * 29) % 56)}%`,
+                "border-radius": "2px 2px 0 0",
+                background: `color-mix(in srgb, ${accent(props.item.kind)} ${22 + ((index() * 7) % 28)}%, transparent)`,
+              }}
+            />
+          )}
+        </For>
+      </div>
+      <span
+        style={{
+          position: "absolute",
+          top: "10px",
+          left: "11px",
+          "font-family": FONT_MONO,
+          "font-size": "9px",
+          "font-weight": 650,
+          color: accent(props.item.kind),
+          "letter-spacing": "0.08em",
+        }}
+      >
+        {props.item.kind.toUpperCase()}
+      </span>
+      <span
+        style={{
+          position: "absolute",
+          right: "10px",
+          bottom: "8px",
+          color: `color-mix(in srgb, ${accent(props.item.kind)} 70%, var(--color-text-faint))`,
+          opacity: 0.8,
+        }}
+      >
+        <KindIcon kind={props.item.kind} size={20} />
+      </span>
+    </div>
+  )
+}
+
+function ArtifactDetail(props: {
+  item: ArtifactInfo
+  directory: string
+  url: (route: string, path?: string) => string
+  request: typeof fetch
+  onClose: () => void
+  onOpen: () => void
+  onDownload: () => void
+  onCopy: () => void
+  onAttach: () => void
+}): JSX.Element {
+  const [provenance] = createResource(
+    () => [props.directory, props.item.path] as const,
+    async () => {
+      const response = await props.request(props.url("/file/provenance", props.item.path))
+      if (!response.ok) throw new Error(`${response.status}`)
+      return (await response.json()) as Provenance
+    },
+  )
+  return (
+    <aside
+      data-component="artifact-detail"
+      style={{
+        width: "310px",
+        "max-width": "42%",
+        "flex-shrink": 0,
+        border: "0",
+        "border-left": "1px solid var(--color-border)",
+        background: "var(--color-bg)",
+        display: "flex",
+        "flex-direction": "column",
+        overflow: "hidden",
+      }}
+    >
+      <div
+        style={{
+          display: "flex",
+          "align-items": "center",
+          gap: "8px",
+          padding: "11px 12px",
+          "border-bottom": "1px solid var(--color-border)",
+        }}
+      >
+        <span style={{ color: accent(props.item.kind), display: "inline-flex" }}>
+          <KindIcon kind={props.item.kind} size={14} />
+        </span>
+        <strong
+          title={props.item.name}
+          style={{
+            flex: 1,
+            "min-width": 0,
+            overflow: "hidden",
+            "text-overflow": "ellipsis",
+            "white-space": "nowrap",
+            "font-family": FONT_SANS,
+            "font-size": "11px",
+            color: "var(--color-text)",
+          }}
+        >
+          {props.item.name}
+        </strong>
+        <button type="button" title="close artifact details" style={iconButton()} onClick={props.onClose}>
+          <IconX size={12} strokeWidth={1.5} />
+        </button>
+      </div>
+      <div
+        class="atlas-scroll"
+        style={{ flex: 1, overflow: "auto", padding: "12px", display: "grid", gap: "12px", "align-content": "start" }}
+      >
+        <div style={{ display: "grid", "grid-template-columns": "1fr 1fr", gap: "7px" }}>
+          <button type="button" style={primaryButton()} onClick={props.onOpen}>
+            <IconBookOpen size={11} /> open
+          </button>
+          <button type="button" style={actionButton()} onClick={props.onAttach}>
+            <IconFlask size={11} /> add to context
+          </button>
+          <button type="button" style={actionButton()} onClick={props.onDownload}>
+            <IconDownload size={11} /> download
+          </button>
+          <button type="button" style={actionButton()} onClick={props.onCopy}>
+            <IconCopy size={11} /> copy path
+          </button>
+        </div>
+        <Section title="File">
+          <Fact label="path" value={props.item.path} mono />
+          <Fact label="kind" value={formatArtifactKind(props.item.kind)} />
+          <Fact label="format" value={props.item.format.toUpperCase()} mono />
+          <Fact label="size" value={formatBytes(props.item.size)} />
+          <Fact label="modified" value={new Date(props.item.modified).toLocaleString()} />
+        </Section>
+        <Section title="Provenance">
+          <Show when={!provenance.loading} fallback={<span style={muted()}>reading Git history…</span>}>
+            <Show when={provenance()} fallback={<span style={muted()}>local file · no Git provenance</span>}>
+              {(value) => (
+                <>
+                  <Show when={value().status === "local"}>
+                    <span style={muted()}>local file · no Git provenance</span>
+                  </Show>
+                  <div style={{ display: "flex", gap: "6px", "align-items": "center", "margin-bottom": "9px" }}>
+                    <Status status={value().status} />
+                    <Show when={value().branch}>
+                      <span style={badge("var(--color-text-faint)")}>{value().branch}</span>
+                    </Show>
+                  </div>
+                  <Show when={value().commit} fallback={<span style={muted()}>Not committed yet</span>}>
+                    {(commit) => (
+                      <div style={{ display: "grid", gap: "6px" }}>
+                        <strong
+                          style={{
+                            "font-family": FONT_SANS,
+                            "font-size": "10px",
+                            color: "var(--color-text)",
+                            "line-height": 1.4,
+                          }}
+                        >
+                          {commit().message}
+                        </strong>
+                        <span style={muted()}>
+                          {commit().author} · {new Date(commit().date).toLocaleString()}
+                        </span>
+                        <button
+                          type="button"
+                          style={shaButton()}
+                          onClick={() => void navigator.clipboard?.writeText(commit().sha)}
+                          title="copy commit SHA"
+                        >
+                          {commit().sha.slice(0, 9)}
+                        </button>
+                      </div>
+                    )}
+                  </Show>
+                </>
+              )}
+            </Show>
+          </Show>
+        </Section>
+        <Section title="Reproducibility">
+          <div style={{ display: "grid", gap: "8px" }}>
+            <Check
+              ok={!provenance()?.dirty}
+              label={provenance()?.dirty ? "working copy has changes" : "working copy matches Git"}
+            />
+            <Check
+              ok={Boolean(provenance()?.commit)}
+              label={provenance()?.commit ? "commit provenance available" : "not committed"}
+            />
+            <Check ok={props.item.size > 0} label="artifact is non-empty" />
+          </div>
+        </Section>
+      </div>
+    </aside>
+  )
+}
+
+function Section(props: { title: string; children: JSX.Element }): JSX.Element {
+  return (
+    <section
+      style={{
+        padding: "11px",
+        border: "1px solid var(--color-border)",
+        "border-radius": "7px",
+        background: "var(--color-bg-subtle)",
+      }}
+    >
+      <h3
+        style={{
+          margin: "0 0 10px",
+          "font-family": FONT_MONO,
+          "font-size": "9px",
+          "font-weight": 600,
+          color: "var(--color-text-faint)",
+          "text-transform": "uppercase",
+          "letter-spacing": "0.07em",
+        }}
+      >
+        {props.title}
+      </h3>
+      <div style={{ display: "grid", gap: "7px" }}>{props.children}</div>
+    </section>
+  )
+}
+
+function Fact(props: { label: string; value: string; mono?: boolean }): JSX.Element {
+  return (
+    <div style={{ display: "grid", "grid-template-columns": "68px 1fr", gap: "7px", "align-items": "baseline" }}>
+      <span style={muted()}>{props.label}</span>
+      <span
+        title={props.value}
+        style={{
+          "font-family": props.mono ? FONT_CODE : FONT_SANS,
+          "font-size": "9px",
+          color: "var(--color-text-muted)",
+          overflow: "hidden",
+          "text-overflow": "ellipsis",
+          "white-space": "nowrap",
+        }}
+      >
+        {props.value}
+      </span>
+    </div>
+  )
+}
+
+function Check(props: { ok: boolean; label: string }): JSX.Element {
+  return (
+    <div
+      style={{
+        display: "flex",
+        gap: "7px",
+        "align-items": "center",
+        "font-family": FONT_SANS,
+        "font-size": "9px",
+        color: "var(--color-text-muted)",
+      }}
+    >
+      <span style={{ color: props.ok ? "#4ca56a" : "#b07a00" }}>{props.ok ? "●" : "◇"}</span>
+      {props.label}
+    </div>
+  )
+}
+
+function Status(props: { status: string }): JSX.Element {
+  const clean = props.status === "clean"
+  return (
+    <span
+      style={{
+        ...badge(clean ? "#4ca56a" : "#b07a00"),
+        background: clean
+          ? "color-mix(in srgb, #4ca56a 9%, transparent)"
+          : "color-mix(in srgb, #d4a72c 9%, transparent)",
+      }}
+    >
+      {props.status}
+    </span>
+  )
+}
+
+function KindIcon(props: { kind: ArtifactKind; size: number }): JSX.Element {
+  if (props.kind === "notebook" || props.kind === "report") return <IconBookOpen size={props.size} strokeWidth={1.5} />
+  if (props.kind === "archive") return <IconArchive size={props.size} strokeWidth={1.5} />
+  if (["structure", "sequence", "genomics", "spectrum"].includes(props.kind))
+    return <IconFlask size={props.size} strokeWidth={1.5} />
+  return <IconFile size={props.size} strokeWidth={1.5} />
+}
+
+function accent(kind: ArtifactKind): string {
+  const colors: Record<ArtifactKind, string> = {
+    notebook: "#e07836",
+    dataset: "#2f8f83",
+    figure: "#825dc7",
+    report: "#d15151",
+    structure: "#2786b8",
+    sequence: "#5a9b4d",
+    genomics: "#3b7f67",
+    spectrum: "#b07822",
+    model: "#6977b8",
+    archive: "#7e7b75",
+  }
+  return colors[kind]
+}
+
+function formatBytes(bytes: number): string {
+  if (bytes < 1024) return `${bytes} B`
+  const units = ["KB", "MB", "GB", "TB"]
+  const order = Math.min(units.length - 1, Math.floor(Math.log(bytes) / Math.log(1024)) - 1)
+  const value = bytes / 1024 ** (order + 1)
+  return `${Math.round(value * 10) / 10} ${units[order]}`
+}
+
+function search(): JSX.CSSProperties {
+  return {
+    display: "flex",
+    "align-items": "center",
+    gap: "6px",
+    padding: "6px 8px",
+    border: "1px solid var(--color-border)",
+    "border-radius": "5px",
+    background: "var(--color-bg-subtle)",
+    color: "var(--color-text-faint)",
+  }
+}
+
+function select(): JSX.CSSProperties {
+  return {
+    padding: "6px 8px",
+    border: "1px solid var(--color-border)",
+    "border-radius": "5px",
+    background: "var(--color-bg-subtle)",
+    color: "var(--color-text-muted)",
+    "font-family": FONT_SANS,
+    "font-size": "10px",
+    outline: "none",
+  }
+}
+
+function filterButton(active: boolean): JSX.CSSProperties {
+  return {
+    padding: "4px 8px",
+    border: `1px solid ${active ? "var(--color-border-strong)" : "var(--color-border)"}`,
+    "border-radius": "99px",
+    background: active ? "var(--color-bg-subtle)" : "transparent",
+    color: active ? "var(--color-text)" : "var(--color-text-muted)",
+    "font-family": FONT_SANS,
+    "font-size": "9px",
+    cursor: "pointer",
+    "white-space": "nowrap",
+  }
+}
+
+function badge(color: string): JSX.CSSProperties {
+  return {
+    width: "fit-content",
+    padding: "2px 6px",
+    "border-radius": "4px",
+    background: `color-mix(in srgb, ${color} 10%, transparent)`,
+    color,
+    "font-family": FONT_MONO,
+    "font-size": "8px",
+    "font-weight": 600,
+    "letter-spacing": "0.04em",
+    "white-space": "nowrap",
+  }
+}
+
+function muted(): JSX.CSSProperties {
+  return { "font-family": FONT_MONO, "font-size": "9px", color: "var(--color-text-faint)" }
+}
+
+function iconButton(): JSX.CSSProperties {
+  return {
+    all: "unset",
+    width: "27px",
+    height: "27px",
+    display: "grid",
+    "place-items": "center",
+    "border-radius": "4px",
+    cursor: "pointer",
+    color: "var(--color-text-faint)",
+  }
+}
+
+function actionButton(): JSX.CSSProperties {
+  return {
+    display: "inline-flex",
+    "align-items": "center",
+    "justify-content": "center",
+    gap: "5px",
+    padding: "6px 8px",
+    border: "1px solid var(--color-border)",
+    "border-radius": "5px",
+    background: "var(--color-bg)",
+    color: "var(--color-text-muted)",
+    "font-family": FONT_SANS,
+    "font-size": "9px",
+    cursor: "pointer",
+  }
+}
+
+function primaryButton(): JSX.CSSProperties {
+  return {
+    ...actionButton(),
+    background: "var(--color-text)",
+    color: "var(--color-bg)",
+    border: "1px solid var(--color-text)",
+  }
+}
+
+function shaButton(): JSX.CSSProperties {
+  return {
+    width: "fit-content",
+    padding: "3px 6px",
+    border: "1px solid var(--color-border)",
+    "border-radius": "4px",
+    background: "var(--color-bg)",
+    color: "var(--color-text-faint)",
+    "font-family": FONT_CODE,
+    "font-size": "9px",
+    cursor: "copy",
+  }
+}
+
+function empty(): JSX.CSSProperties {
+  return {
+    flex: 1,
+    display: "grid",
+    "place-items": "center",
+    "align-content": "center",
+    gap: "8px",
+    padding: "40px 24px",
+    color: "var(--color-text-faint)",
+    "text-align": "center",
+  }
+}
+
+function emptyTitle(): JSX.CSSProperties {
+  return { "font-family": FONT_SANS, "font-size": "13px", color: "var(--color-text)" }
+}
+
+export default ArtifactGallery
diff --git a/frontend/workspace/src/artifacts/model.test.ts b/frontend/workspace/src/artifacts/model.test.ts
new file mode 100644
index 00000000..9e1ec184
--- /dev/null
+++ b/frontend/workspace/src/artifacts/model.test.ts
@@ -0,0 +1,35 @@
+import { describe, expect, test } from "bun:test"
+import { filterArtifacts, groupArtifacts, normalizeArtifacts, sortArtifacts } from "./model"
+
+const rows = normalizeArtifacts([
+  { name: "analysis.ipynb", path: "analysis.ipynb", kind: "notebook", format: "ipynb", size: 20, modified: 10 },
+  { name: "figure.png", path: "results/figure.png", kind: "figure", format: "png", size: 30, modified: 30 },
+  { name: "counts.csv", path: "results/counts.csv", kind: "dataset", format: "csv", size: 10, modified: 20 },
+])
+
+describe("artifact gallery model", () => {
+  test("normalizes only valid artifact rows", () => {
+    expect(normalizeArtifacts([{ kind: "nope" }, null, ...rows])).toHaveLength(3)
+  })
+
+  test("filters by kind and searches names, paths, and formats", () => {
+    expect(filterArtifacts(rows, "figure", "result")).toEqual([rows[1]])
+    expect(filterArtifacts(rows, "all", "IPYNB")).toEqual([rows[0]])
+    expect(filterArtifacts(rows, "dataset", "")).toEqual([rows[2]])
+  })
+
+  test("groups artifact counts by kind", () => {
+    expect(groupArtifacts(rows)).toEqual([
+      { kind: "dataset", count: 1 },
+      { kind: "figure", count: 1 },
+      { kind: "notebook", count: 1 },
+    ])
+  })
+
+  test("sorts by recency, size, and name without mutating input", () => {
+    expect(sortArtifacts(rows, "recent").map((row) => row.name)).toEqual(["figure.png", "counts.csv", "analysis.ipynb"])
+    expect(sortArtifacts(rows, "size").map((row) => row.name)).toEqual(["figure.png", "analysis.ipynb", "counts.csv"])
+    expect(sortArtifacts(rows, "name").map((row) => row.name)).toEqual(["analysis.ipynb", "counts.csv", "figure.png"])
+    expect(rows[0]?.name).toBe("analysis.ipynb")
+  })
+})
diff --git a/frontend/workspace/src/artifacts/model.ts b/frontend/workspace/src/artifacts/model.ts
new file mode 100644
index 00000000..6e87c8a7
--- /dev/null
+++ b/frontend/workspace/src/artifacts/model.ts
@@ -0,0 +1,87 @@
+export const artifactKinds = [
+  "notebook",
+  "dataset",
+  "figure",
+  "report",
+  "structure",
+  "sequence",
+  "genomics",
+  "spectrum",
+  "model",
+  "archive",
+] as const
+
+export type ArtifactKind = (typeof artifactKinds)[number]
+export type ArtifactSort = "recent" | "size" | "name"
+
+export interface ArtifactInfo {
+  name: string
+  path: string
+  kind: ArtifactKind
+  format: string
+  size: number
+  modified: number
+}
+
+const kinds = new Set<string>(artifactKinds)
+
+export function normalizeArtifacts(value: unknown): ArtifactInfo[] {
+  if (!Array.isArray(value)) return []
+  return value.flatMap((item): ArtifactInfo[] => {
+    if (!item || typeof item !== "object") return []
+    const row = item as Record<string, unknown>
+    if (
+      typeof row.name !== "string" ||
+      typeof row.path !== "string" ||
+      typeof row.kind !== "string" ||
+      !kinds.has(row.kind) ||
+      typeof row.format !== "string" ||
+      typeof row.size !== "number" ||
+      typeof row.modified !== "number"
+    )
+      return []
+    return [
+      {
+        name: row.name,
+        path: row.path,
+        kind: row.kind as ArtifactKind,
+        format: row.format,
+        size: row.size,
+        modified: row.modified,
+      },
+    ]
+  })
+}
+
+export function filterArtifacts(rows: ArtifactInfo[], kind: ArtifactKind | "all", query: string): ArtifactInfo[] {
+  const term = query.trim().toLowerCase()
+  return rows.filter((row) => {
+    if (kind !== "all" && row.kind !== kind) return false
+    if (!term) return true
+    return `${row.name}\n${row.path}\n${row.format}\n${row.kind}`.toLowerCase().includes(term)
+  })
+}
+
+export function sortArtifacts(rows: ArtifactInfo[], sort: ArtifactSort): ArtifactInfo[] {
+  return rows.toSorted((a, b) => {
+    if (sort === "recent") return b.modified - a.modified || a.name.localeCompare(b.name)
+    if (sort === "size") return b.size - a.size || a.name.localeCompare(b.name)
+    return a.name.localeCompare(b.name)
+  })
+}
+
+export function groupArtifacts(rows: ArtifactInfo[]): { kind: ArtifactKind; count: number }[] {
+  const counts = rows.reduce<Partial<Record<ArtifactKind, number>>>(
+    (all, row) => ({ ...all, [row.kind]: (all[row.kind] ?? 0) + 1 }),
+    {},
+  )
+  return Object.entries(counts)
+    .map(([kind, count]) => ({ kind: kind as ArtifactKind, count }))
+    .toSorted((a, b) => a.kind.localeCompare(b.kind))
+}
+
+export function formatArtifactKind(kind: ArtifactKind): string {
+  if (kind === "genomics") return "genomics"
+  if (kind === "spectrum") return "mass spec"
+  return kind
+}
diff --git a/frontend/workspace/src/atlas/FileExplorer.tsx b/frontend/workspace/src/atlas/FileExplorer.tsx
index af5a1bdb..1612880f 100644
--- a/frontend/workspace/src/atlas/FileExplorer.tsx
+++ b/frontend/workspace/src/atlas/FileExplorer.tsx
@@ -3,7 +3,7 @@ import { useSDK } from "@/context/sdk"
 import { useSync } from "@/context/sync"
 import { FONT_MONO, FONT_SANS } from "@/styles/tokens"
 import { centerTabs } from "@/atlas/store/centerTabs"
-import { createAtlasAPI, type AtlasNode } from "@/atlas/api/atlas"
+import { ArtifactGallery } from "@/artifacts/ArtifactGallery"
 import {
   IconFolder,
   IconFile,
@@ -314,7 +314,10 @@ export function FileExplorer(): JSX.Element {
         </Show>
       </div>
 
-      <Show when={mode() === "host"} fallback={<ArtifactsPanel />}>
+      <Show
+        when={mode() === "host"}
+        fallback={<ArtifactGallery directory={cwd()} onOpen={(path) => centerTabs.openFile(cwd(), path)} />}
+      >
         {/* toolbar row 2: back / up / path bar / refresh */}
         <div
           style={{
@@ -569,134 +572,6 @@ function GridBody(props: { nodes: FileNode[]; onClick: (n: FileNode) => void }):
   )
 }
 
-// ── Artifacts (project Atlas graph) ────────────────────────────────
-type ArtifactRow = { node: AtlasNode; artifact: { name?: string; kind?: string; uri?: string } }
-
-async function mapSettledBounded<T, R>(
-  items: T[],
-  limit: number,
-  visit: (item: T) => Promise<R>,
-): Promise<PromiseSettledResult<R>[]> {
-  const results = new Array<PromiseSettledResult<R>>(items.length)
-  let cursor = 0
-  const workers = Array.from({ length: Math.min(Math.max(1, limit), items.length) }, async () => {
-    while (cursor < items.length) {
-      const index = cursor++
-      try {
-        results[index] = { status: "fulfilled", value: await visit(items[index]) }
-      } catch (reason) {
-        results[index] = { status: "rejected", reason }
-      }
-    }
-  })
-  await Promise.all(workers)
-  return results
-}
-
-function ArtifactsPanel(): JSX.Element {
-  const sync = useSync()
-  const sdk = useSDK()
-  const atlas = createAtlasAPI(() => sdk.url)
-  const directory = () => sync.project?.worktree || sync.data.path.directory || sdk.directory
-  const [loadError, setLoadError] = createSignal<Error>()
-  const [partialLoadWarning, setPartialLoadWarning] = createSignal<string>()
-  const [data] = createResource(directory, async (dir) => {
-    try {
-      const pid = (await atlas.resolveProject(dir)).project_id
-      if (!pid) {
-        setLoadError(undefined)
-        setPartialLoadWarning(undefined)
-        return [] as ArtifactRow[]
-      }
-      const tree = await atlas.getGraphTree(pid)
-      const rows: ArtifactRow[] = []
-      const nodes = tree.nodes ?? []
-      const settled = await mapSettledBounded(nodes, 8, async (node) => {
-        const response = await atlas.listArtifacts(node.node_id)
-        return { node, artifacts: Array.isArray(response) ? response : (response.artifacts ?? []) }
-      })
-      const rejected = settled.filter((result) => result.status === "rejected")
-      for (const result of settled) {
-        if (result.status !== "fulfilled") continue
-        for (const artifact of result.value.artifacts) rows.push({ node: result.value.node, artifact })
-      }
-      setLoadError(undefined)
-      setPartialLoadWarning(
-        rejected.length > 0
-          ? `${rejected.length} of ${nodes.length} node artifact requests failed; showing the results that loaded`
-          : undefined,
-      )
-      return rows
-    } catch (error) {
-      setLoadError(error instanceof Error ? error : new Error(String(error)))
-      setPartialLoadWarning(undefined)
-      return [] as ArtifactRow[]
-    }
-  })
-  return (
-    <div class="atlas-scroll" style={{ flex: 1, "min-height": 0, "overflow-y": "auto", padding: "8px 4px" }}>
-      <Show
-        when={(data.latest ?? []).length > 0}
-        fallback={
-          <div style={emptyMsg()}>
-            {loadError()
-              ? `artifacts unavailable · ${loadError()!.message}`
-              : partialLoadWarning()
-                ? `artifacts partially unavailable · ${partialLoadWarning()}`
-                : data.loading
-                  ? "loading artifacts…"
-                  : "no artifacts yet · attach a file to seed one"}
-          </div>
-        }
-      >
-        <Show when={partialLoadWarning()}>
-          {(warning) => (
-            <div role="status" style={{ ...emptyMsg(), padding: "8px 12px", "text-align": "left" }}>
-              artifacts partially unavailable · {warning()}
-            </div>
-          )}
-        </Show>
-        <div style={colHeader()}>
-          <span style={{ width: "60px" }}>Kind</span>
-          <span style={{ flex: 1 }}>Name</span>
-          <span style={{ width: "120px", "text-align": "right" }}>Node</span>
-        </div>
-        <For each={data.latest ?? []}>
-          {(r) => (
-            <div style={{ ...row(false), cursor: "default" }}>
-              <span
-                style={{
-                  width: "60px",
-                  "font-family": FONT_MONO,
-                  "font-size": "10px",
-                  color: "var(--color-text-faint)",
-                  "flex-shrink": 0,
-                }}
-              >
-                {r.artifact.kind ?? "—"}
-              </span>
-              <span
-                style={{
-                  flex: 1,
-                  "min-width": 0,
-                  overflow: "hidden",
-                  "text-overflow": "ellipsis",
-                  "white-space": "nowrap",
-                }}
-              >
-                {r.artifact.name ?? r.artifact.uri ?? "?"}
-              </span>
-              <span style={{ ...cell(), width: "120px", color: "var(--color-text-muted)" }}>
-                {r.node.title?.slice(0, 20) ?? r.node.slug_name ?? "—"}
-              </span>
-            </div>
-          )}
-        </For>
-      </Show>
-    </div>
-  )
-}
-
 // ── styles ─────────────────────────────────────────────────────────
 function machineBtn(): JSX.CSSProperties {
   return {
diff --git a/tooling/sdk/js/src/v2/gen/sdk.gen.ts b/tooling/sdk/js/src/v2/gen/sdk.gen.ts
index d22f41af..b1b1056c 100644
--- a/tooling/sdk/js/src/v2/gen/sdk.gen.ts
+++ b/tooling/sdk/js/src/v2/gen/sdk.gen.ts
@@ -32,10 +32,12 @@ import type {
   ConfigUpdateResponses,
   EventSubscribeResponses,
   ExperimentalResourceListResponses,
+  FileArtifactsResponses,
   FileInspectResponses,
   FileListResponses,
   FilePartInput,
   FilePartSource,
+  FileProvenanceResponses,
   FileRawResponses,
   FileReadResponses,
   FileStatusResponses,
@@ -3376,6 +3378,55 @@ export class File extends HeyApiClient {
     })
   }
 
+  /**
+   * List local research artifacts
+   *
+   * Discover notebooks, datasets, figures, reports, models, and scientific files in the project.
+   */
+  public artifacts<ThrowOnError extends boolean = false>(
+    parameters?: {
+      directory?: string
+    },
+    options?: Options<never, ThrowOnError>,
+  ) {
+    const params = buildClientParams([parameters], [{ args: [{ in: "query", key: "directory" }] }])
+    return (options?.client ?? this.client).get<FileArtifactsResponses, unknown, ThrowOnError>({
+      url: "/file/artifacts",
+      ...options,
+      ...params,
+    })
+  }
+
+  /**
+   * Get local file provenance
+   *
+   * Read Git branch, dirty state, and latest commit metadata for a project file.
+   */
+  public provenance<ThrowOnError extends boolean = false>(
+    parameters: {
+      directory?: string
+      path: string
+    },
+    options?: Options<never, ThrowOnError>,
+  ) {
+    const params = buildClientParams(
+      [parameters],
+      [
+        {
+          args: [
+            { in: "query", key: "directory" },
+            { in: "query", key: "path" },
+          ],
+        },
+      ],
+    )
+    return (options?.client ?? this.client).get<FileProvenanceResponses, unknown, ThrowOnError>({
+      url: "/file/provenance",
+      ...options,
+      ...params,
+    })
+  }
+
   /**
    * Get file status
    *
diff --git a/tooling/sdk/js/src/v2/gen/types.gen.ts b/tooling/sdk/js/src/v2/gen/types.gen.ts
index 9e89d242..3879b8ab 100644
--- a/tooling/sdk/js/src/v2/gen/types.gen.ts
+++ b/tooling/sdk/js/src/v2/gen/types.gen.ts
@@ -5342,6 +5342,73 @@ export type FileRawResponses = {
   200: unknown
 }
 
+export type FileArtifactsData = {
+  body?: never
+  path?: never
+  query?: {
+    directory?: string
+  }
+  url: "/file/artifacts"
+}
+
+export type FileArtifactsResponses = {
+  /**
+   * Research artifacts
+   */
+  200: Array<{
+    name: string
+    path: string
+    kind:
+      | "notebook"
+      | "dataset"
+      | "figure"
+      | "report"
+      | "structure"
+      | "sequence"
+      | "genomics"
+      | "spectrum"
+      | "model"
+      | "archive"
+    format: string
+    size: number
+    modified: number
+  }>
+}
+
+export type FileArtifactsResponse = FileArtifactsResponses[keyof FileArtifactsResponses]
+
+export type FileProvenanceData = {
+  body?: never
+  path?: never
+  query: {
+    directory?: string
+    path: string
+  }
+  url: "/file/provenance"
+}
+
+export type FileProvenanceResponses = {
+  /**
+   * Local provenance
+   */
+  200: {
+    path: string
+    tracked: boolean
+    dirty: boolean
+    status: "clean" | "modified" | "added" | "deleted" | "untracked" | "local"
+    branch?: string
+    commit?: {
+      sha: string
+      author: string
+      email: string
+      date: string
+      message: string
+    }
+  }
+}
+
+export type FileProvenanceResponse = FileProvenanceResponses[keyof FileProvenanceResponses]
+
 export type FileStatusData = {
   body?: never
   path?: never
diff --git a/tooling/sdk/openapi.json b/tooling/sdk/openapi.json
index 5f6d6ee2..1bef936a 100644
--- a/tooling/sdk/openapi.json
+++ b/tooling/sdk/openapi.json
@@ -7418,6 +7418,183 @@
         ]
       }
     },
+    "/file/artifacts": {
+      "get": {
+        "operationId": "file.artifacts",
+        "parameters": [
+          {
+            "in": "query",
+            "name": "directory",
+            "schema": {
+              "type": "string"
+            }
+          }
+        ],
+        "summary": "List local research artifacts",
+        "description": "Discover notebooks, datasets, figures, reports, models, and scientific files in the project.",
+        "responses": {
+          "200": {
+            "description": "Research artifacts",
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "type": "object",
+                    "properties": {
+                      "name": {
+                        "type": "string"
+                      },
+                      "path": {
+                        "type": "string"
+                      },
+                      "kind": {
+                        "type": "string",
+                        "enum": [
+                          "notebook",
+                          "dataset",
+                          "figure",
+                          "report",
+                          "structure",
+                          "sequence",
+                          "genomics",
+                          "spectrum",
+                          "model",
+                          "archive"
+                        ]
+                      },
+                      "format": {
+                        "type": "string"
+                      },
+                      "size": {
+                        "type": "number"
+                      },
+                      "modified": {
+                        "type": "number"
+                      }
+                    },
+                    "required": [
+                      "name",
+                      "path",
+                      "kind",
+                      "format",
+                      "size",
+                      "modified"
+                    ]
+                  }
+                }
+              }
+            }
+          }
+        },
+        "x-codeSamples": [
+          {
+            "lang": "js",
+            "source": "import { createOpenScienceClient } from \"@synsci/sdk\"\n\nconst client = createOpenScienceClient()\nawait client.file.artifacts({\n  ...\n})"
+          }
+        ]
+      }
+    },
+    "/file/provenance": {
+      "get": {
+        "operationId": "file.provenance",
+        "parameters": [
+          {
+            "in": "query",
+            "name": "directory",
+            "schema": {
+              "type": "string"
+            }
+          },
+          {
+            "in": "query",
+            "name": "path",
+            "schema": {
+              "type": "string"
+            },
+            "required": true
+          }
+        ],
+        "summary": "Get local file provenance",
+        "description": "Read Git branch, dirty state, and latest commit metadata for a project file.",
+        "responses": {
+          "200": {
+            "description": "Local provenance",
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "object",
+                  "properties": {
+                    "path": {
+                      "type": "string"
+                    },
+                    "tracked": {
+                      "type": "boolean"
+                    },
+                    "dirty": {
+                      "type": "boolean"
+                    },
+                    "status": {
+                      "type": "string",
+                      "enum": [
+                        "clean",
+                        "modified",
+                        "added",
+                        "deleted",
+                        "untracked",
+                        "local"
+                      ]
+                    },
+                    "branch": {
+                      "type": "string"
+                    },
+                    "commit": {
+                      "type": "object",
+                      "properties": {
+                        "sha": {
+                          "type": "string"
+                        },
+                        "author": {
+                          "type": "string"
+                        },
+                        "email": {
+                          "type": "string"
+                        },
+                        "date": {
+                          "type": "string"
+                        },
+                        "message": {
+                          "type": "string"
+                        }
+                      },
+                      "required": [
+                        "sha",
+                        "author",
+                        "email",
+                        "date",
+                        "message"
+                      ]
+                    }
+                  },
+                  "required": [
+                    "path",
+                    "tracked",
+                    "dirty",
+                    "status"
+                  ]
+                }
+              }
+            }
+          }
+        },
+        "x-codeSamples": [
+          {
+            "lang": "js",
+            "source": "import { createOpenScienceClient } from \"@synsci/sdk\"\n\nconst client = createOpenScienceClient()\nawait client.file.provenance({\n  ...\n})"
+          }
+        ]
+      }
+    },
     "/file/status": {
       "get": {
         "operationId": "file.status",

From f296fb1352076e149f867614f09f53c56913cffc Mon Sep 17 00:00:00 2001
From: Aayam Bansal <aayambansal@gmail.com>
Date: Wed, 29 Jul 2026 06:45:12 +0800
Subject: [PATCH 10/40] feat: add research mission control

---
 frontend/ui/src/styles/theme.css              |  10 +-
 .../workspace/e2e/research-launchpad.spec.ts  |  18 +
 frontend/workspace/src/atlas/store/ui.ts      |   6 +-
 .../workspace/src/components/prompt-input.tsx |  17 +
 .../session/research-launchpad.test.ts        |  36 ++
 .../components/session/research-launchpad.ts  | 111 ++++
 .../components/session/session-new-view.tsx   | 255 +++++++---
 frontend/workspace/src/index.css              |  19 +-
 frontend/workspace/src/styles/atlas.css       | 473 +++++++++++++++++-
 frontend/workspace/src/styles/tokens.ts       |  11 +-
 10 files changed, 864 insertions(+), 92 deletions(-)
 create mode 100644 frontend/workspace/e2e/research-launchpad.spec.ts
 create mode 100644 frontend/workspace/src/components/session/research-launchpad.test.ts
 create mode 100644 frontend/workspace/src/components/session/research-launchpad.ts

diff --git a/frontend/ui/src/styles/theme.css b/frontend/ui/src/styles/theme.css
index d1409c72..4c423e12 100644
--- a/frontend/ui/src/styles/theme.css
+++ b/frontend/ui/src/styles/theme.css
@@ -1,9 +1,9 @@
 :root {
-  /* Computer Modern (Latin Modern Roman) is the single UI typeface across the
-     whole product — sans AND serif resolve to it so nothing in the shared UI
-     drifts to a different family. Keep this in lockstep with FONT_SANS/SERIF in
-     frontend/workspace/src/styles/tokens.ts. NEVER swap the family; only sizes change. */
-  --font-family-sans: "Computer Modern", "Latin Modern Roman", Georgia, "Times New Roman", serif;
+  /* Native application typography for controls and dense working surfaces.
+     Computer Modern remains the editorial serif for papers and long-form
+     scientific output. Keep this in lockstep with workspace style tokens. */
+  --font-family-sans:
+    "Avenir Next", "SF Pro Text", -apple-system, BlinkMacSystemFont, "Segoe UI", Helvetica, Arial, sans-serif;
   --font-family-sans--font-feature-settings: normal;
   --font-family-mono: "IBM Plex Mono", "IBM Plex Mono Fallback";
   --font-family-mono--font-feature-settings: "ss01" 1;
diff --git a/frontend/workspace/e2e/research-launchpad.spec.ts b/frontend/workspace/e2e/research-launchpad.spec.ts
new file mode 100644
index 00000000..ca545988
--- /dev/null
+++ b/frontend/workspace/e2e/research-launchpad.spec.ts
@@ -0,0 +1,18 @@
+import { expect, test } from "./fixtures"
+
+test("turns a scientific workflow into an editable research brief", async ({ page, gotoSession }) => {
+  await gotoSession()
+
+  const launchpad = page.locator('[data-component="research-launchpad"]')
+  await expect(launchpad).toBeVisible()
+  await expect(launchpad.getByRole("heading", { name: "What are we trying to find out?" })).toBeVisible()
+  await expect(launchpad.locator("[data-workflow]")).toHaveCount(8)
+  await expect(launchpad.getByText("Research artifacts", { exact: true })).toBeVisible()
+  await expect(page.locator(".session-right-pane")).toHaveCount(0)
+
+  await launchpad.locator('[data-workflow="analyze-data"]').click()
+
+  const composer = page.locator('[data-component="prompt-input"]')
+  await expect(composer).toBeFocused()
+  await expect(composer).toContainText("Analyze the relevant dataset in this project")
+})
diff --git a/frontend/workspace/src/atlas/store/ui.ts b/frontend/workspace/src/atlas/store/ui.ts
index 49e56443..f9618611 100644
--- a/frontend/workspace/src/atlas/store/ui.ts
+++ b/frontend/workspace/src/atlas/store/ui.ts
@@ -2,7 +2,7 @@ import { createSignal } from "solid-js"
 
 export type RightPaneTab = "canvas" | "terminal"
 
-const PANE_OPEN_KEY = "thesis-rightpane-open-v1"
+const PANE_OPEN_KEY = "openscience-rightpane-open-v2"
 const HIDDEN_TABS_KEY = "thesis-rightpane-hidden-tabs-v1"
 const AGENT_KEY = "thesis-agent-v1"
 
@@ -21,9 +21,9 @@ function readAgent(): string {
 
 function readPaneOpen(): boolean {
   try {
-    return localStorage.getItem(PANE_OPEN_KEY) !== "0"
+    return localStorage.getItem(PANE_OPEN_KEY) === "1"
   } catch {
-    return true
+    return false
   }
 }
 
diff --git a/frontend/workspace/src/components/prompt-input.tsx b/frontend/workspace/src/components/prompt-input.tsx
index eecb7a9b..493aa80d 100644
--- a/frontend/workspace/src/components/prompt-input.tsx
+++ b/frontend/workspace/src/components/prompt-input.tsx
@@ -60,6 +60,7 @@ import { createOpenScienceClient, type Message, type Part } from "@synsci/sdk/v2
 import { Binary } from "@synsci/util/binary"
 import { showToast } from "@synsci/ui/toast"
 import { base64Encode } from "@synsci/util/encode"
+import { uiStore } from "@/atlas/store/ui"
 
 const ACCEPTED_IMAGE_TYPES = ["image/png", "image/jpeg", "image/gif", "image/webp"]
 const ACCEPTED_TEXT_TYPES = ["text/markdown", "text/plain"]
@@ -1655,6 +1656,22 @@ export const PromptInput: Component<PromptInputProps> = (props) => {
     })
   }
 
+  createEffect(() => {
+    const text = uiStore.prefill()
+    if (!text || !editorRef) return
+    const send = uiStore.prefillSend()
+    editorRef.textContent = text
+    prompt.set([{ type: "text", content: text, start: 0, end: text.length }], text.length)
+    uiStore.setPrefill(undefined)
+    uiStore.setPrefillSend(false)
+    requestAnimationFrame(() => {
+      editorRef.focus()
+      setCursorPosition(editorRef, text.length)
+      queueScroll()
+      if (send) void handleSubmit(new Event("submit"))
+    })
+  })
+
   return (
     <div class="relative size-full flex flex-col gap-3">
       <Show when={store.popover}>
diff --git a/frontend/workspace/src/components/session/research-launchpad.test.ts b/frontend/workspace/src/components/session/research-launchpad.test.ts
new file mode 100644
index 00000000..797fe434
--- /dev/null
+++ b/frontend/workspace/src/components/session/research-launchpad.test.ts
@@ -0,0 +1,36 @@
+import { describe, expect, test } from "bun:test"
+import { researchWorkflows, workflowGroups, workflowPrompt } from "./research-launchpad"
+
+describe("research launchpad", () => {
+  test("ships launch-ready workflows across the core scientific loop", () => {
+    expect(researchWorkflows.map((workflow) => workflow.id)).toEqual([
+      "analyze-data",
+      "run-notebook",
+      "inspect-structure",
+      "sequence-qc",
+      "survey-literature",
+      "reproduce-result",
+      "compare-runs",
+      "write-report",
+    ])
+    expect(new Set(researchWorkflows.map((workflow) => workflow.group))).toEqual(
+      new Set(["analyze", "compute", "discover", "communicate"]),
+    )
+  })
+
+  test("groups workflows without losing their authored order", () => {
+    expect(workflowGroups().map((group) => group.id)).toEqual(["analyze", "compute", "discover", "communicate"])
+    expect(
+      workflowGroups()
+        .find((group) => group.id === "analyze")
+        ?.workflows.map((workflow) => workflow.id),
+    ).toEqual(["analyze-data", "inspect-structure", "sequence-qc"])
+  })
+
+  test("adds project context to workflow prompts when artifacts are available", () => {
+    const workflow = researchWorkflows[0]
+    expect(workflowPrompt(workflow, 0)).toBe(workflow.prompt)
+    expect(workflowPrompt(workflow, 12)).toContain("12 research artifacts")
+    expect(workflowPrompt(workflow, 12)).toContain(workflow.prompt)
+  })
+})
diff --git a/frontend/workspace/src/components/session/research-launchpad.ts b/frontend/workspace/src/components/session/research-launchpad.ts
new file mode 100644
index 00000000..5ec8390a
--- /dev/null
+++ b/frontend/workspace/src/components/session/research-launchpad.ts
@@ -0,0 +1,111 @@
+export type ResearchWorkflow = {
+  id: string
+  group: "analyze" | "compute" | "discover" | "communicate"
+  title: string
+  description: string
+  prompt: string
+  shortcut: string
+  icon: "table" | "notebook" | "atom" | "sequence" | "search" | "reproduce" | "compare" | "report"
+}
+
+export const researchWorkflows: ResearchWorkflow[] = [
+  {
+    id: "analyze-data",
+    group: "analyze",
+    title: "Analyze a dataset",
+    description: "Profile columns, find quality issues, visualize patterns, and produce a defensible result.",
+    prompt:
+      "Analyze the relevant dataset in this project. Inspect its schema and quality first, then compute useful summaries and visualizations. Explain every assumption and save any reusable analysis as a notebook.",
+    shortcut: "CSV · TSV · JSONL · HDF5",
+    icon: "table",
+  },
+  {
+    id: "run-notebook",
+    group: "compute",
+    title: "Run a notebook",
+    description: "Open an existing notebook or build one with live Python or R outputs.",
+    prompt:
+      "Find the most relevant notebook in this project, inspect it before running anything, then execute or repair it cell by cell. Preserve outputs and summarize the result and environment.",
+    shortcut: "Jupyter · Python · R",
+    icon: "notebook",
+  },
+  {
+    id: "inspect-structure",
+    group: "analyze",
+    title: "Inspect a structure",
+    description: "Render proteins or molecules, check chemistry, and investigate structural features.",
+    prompt:
+      "Inspect the relevant molecular or protein structure in this project. Render it, identify important chains, ligands, residues, or conformers, and explain any structural quality issues before drawing conclusions.",
+    shortcut: "PDB · CIF · SDF · MOL",
+    icon: "atom",
+  },
+  {
+    id: "sequence-qc",
+    group: "analyze",
+    title: "Quality-check sequences",
+    description: "Review reads, variants, intervals, alignments, and per-cycle quality.",
+    prompt:
+      "Quality-check the relevant sequencing or genomics files in this project. Report read and base counts, quality and GC patterns, sample or contig coverage, and any concrete anomalies worth investigating.",
+    shortcut: "FASTQ · VCF · BAM · GFF",
+    icon: "sequence",
+  },
+  {
+    id: "survey-literature",
+    group: "discover",
+    title: "Survey the literature",
+    description: "Turn a research question into a sourced map of claims, methods, and open gaps.",
+    prompt:
+      "Build a focused literature survey for my research question. Separate established evidence from inference, compare methods and datasets, capture citations, and finish with the highest-value unanswered questions.",
+    shortcut: "papers · citations · claims",
+    icon: "search",
+  },
+  {
+    id: "reproduce-result",
+    group: "discover",
+    title: "Reproduce a result",
+    description: "Trace a claim to code and data, define a criterion, run checks, and record evidence.",
+    prompt:
+      "Reproduce the target result in this project. Identify the exact claim, code, data, configuration, and success criterion before running it. Record failures as evidence and finish with a supported, weakened, rejected, or not-tested verdict.",
+    shortcut: "claim · code · evidence",
+    icon: "reproduce",
+  },
+  {
+    id: "compare-runs",
+    group: "compute",
+    title: "Compare experiments",
+    description: "Normalize metrics, surface confounders, and choose a winner without hiding failures.",
+    prompt:
+      "Compare the experiment runs in this project. Normalize their configurations and metrics, flag confounders and failed runs, visualize the decision-relevant differences, and recommend the next experiment.",
+    shortcut: "metrics · configs · failures",
+    icon: "compare",
+  },
+  {
+    id: "write-report",
+    group: "communicate",
+    title: "Write a research report",
+    description: "Synthesize project evidence into a clear report with figures, caveats, and citations.",
+    prompt:
+      "Draft a research report from the evidence in this project. Use a concise abstract, methods, results, limitations, and next steps. Cite source files and claims precisely, and reuse existing figures where they support the text.",
+    shortcut: "Markdown · LaTeX · PDF",
+    icon: "report",
+  },
+]
+
+const groups: Array<{ id: ResearchWorkflow["group"]; title: string }> = [
+  { id: "analyze", title: "Analyze" },
+  { id: "compute", title: "Compute" },
+  { id: "discover", title: "Discover" },
+  { id: "communicate", title: "Communicate" },
+]
+
+export function workflowGroups() {
+  return groups.map((group) => ({
+    ...group,
+    workflows: researchWorkflows.filter((workflow) => workflow.group === group.id),
+  }))
+}
+
+export function workflowPrompt(workflow: ResearchWorkflow, artifacts: number) {
+  if (artifacts <= 0) return workflow.prompt
+  return `Your workspace contains ${artifacts.toLocaleString("en-US")} research artifacts. ${workflow.prompt}`
+}
diff --git a/frontend/workspace/src/components/session/session-new-view.tsx b/frontend/workspace/src/components/session/session-new-view.tsx
index 530c3722..e63ff160 100644
--- a/frontend/workspace/src/components/session/session-new-view.tsx
+++ b/frontend/workspace/src/components/session/session-new-view.tsx
@@ -1,10 +1,27 @@
-import { Show, createMemo } from "solid-js"
+import { For, Show, createMemo, createResource, type JSX } from "solid-js"
 import { DateTime } from "luxon"
 import { useSync } from "@/context/sync"
-import { useLanguage } from "@/context/language"
 import { useModels } from "@/context/models"
-import { Icon } from "@synsci/ui/icon"
+import { useSDK } from "@/context/sdk"
+import { useDialog } from "@synsci/ui/context/dialog"
 import { getDirectory, getFilename } from "@synsci/util/path"
+import { DialogSettings } from "@/components/dialog-settings"
+import { centerTabs } from "@/atlas/store/centerTabs"
+import { uiStore } from "@/atlas/store/ui"
+import {
+  IconActivity,
+  IconArrowRight,
+  IconAtom,
+  IconBraces,
+  IconCheckCircle,
+  IconFile,
+  IconFolder,
+  IconLayoutGrid,
+  IconNetwork,
+  IconRefresh,
+  IconSearch,
+} from "@/atlas/shared/Icon"
+import { researchWorkflows, workflowPrompt, type ResearchWorkflow } from "@/components/session/research-launchpad"
 
 const MAIN_WORKTREE = "main"
 const CREATE_WORKTREE = "create"
@@ -14,82 +31,194 @@ interface NewSessionViewProps {
   onWorktreeChange: (value: string) => void
 }
 
+const icons: Record<ResearchWorkflow["icon"], (props: { size?: number; strokeWidth?: number }) => JSX.Element> = {
+  table: IconLayoutGrid,
+  notebook: IconBraces,
+  atom: IconAtom,
+  sequence: IconActivity,
+  search: IconSearch,
+  reproduce: IconRefresh,
+  compare: IconNetwork,
+  report: IconFile,
+}
+
 export function NewSessionView(props: NewSessionViewProps) {
   const sync = useSync()
-  const language = useLanguage()
   const models = useModels()
-  // No connected provider ⇒ no models ⇒ nothing to send. On BYOK this most
-  // often means no key is set (or the only synced credential was the managed
-  // wallet, which byok deliberately drops). Tell the user plainly instead of
-  // leaving them at a dead composer.
+  const sdk = useSDK()
+  const dialog = useDialog()
   const noModel = createMemo(() => models.list().length === 0)
-
   const sandboxes = createMemo(() => sync.project?.sandboxes ?? [])
   const options = createMemo(() => [MAIN_WORKTREE, ...sandboxes(), CREATE_WORKTREE])
-  const current = createMemo(() => {
-    const selection = props.worktree
-    if (options().includes(selection)) return selection
-    return MAIN_WORKTREE
-  })
+  const current = createMemo(() => (options().includes(props.worktree) ? props.worktree : MAIN_WORKTREE))
   const projectRoot = createMemo(() => sync.project?.worktree ?? sync.data.path.directory)
-  const isWorktree = createMemo(() => {
-    const project = sync.project
-    if (!project) return false
-    return sync.data.path.directory !== project.worktree
-  })
-
-  const label = (value: string) => {
-    if (value === MAIN_WORKTREE) {
-      if (isWorktree()) return language.t("session.new.worktree.main")
-      const branch = sync.data.vcs?.branch
-      if (branch) return language.t("session.new.worktree.mainWithBranch", { branch })
-      return language.t("session.new.worktree.main")
+  const projectName = createMemo(() => getFilename(projectRoot()) || "research project")
+  const branch = createMemo(() => sync.data.vcs?.branch || "working tree")
+  const [artifacts] = createResource(
+    () => sdk.directory,
+    () =>
+      sdk.client.file
+        .artifacts()
+        .then((response) => response.data ?? [])
+        .catch(() => []),
+  )
+  const local = createMemo(() => {
+    try {
+      const host = new URL(sdk.url).hostname
+      return host === "localhost" || host === "127.0.0.1" || host === "::1" || host === "[::1]"
+    } catch {
+      return false
     }
+  })
 
-    if (value === CREATE_WORKTREE) return language.t("session.new.worktree.create")
-
+  const worktreeLabel = (value: string) => {
+    if (value === MAIN_WORKTREE) return branch()
+    if (value === CREATE_WORKTREE) return "new isolated worktree"
     return getFilename(value)
   }
 
+  const start = (workflow: ResearchWorkflow) => {
+    uiStore.setPrefill(workflowPrompt(workflow, artifacts.latest?.length ?? 0))
+    centerTabs.showChat()
+  }
+
   return (
-    <div class="size-full flex flex-col justify-end items-start gap-4 flex-[1_0_0] self-stretch max-w-200 mx-auto px-6 pb-[calc(var(--prompt-height,11.25rem)+64px)]">
-      <div class="text-20-medium text-text-weaker">{language.t("command.session.new")}</div>
-      <Show when={noModel()}>
-        <div class="flex flex-col gap-1.5 rounded-lg border border-border-base bg-surface-raised-base px-4 py-3 self-stretch max-w-full">
-          <div class="text-13-medium text-text-strong">No model connected</div>
-          <div class="text-12-regular text-text-weak leading-relaxed">
-            You don't have a provider key set. Bring your own with{" "}
-            <code class="text-text-base">openscience keys signin</code> (OpenAI · Anthropic · Gemini, or ChatGPT / Codex
-            — no API key needed), or use managed credits with <code class="text-text-base">openscience login</code>.
+    <main class="atlas-scroll research-launchpad" data-component="research-launchpad">
+      <div class="research-launchpad__inner">
+        <section class="research-launchpad__intro" aria-labelledby="research-launchpad-title">
+          <div>
+            <div class="research-launchpad__eyebrow">Research workspace</div>
+            <h1 id="research-launchpad-title">What are we trying to find out?</h1>
+            <p>
+              Start with a concrete workflow or describe the result you need. OpenScience can inspect project files, run
+              code, edit notebooks, and keep the evidence next to the work.
+            </p>
           </div>
-        </div>
-      </Show>
-      <div class="flex justify-center items-center gap-3">
-        <Icon name="folder" size="small" />
-        <div class="text-12-medium text-text-weak select-text">
-          {getDirectory(projectRoot())}
-          <span class="text-text-strong">{getFilename(projectRoot())}</span>
-        </div>
-      </div>
-      <div class="flex justify-center items-center gap-1">
-        <Icon name="branch" size="small" />
-        <div class="text-12-medium text-text-weak select-text ml-2">{label(current())}</div>
-      </div>
-      <Show when={sync.project}>
-        {(project) => (
-          <div class="flex justify-center items-center gap-3">
-            <Icon name="pencil-line" size="small" />
-            <div class="text-12-medium text-text-weak">
-              {language.t("session.new.lastModified")}&nbsp;
-              <span class="text-text-strong">
-                {DateTime.fromMillis(project().time.updated ?? project().time.created)
-                  .setLocale(language.locale())
-                  .toRelative()}
+          <div class="research-launchpad__project" title={projectRoot()}>
+            <IconFolder size={15} strokeWidth={1.45} />
+            <div>
+              <strong>{projectName()}</strong>
+              <span>
+                {getDirectory(projectRoot())}
+                {projectName()}
               </span>
             </div>
           </div>
-        )}
-      </Show>
-    </div>
+        </section>
+
+        <section class="research-launchpad__status" aria-label="Workspace readiness">
+          <button
+            type="button"
+            class="research-launchpad__status-item"
+            data-state={noModel() ? "attention" : "ready"}
+            onClick={() => {
+              if (noModel()) dialog.show(() => <DialogSettings />)
+            }}
+          >
+            <span class="research-launchpad__status-dot" />
+            <span>
+              <strong>{noModel() ? "Connect a model" : `${models.list().length} models ready`}</strong>
+              <small>{noModel() ? "required before the first run" : "choose one in the composer"}</small>
+            </span>
+          </button>
+          <div class="research-launchpad__status-item" data-state="ready">
+            <span class="research-launchpad__status-dot" />
+            <span>
+              <strong>{local() ? "Local compute ready" : "Remote compute connected"}</strong>
+              <small>{local() ? "terminal and notebook kernels available" : sdk.url}</small>
+            </span>
+          </div>
+          <button type="button" class="research-launchpad__status-item" onClick={() => centerTabs.setActive("files")}>
+            <span class="research-launchpad__status-count">
+              <Show when={!artifacts.loading} fallback="··">
+                {(artifacts.latest?.length ?? 0).toLocaleString()}
+              </Show>
+            </span>
+            <span>
+              <strong>Research artifacts</strong>
+              <small>
+                {artifacts.error ? "scan unavailable · open Files" : "notebooks, data, figures, and models"}
+              </small>
+            </span>
+          </button>
+        </section>
+
+        <Show when={noModel()}>
+          <section class="research-launchpad__notice" role="status">
+            <div>
+              <strong>No model is connected yet</strong>
+              <span>
+                Add OpenAI, Anthropic, Gemini, OpenRouter, or a local model. Your project files stay on the selected
+                compute host.
+              </span>
+            </div>
+            <button type="button" onClick={() => dialog.show(() => <DialogSettings />)}>
+              open model settings
+              <IconArrowRight size={12} strokeWidth={1.7} />
+            </button>
+          </section>
+        </Show>
+
+        <section class="research-launchpad__workflows" aria-labelledby="research-workflows-title">
+          <div class="research-launchpad__section-heading">
+            <div>
+              <h2 id="research-workflows-title">Start from a workflow</h2>
+              <p>Each one writes a detailed, editable brief into the composer.</p>
+            </div>
+            <label class="research-launchpad__worktree">
+              <span>Run on</span>
+              <select value={current()} onChange={(event) => props.onWorktreeChange(event.currentTarget.value)}>
+                <For each={options()}>{(option) => <option value={option}>{worktreeLabel(option)}</option>}</For>
+              </select>
+            </label>
+          </div>
+
+          <div class="research-launchpad__grid">
+            <For each={researchWorkflows}>
+              {(workflow, index) => {
+                const Icon = icons[workflow.icon]
+                return (
+                  <button
+                    type="button"
+                    class="research-launchpad__workflow"
+                    data-workflow={workflow.id}
+                    data-featured={index() === 0 ? "true" : "false"}
+                    onClick={() => start(workflow)}
+                  >
+                    <span class="research-launchpad__workflow-icon">
+                      <Icon size={16} strokeWidth={1.45} />
+                    </span>
+                    <span class="research-launchpad__workflow-copy">
+                      <strong>{workflow.title}</strong>
+                      <span>{workflow.description}</span>
+                      <small>{workflow.shortcut}</small>
+                    </span>
+                    <IconArrowRight class="research-launchpad__workflow-arrow" size={13} strokeWidth={1.7} />
+                  </button>
+                )
+              }}
+            </For>
+          </div>
+        </section>
+
+        <footer class="research-launchpad__footer">
+          <span>
+            <IconCheckCircle size={13} strokeWidth={1.5} />
+            {branch()}
+          </span>
+          <Show when={sync.project}>
+            {(project) => (
+              <span>
+                updated{" "}
+                {DateTime.fromMillis(project().time.updated ?? project().time.created)
+                  .setLocale("en")
+                  .toRelative()}
+              </span>
+            )}
+          </Show>
+          <span>or describe your goal below</span>
+        </footer>
+      </div>
+    </main>
   )
 }
diff --git a/frontend/workspace/src/index.css b/frontend/workspace/src/index.css
index a6835b32..418d000a 100644
--- a/frontend/workspace/src/index.css
+++ b/frontend/workspace/src/index.css
@@ -2,25 +2,21 @@
 @import "./styles/atlas.css";
 
 /*
-  OpenScience editorial typography.
+  OpenScience typography.
 
-  A research-workbench voice: Computer Modern (Latin Modern Roman) is the single
-  UI typeface — headings and body both resolve to it via --font-family-serif /
-  --font-family-sans; JetBrains Mono is reserved for code. Kept in @layer base
-  with bare-element selectors so any component class or inline style still wins —
-  this only sets the resting default.
+  The application shell uses the native sans stack for compact, high-legibility
+  controls. Computer Modern remains available as the editorial serif for papers,
+  reports, and long-form rendered research.
 */
 @layer base {
-  /* Computer Modern ships 400 + 700 only — declare the weights that actually
-     render (intermediate weights would silently map onto these anyway). */
   h1,
   h2,
   h3,
   h4,
   h5,
   h6 {
-    font-family: var(--font-family-serif);
-    font-feature-settings: var(--font-family-serif--font-feature-settings, normal);
+    font-family: var(--font-family-sans);
+    font-feature-settings: var(--font-family-sans--font-feature-settings, normal);
     font-optical-sizing: auto;
     font-weight: 400;
     letter-spacing: -0.011em;
@@ -40,7 +36,7 @@
   notes, markdown). Airy measure and calm rhythm, paper-like.
 */
 .prose-editorial {
-  font-family: var(--font-family-sans);
+  font-family: var(--font-family-serif);
   font-size: var(--font-size-large, 15px);
   line-height: 1.7;
   color: var(--text-base, var(--color-text));
@@ -50,6 +46,7 @@
 .prose-editorial h1,
 .prose-editorial h2,
 .prose-editorial h3 {
+  font-family: var(--font-family-serif);
   margin-top: 1.6em;
   margin-bottom: 0.5em;
 }
diff --git a/frontend/workspace/src/styles/atlas.css b/frontend/workspace/src/styles/atlas.css
index 53b15b11..d4bb50e2 100644
--- a/frontend/workspace/src/styles/atlas.css
+++ b/frontend/workspace/src/styles/atlas.css
@@ -92,15 +92,18 @@
   --text-xl: 16px;
   --text-2xl: 20px;
 
-  --font-sans: "Computer Modern", "Latin Modern Roman", Georgia, "Times New Roman", serif;
+  --font-sans:
+    "Avenir Next", "SF Pro Text", -apple-system, BlinkMacSystemFont, "Segoe UI", Helvetica, Arial, sans-serif;
   --font-serif: "Computer Modern", "Latin Modern Roman", Georgia, "Times New Roman", serif;
   /* Code font: single source. --font-family-mono is owned by @synsci/ui theme.css
      and written at runtime by the Settings mono-font picker (self-hosted Nerd
      Font families) — everything code-shaped routes through it. */
   --font-code: var(--font-family-mono);
-  --font-ui-sans: "Computer Modern", "Latin Modern Roman", Georgia, "Times New Roman", serif;
-  /* Bridge @synsci/ui (SessionTurn chat transcript) typography to Computer Modern */
-  --font-family-sans: "Computer Modern", "Latin Modern Roman", Georgia, serif;
+  --font-ui-sans:
+    "Avenir Next", "SF Pro Text", -apple-system, BlinkMacSystemFont, "Segoe UI", Helvetica, Arial, sans-serif;
+  /* Bridge @synsci/ui and the workspace shell to the same native app stack. */
+  --font-family-sans:
+    "Avenir Next", "SF Pro Text", -apple-system, BlinkMacSystemFont, "Segoe UI", Helvetica, Arial, sans-serif;
 
   --z-header: 20;
   --z-sticky: 50;
@@ -1147,6 +1150,468 @@ html[data-color-scheme="dark"] .atlas-overlay {
   border-right: 1px solid;
 }
 
+/* ==========================================================
+   Research launchpad
+
+   The empty chat state is a working surface: it reports readiness, exposes
+   real local artifacts, and turns repeatable scientific workflows into
+   editable briefs in the composer.
+   ========================================================== */
+.research-launchpad {
+  flex: 1;
+  min-height: 0;
+  overflow-y: auto;
+  padding: clamp(34px, 6vh, 74px) clamp(22px, 5vw, 64px) calc(var(--prompt-height, 11.25rem) + 96px);
+  background:
+    radial-gradient(circle at 8% 6%, color-mix(in srgb, var(--color-text) 3.5%, transparent), transparent 25rem),
+    var(--color-bg);
+}
+
+.research-launchpad__inner {
+  width: min(100%, 940px);
+  margin: 0 auto;
+  display: grid;
+  gap: 28px;
+}
+
+.research-launchpad__intro {
+  display: grid;
+  grid-template-columns: minmax(0, 1fr) auto;
+  align-items: end;
+  gap: 36px;
+}
+
+.research-launchpad__eyebrow {
+  margin-bottom: 9px;
+  font-family: var(--font-family-mono);
+  font-size: 10px;
+  letter-spacing: 0.1em;
+  text-transform: uppercase;
+  color: var(--color-text-faint);
+}
+
+.research-launchpad__intro h1 {
+  margin: 0;
+  max-width: 700px;
+  font-family: var(--font-family-sans);
+  font-size: clamp(30px, 4vw, 46px);
+  font-weight: 500;
+  letter-spacing: -0.045em;
+  line-height: 1.02;
+  text-wrap: balance;
+}
+
+.research-launchpad__intro p {
+  max-width: 660px;
+  margin: 14px 0 0;
+  font-family: var(--font-family-sans);
+  font-size: 14px;
+  line-height: 1.55;
+  color: var(--color-text-muted);
+  text-wrap: pretty;
+}
+
+.research-launchpad__project {
+  max-width: 240px;
+  display: flex;
+  align-items: center;
+  gap: 10px;
+  padding-bottom: 4px;
+  color: var(--color-text-faint);
+}
+
+.research-launchpad__project > div {
+  min-width: 0;
+  display: grid;
+  gap: 2px;
+}
+
+.research-launchpad__project strong,
+.research-launchpad__project span {
+  overflow: hidden;
+  text-overflow: ellipsis;
+  white-space: nowrap;
+}
+
+.research-launchpad__project strong {
+  font-family: var(--font-family-sans);
+  font-size: 12px;
+  font-weight: 550;
+  color: var(--color-text);
+}
+
+.research-launchpad__project span {
+  font-family: var(--font-family-mono);
+  font-size: 9px;
+  color: var(--color-text-faint);
+}
+
+.research-launchpad__status {
+  display: grid;
+  grid-template-columns: repeat(3, minmax(0, 1fr));
+  border-top: 1px solid var(--color-border);
+  border-bottom: 1px solid var(--color-border);
+}
+
+.research-launchpad__status-item {
+  all: unset;
+  box-sizing: border-box;
+  min-width: 0;
+  display: flex;
+  align-items: center;
+  gap: 10px;
+  padding: 13px 15px;
+  color: var(--color-text-faint);
+}
+
+button.research-launchpad__status-item {
+  cursor: pointer;
+  transition:
+    background 160ms ease,
+    color 160ms ease;
+}
+
+button.research-launchpad__status-item:hover {
+  background: var(--color-accent-subtle);
+  color: var(--color-text);
+}
+
+.research-launchpad__status-item + .research-launchpad__status-item {
+  border-left: 1px solid var(--color-border);
+}
+
+.research-launchpad__status-dot {
+  width: 7px;
+  height: 7px;
+  flex: 0 0 auto;
+  border-radius: 50%;
+  background: var(--color-success);
+  box-shadow: 0 0 0 3px color-mix(in srgb, var(--color-success) 12%, transparent);
+}
+
+.research-launchpad__status-item[data-state="attention"] .research-launchpad__status-dot {
+  background: var(--color-warning);
+  box-shadow: 0 0 0 3px color-mix(in srgb, var(--color-warning) 13%, transparent);
+}
+
+.research-launchpad__status-count {
+  min-width: 25px;
+  font-family: var(--font-family-mono);
+  font-size: 15px;
+  font-variant-numeric: tabular-nums;
+  color: var(--color-text);
+}
+
+.research-launchpad__status-item > span:last-child {
+  min-width: 0;
+  display: grid;
+  gap: 2px;
+}
+
+.research-launchpad__status-item strong {
+  overflow: hidden;
+  font-family: var(--font-family-sans);
+  font-size: 11px;
+  font-weight: 550;
+  color: var(--color-text);
+  text-overflow: ellipsis;
+  white-space: nowrap;
+}
+
+.research-launchpad__status-item small {
+  overflow: hidden;
+  font-family: var(--font-family-sans);
+  font-size: 10px;
+  color: var(--color-text-faint);
+  text-overflow: ellipsis;
+  white-space: nowrap;
+}
+
+.research-launchpad__notice {
+  display: flex;
+  align-items: center;
+  gap: 20px;
+  padding: 14px 16px;
+  border: 1px solid color-mix(in srgb, var(--color-warning) 35%, var(--color-border));
+  border-radius: 8px;
+  background: color-mix(in srgb, var(--color-warning-muted) 55%, transparent);
+}
+
+.research-launchpad__notice > div {
+  min-width: 0;
+  flex: 1;
+  display: grid;
+  gap: 3px;
+}
+
+.research-launchpad__notice strong {
+  font-family: var(--font-family-sans);
+  font-size: 12px;
+  font-weight: 600;
+}
+
+.research-launchpad__notice span {
+  font-family: var(--font-family-sans);
+  font-size: 11px;
+  line-height: 1.45;
+  color: var(--color-text-muted);
+}
+
+.research-launchpad__notice button {
+  all: unset;
+  box-sizing: border-box;
+  flex: 0 0 auto;
+  display: inline-flex;
+  align-items: center;
+  gap: 7px;
+  padding: 7px 10px;
+  border: 1px solid var(--color-border-strong);
+  border-radius: 5px;
+  background: var(--color-surface-solid);
+  font-family: var(--font-family-sans);
+  font-size: 11px;
+  font-weight: 550;
+  color: var(--color-text);
+  cursor: pointer;
+  transition:
+    transform 150ms ease,
+    background 150ms ease;
+}
+
+.research-launchpad__notice button:hover {
+  background: var(--color-bg-elevated);
+}
+
+.research-launchpad__notice button:active {
+  transform: translateY(1px);
+}
+
+.research-launchpad__workflows {
+  display: grid;
+  gap: 14px;
+}
+
+.research-launchpad__section-heading {
+  display: flex;
+  align-items: end;
+  justify-content: space-between;
+  gap: 18px;
+}
+
+.research-launchpad__section-heading h2 {
+  margin: 0;
+  font-family: var(--font-family-sans);
+  font-size: 15px;
+  font-weight: 600;
+  letter-spacing: -0.015em;
+}
+
+.research-launchpad__section-heading p {
+  margin: 3px 0 0;
+  font-family: var(--font-family-sans);
+  font-size: 11px;
+  color: var(--color-text-faint);
+}
+
+.research-launchpad__worktree {
+  flex: 0 0 auto;
+  display: flex;
+  align-items: center;
+  gap: 8px;
+  font-family: var(--font-family-sans);
+  font-size: 10px;
+  color: var(--color-text-faint);
+}
+
+.research-launchpad__worktree select {
+  max-width: 210px;
+  padding: 6px 26px 6px 9px;
+  border: 1px solid var(--color-border);
+  border-radius: 5px;
+  background: var(--color-surface-solid);
+  font-family: var(--font-family-mono);
+  font-size: 10px;
+  color: var(--color-text);
+}
+
+.research-launchpad__grid {
+  display: grid;
+  grid-template-columns: repeat(2, minmax(0, 1fr));
+  gap: 8px;
+}
+
+.research-launchpad__workflow {
+  all: unset;
+  box-sizing: border-box;
+  position: relative;
+  min-width: 0;
+  display: grid;
+  grid-template-columns: auto minmax(0, 1fr) auto;
+  align-items: start;
+  gap: 12px;
+  padding: 15px;
+  border: 1px solid var(--color-border);
+  border-radius: 8px;
+  background: color-mix(in srgb, var(--color-surface-solid) 74%, transparent);
+  cursor: pointer;
+  transition:
+    transform 180ms cubic-bezier(0.16, 1, 0.3, 1),
+    border-color 180ms ease,
+    background 180ms ease,
+    box-shadow 180ms ease;
+}
+
+.research-launchpad__workflow[data-featured="true"] {
+  grid-column: 1 / -1;
+  padding: 18px;
+  background:
+    radial-gradient(circle at 90% 15%, color-mix(in srgb, var(--color-text) 5%, transparent), transparent 16rem),
+    color-mix(in srgb, var(--color-surface-solid) 88%, transparent);
+}
+
+.research-launchpad__workflow:hover {
+  transform: translateY(-2px);
+  border-color: var(--color-border-strong);
+  background: var(--color-surface-solid);
+  box-shadow: 0 12px 28px color-mix(in srgb, var(--color-text) 7%, transparent);
+}
+
+.research-launchpad__workflow:active {
+  transform: translateY(0);
+}
+
+.research-launchpad__workflow-icon {
+  width: 31px;
+  height: 31px;
+  display: inline-grid;
+  place-items: center;
+  border: 1px solid var(--color-border);
+  border-radius: 7px;
+  background: var(--color-bg);
+  color: var(--color-text-muted);
+}
+
+.research-launchpad__workflow-copy {
+  min-width: 0;
+  display: grid;
+  gap: 5px;
+}
+
+.research-launchpad__workflow-copy strong {
+  font-family: var(--font-family-sans);
+  font-size: 12px;
+  font-weight: 600;
+  color: var(--color-text);
+}
+
+.research-launchpad__workflow-copy > span {
+  max-width: 58ch;
+  font-family: var(--font-family-sans);
+  font-size: 11px;
+  line-height: 1.45;
+  color: var(--color-text-muted);
+  text-wrap: pretty;
+}
+
+.research-launchpad__workflow-copy small {
+  margin-top: 2px;
+  font-family: var(--font-family-mono);
+  font-size: 9px;
+  letter-spacing: 0.025em;
+  color: var(--color-text-faint);
+}
+
+.research-launchpad__workflow-arrow {
+  margin-top: 7px;
+  color: var(--color-text-faint);
+  transition:
+    color 160ms ease,
+    transform 160ms ease;
+}
+
+.research-launchpad__workflow:hover .research-launchpad__workflow-arrow {
+  transform: translateX(2px);
+  color: var(--color-text);
+}
+
+.research-launchpad__footer {
+  display: flex;
+  align-items: center;
+  gap: 14px;
+  padding-top: 2px;
+  font-family: var(--font-family-mono);
+  font-size: 9px;
+  color: var(--color-text-faint);
+}
+
+.research-launchpad__footer span {
+  display: inline-flex;
+  align-items: center;
+  gap: 5px;
+}
+
+.research-launchpad__footer span:last-child {
+  margin-left: auto;
+}
+
+@media (max-width: 820px) {
+  .research-launchpad__intro {
+    grid-template-columns: 1fr;
+    gap: 16px;
+  }
+
+  .research-launchpad__project {
+    max-width: 100%;
+  }
+
+  .research-launchpad__status {
+    grid-template-columns: 1fr;
+  }
+
+  .research-launchpad__status-item + .research-launchpad__status-item {
+    border-left: 0;
+    border-top: 1px solid var(--color-border);
+  }
+}
+
+@media (max-width: 640px) {
+  .research-launchpad {
+    padding: 28px 16px calc(var(--prompt-height, 11.25rem) + 78px);
+  }
+
+  .research-launchpad__intro h1 {
+    font-size: 31px;
+  }
+
+  .research-launchpad__notice,
+  .research-launchpad__section-heading {
+    align-items: stretch;
+    flex-direction: column;
+  }
+
+  .research-launchpad__worktree {
+    justify-content: space-between;
+  }
+
+  .research-launchpad__grid {
+    grid-template-columns: 1fr;
+  }
+
+  .research-launchpad__workflow[data-featured="true"] {
+    grid-column: auto;
+  }
+
+  .research-launchpad__footer {
+    align-items: flex-start;
+    flex-direction: column;
+    gap: 6px;
+  }
+
+  .research-launchpad__footer span:last-child {
+    margin-left: 0;
+  }
+}
+
 /* ==========================================================
    Compact workspace shell
 
diff --git a/frontend/workspace/src/styles/tokens.ts b/frontend/workspace/src/styles/tokens.ts
index ae427328..76abff55 100644
--- a/frontend/workspace/src/styles/tokens.ts
+++ b/frontend/workspace/src/styles/tokens.ts
@@ -1,15 +1,14 @@
 import type { JSX } from "solid-js"
 
-export const FONT_SANS = "'Computer Modern', 'Latin Modern Roman', Georgia, 'Times New Roman', serif"
-export const FONT_SERIF = FONT_SANS
+export const FONT_SANS =
+  "'Avenir Next', 'SF Pro Text', -apple-system, BlinkMacSystemFont, 'Segoe UI', Helvetica, Arial, sans-serif"
+export const FONT_SERIF = "'Computer Modern', 'Latin Modern Roman', Georgia, 'Times New Roman', serif"
 /** Code font — resolves through the theme/Settings-owned mono variable so the
  *  user's mono-font choice applies everywhere code renders. */
 export const FONT_CODE = "var(--font-family-mono, ui-monospace, monospace)"
-/** HISTORICAL TRAP: "mono" here is the one product typeface (Computer Modern,
- *  a serif) — NOT a monospace face. Use FONT_CODE for anything code-shaped. */
+/** Historical alias: this is UI text, not a monospace face. Use FONT_CODE for code. */
 export const FONT_MONO = FONT_SANS
-/** Alias kept for call sites that reference a "UI sans" token. Resolves to the
- *  one product typeface (Computer Modern) so nothing can drift to a second family. */
+/** Alias kept for call sites that reference the UI sans token. */
 export const FONT_UI_SANS = FONT_SANS
 
 /** Control radius in px — keep in lockstep with --radius in atlas.css. */

From aa9b31424b77ae5e03ac885201b7b1177afd2632 Mon Sep 17 00:00:00 2001
From: Aayam Bansal <aayambansal@gmail.com>
Date: Wed, 29 Jul 2026 07:01:36 +0800
Subject: [PATCH 11/40] feat: add managed compute jobs

---
 backend/cli/src/compute/jobs.ts               |  500 ++++++++
 .../cli/src/server/routes/settings/compute.ts |  124 +-
 backend/cli/test/compute/jobs.test.ts         |  109 ++
 .../cli/test/server/settings-compute.test.ts  |   45 +
 frontend/workspace/e2e/compute-jobs.spec.ts   |   18 +
 frontend/workspace/src/atlas/ComputeJobs.tsx  |  662 +++++++++++
 frontend/workspace/src/atlas/RightPane.tsx    |    6 +
 frontend/workspace/src/atlas/store/ui.ts      |    2 +-
 .../src/components/settings/Compute.tsx       |  101 +-
 tooling/sdk/js/src/v2/gen/sdk.gen.ts          |  152 +++
 tooling/sdk/js/src/v2/gen/types.gen.ts        |  263 ++++-
 tooling/sdk/openapi.json                      | 1040 ++++++++++++++---
 12 files changed, 2855 insertions(+), 167 deletions(-)
 create mode 100644 backend/cli/src/compute/jobs.ts
 create mode 100644 backend/cli/test/compute/jobs.test.ts
 create mode 100644 frontend/workspace/e2e/compute-jobs.spec.ts
 create mode 100644 frontend/workspace/src/atlas/ComputeJobs.tsx

diff --git a/backend/cli/src/compute/jobs.ts b/backend/cli/src/compute/jobs.ts
new file mode 100644
index 00000000..4362a73a
--- /dev/null
+++ b/backend/cli/src/compute/jobs.ts
@@ -0,0 +1,500 @@
+import { spawn, type ChildProcess } from "node:child_process"
+import crypto from "node:crypto"
+import fs from "node:fs/promises"
+import path from "node:path"
+import z from "zod"
+import { Global } from "../global"
+import { OpenScience } from "../openscience"
+import { Shell } from "../shell/shell"
+
+export namespace ComputeJobs {
+  export const Scheduler = z.enum(["none", "slurm", "pbs"])
+  export type Scheduler = z.infer<typeof Scheduler>
+
+  export const Host = z.object({
+    id: z.string(),
+    label: z.string(),
+    host: z.string(),
+    user: z.string().optional(),
+    port: z.number().int().positive().optional(),
+    scheduler: Scheduler.default("none"),
+    workdir: z.string().optional(),
+  })
+  export type Host = z.infer<typeof Host>
+
+  export const Probe = z.object({
+    ok: z.boolean(),
+    host: z.string(),
+    latency_ms: z.number().nonnegative(),
+    hostname: z.string().optional(),
+    python: z.boolean(),
+    gpu: z.boolean(),
+    slurm: z.boolean(),
+    pbs: z.boolean(),
+    error: z.string().optional(),
+  })
+  export type Probe = z.infer<typeof Probe>
+
+  export const Target = z.discriminatedUnion("kind", [
+    z.object({ kind: z.literal("local") }),
+    z.object({ kind: z.literal("ssh"), host_id: z.string() }),
+  ])
+  export type Target = z.infer<typeof Target>
+
+  export const Input = z.object({
+    name: z.string().trim().min(1).max(120),
+    command: z.string().trim().min(1).max(100_000),
+    cwd: z.string().optional(),
+    target: Target,
+  })
+  export type Input = z.infer<typeof Input>
+
+  export const Status = z.enum(["queued", "running", "succeeded", "failed", "cancelled", "interrupted"])
+  export type Status = z.infer<typeof Status>
+
+  export const Job = z.object({
+    id: z.string(),
+    name: z.string(),
+    command: z.string(),
+    cwd: z.string().optional(),
+    target: Target,
+    target_label: z.string(),
+    scheduler: Scheduler,
+    status: Status,
+    created_at: z.string(),
+    started_at: z.string().optional(),
+    completed_at: z.string().optional(),
+    exit_code: z.number().int().nullable().optional(),
+    pid: z.number().int().positive().optional(),
+    error: z.string().optional(),
+  })
+  export type Job = z.infer<typeof Job>
+
+  type Options = {
+    root?: string
+    hosts?: Host[]
+  }
+
+  type Runtime = {
+    process: ChildProcess
+    detached: boolean
+    host?: Host
+  }
+
+  const active = new Map<string, Runtime>()
+  const locks = new Map<string, Promise<void>>()
+  const terminal = new Set<Status>(["succeeded", "failed", "cancelled", "interrupted"])
+
+  const rootOf = (root?: string) => root ?? path.join(Global.Path.data, "compute")
+  const metaOf = (root: string) => path.join(root, "jobs.json")
+  const logsOf = (root: string) => path.join(root, "jobs")
+  const exitOf = (root: string, id: string) => path.join(logsOf(root), `${id}.exit`)
+  const keyOf = (root: string, id: string) => `${root}\0${id}`
+
+  async function read(root: string): Promise<Job[]> {
+    const value = await Bun.file(metaOf(root))
+      .json()
+      .catch(() => [])
+    const result = Job.array().safeParse(value)
+    return result.success ? result.data : []
+  }
+
+  async function write(root: string, jobs: Job[]): Promise<void> {
+    await fs.mkdir(root, { recursive: true })
+    await Bun.write(metaOf(root), JSON.stringify(jobs, null, 2), { mode: 0o600 })
+  }
+
+  async function change<T>(root: string, edit: (jobs: Job[]) => T | Promise<T>): Promise<T> {
+    const prior = locks.get(root) ?? Promise.resolve()
+    const task = prior
+      .catch(() => undefined)
+      .then(async () => {
+        const jobs = await read(root)
+        const result = await edit(jobs)
+        await write(root, jobs)
+        return result
+      })
+    locks.set(
+      root,
+      task.then(
+        () => undefined,
+        () => undefined,
+      ),
+    )
+    return task
+  }
+
+  async function patch(root: string, id: string, value: Partial<Job>): Promise<Job> {
+    return change(root, (jobs) => {
+      const index = jobs.findIndex((job) => job.id === id)
+      if (index < 0) throw new Error(`Compute job ${id} was not found`)
+      const next = Job.parse({ ...jobs[index], ...value })
+      jobs[index] = next
+      return next
+    })
+  }
+
+  function alive(pid: number): boolean {
+    try {
+      process.kill(pid, 0)
+      return true
+    } catch {
+      return false
+    }
+  }
+
+  async function sync(root: string): Promise<void> {
+    const jobs = await read(root)
+    const updates = (
+      await Promise.all(
+        jobs.map(async (job): Promise<{ id: string; value: Partial<Job> } | undefined> => {
+          if (terminal.has(job.status) || active.has(keyOf(root, job.id))) return
+          if (job.status === "queued" && Date.now() - Date.parse(job.created_at) < 5_000) return
+          const marker = await Bun.file(exitOf(root, job.id))
+            .text()
+            .catch(() => undefined)
+          const exit = marker?.trim().match(/^-?\d+$/) ? Number(marker.trim()) : undefined
+          if (job.target.kind === "local" && exit !== undefined) {
+            return {
+              id: job.id,
+              value: {
+                status: exit === 0 ? "succeeded" : "failed",
+                completed_at: new Date().toISOString(),
+                exit_code: exit,
+                pid: undefined,
+              },
+            }
+          }
+          if (job.target.kind === "local" && job.pid && alive(job.pid)) return
+          return {
+            id: job.id,
+            value: {
+              status: "interrupted",
+              completed_at: new Date().toISOString(),
+              exit_code: null,
+              pid: undefined,
+              error:
+                job.target.kind === "ssh"
+                  ? "The app connection ended before this remote job reported a result. Check the remote scheduler before rerunning it."
+                  : "The job process ended before it could report a result.",
+            },
+          }
+        }),
+      )
+    ).filter((item): item is { id: string; value: Partial<Job> } => !!item)
+    if (!updates.length) return
+    await change(root, (current) => {
+      for (const update of updates) {
+        const index = current.findIndex((job) => job.id === update.id)
+        if (index < 0 || terminal.has(current[index]!.status) || active.has(keyOf(root, update.id))) continue
+        current[index] = Job.parse({ ...current[index], ...update.value })
+      }
+    })
+  }
+
+  export function quote(value: string): string {
+    return `'${value.replaceAll("'", `'\"'\"'`)}'`
+  }
+
+  function name(value: string): string {
+    const clean = value
+      .toLowerCase()
+      .replace(/[^a-z0-9_-]+/g, "-")
+      .replace(/^-+|-+$/g, "")
+      .slice(0, 42)
+    return clean || "job"
+  }
+
+  function remote(input: { id: string; name: string; command: string; cwd?: string }, host: Host): string {
+    const cwd = input.cwd || host.workdir || "."
+    const job = `os-${input.id}`
+    const folder = `.openscience/jobs`
+    const log = `${folder}/${input.id}.log`
+    const enter = `cd ${quote(cwd)} && mkdir -p ${quote(folder)}`
+    if (host.scheduler === "slurm") {
+      return [
+        enter,
+        `sbatch --wait --parsable --job-name=${quote(job)} --output=${quote(log)} --error=${quote(log)} --wrap=${quote(input.command)}`,
+        "code=$?",
+        `test -f ${quote(log)} && cat ${quote(log)}`,
+        "exit $code",
+      ].join("; ")
+    }
+    if (host.scheduler === "pbs") {
+      const script = `#!/usr/bin/env bash\nset -o pipefail\n${input.command}\n`
+      return [
+        enter,
+        `printf %s ${quote(script)} | qsub -W block=true -N ${quote(name(job))} -j oe -o ${quote(log)}`,
+        "code=$?",
+        `test -f ${quote(log)} && cat ${quote(log)}`,
+        "exit $code",
+      ].join("; ")
+    }
+    return `${enter} && exec bash -lc ${quote(input.command)}`
+  }
+
+  function ssh(host: Host, script: string): string[] {
+    const destination = host.user ? `${host.user}@${host.host}` : host.host
+    if (destination.startsWith("-")) throw new Error("SSH destinations cannot begin with a hyphen")
+    const port = host.port ? ["-p", String(host.port)] : []
+    return ["ssh", "-o", "BatchMode=yes", "-o", "ConnectTimeout=8", ...port, "--", destination, script]
+  }
+
+  export function command(
+    input: { id: string; name: string; command: string; cwd?: string },
+    host?: Host,
+  ): { argv: string[]; scheduler: Scheduler; label: string } {
+    if (!host) {
+      return {
+        argv: [Shell.acceptable(), "-lc", input.command],
+        scheduler: "none",
+        label: "This computer",
+      }
+    }
+    return {
+      argv: ssh(host, remote(input, host)),
+      scheduler: host.scheduler,
+      label: host.label,
+    }
+  }
+
+  export async function probe(host: Host): Promise<Probe> {
+    const parsed = Host.parse(host)
+    const started = performance.now()
+    const script = [
+      "printf 'connected=1\\n'",
+      "printf 'hostname='; hostname 2>/dev/null || true",
+      "command -v python3 >/dev/null 2>&1 && printf 'python=1\\n' || true",
+      "command -v nvidia-smi >/dev/null 2>&1 && printf 'gpu=1\\n' || true",
+      "command -v sbatch >/dev/null 2>&1 && printf 'slurm=1\\n' || true",
+      "command -v qsub >/dev/null 2>&1 && printf 'pbs=1\\n' || true",
+    ].join("; ")
+    const argv = ssh(parsed, script)
+    const proc = spawn(argv[0]!, argv.slice(1), {
+      env: await OpenScience.subprocessEnv(process.env),
+      windowsHide: true,
+      stdio: ["ignore", "pipe", "pipe"],
+    })
+    const output: Buffer[] = []
+    const errors: Buffer[] = []
+    proc.stdout?.on("data", (chunk: Buffer) => output.push(chunk))
+    proc.stderr?.on("data", (chunk: Buffer) => errors.push(chunk))
+    const done = new Promise<{ code: number | null; error?: string }>((resolve) => {
+      proc.once("error", (error) => resolve({ code: null, error: error.message }))
+      proc.once("exit", (code) => resolve({ code }))
+    })
+    const result = await Promise.race([
+      done,
+      Bun.sleep(12_000).then(() => ({ code: null, error: "Connection timed out" })),
+    ])
+    if (proc.exitCode === null) {
+      await Shell.killTree(proc, {
+        detached: false,
+        exited: () => proc.exitCode !== null,
+      })
+    }
+    const text = Buffer.concat(output).toString("utf8")
+    const error = result.error || (result.code === 0 ? undefined : Buffer.concat(errors).toString("utf8").trim())
+    return Probe.parse({
+      ok: result.code === 0 && text.includes("connected=1"),
+      host: parsed.label,
+      latency_ms: Math.round(performance.now() - started),
+      hostname: text.match(/^hostname=(.+)$/m)?.[1]?.trim(),
+      python: text.includes("python=1"),
+      gpu: text.includes("gpu=1"),
+      slurm: text.includes("slurm=1"),
+      pbs: text.includes("pbs=1"),
+      error: error || undefined,
+    })
+  }
+
+  async function execute(job: Job, host: Host | undefined, root: string): Promise<void> {
+    await fs.mkdir(logsOf(root), { recursive: true })
+    await fs.rm(exitOf(root, job.id), { force: true })
+    const wrapped = host
+      ? job.command
+      : `(${job.command}\n); code=$?; printf %s "$code" > ${quote(exitOf(root, job.id))}; exit "$code"`
+    const spec = command({ ...job, command: wrapped }, host)
+    const log = path.join(logsOf(root), `${job.id}.log`)
+    const output = await fs.open(log, "a", 0o600)
+    const env = await OpenScience.subprocessEnv(process.env)
+    const queued = await get(job.id, { root })
+    if (queued?.status === "cancelled") {
+      await output.close()
+      return
+    }
+    const detached = process.platform !== "win32"
+    const proc = spawn(spec.argv[0]!, spec.argv.slice(1), {
+      cwd: host ? undefined : job.cwd,
+      env,
+      detached,
+      windowsHide: true,
+      stdio: ["ignore", output.fd, output.fd],
+    })
+    await output.close()
+    const current = await get(job.id, { root })
+    if (current?.status === "cancelled") {
+      await Shell.killTree(proc, {
+        detached,
+        exited: () => proc.exitCode !== null,
+      })
+      return
+    }
+    active.set(keyOf(root, job.id), { process: proc, detached, host })
+    await patch(root, job.id, {
+      status: "running",
+      started_at: new Date().toISOString(),
+      pid: proc.pid,
+    })
+    const result = await new Promise<{ code: number | null; error?: string }>((resolve) => {
+      proc.once("error", (error) => resolve({ code: null, error: error.message }))
+      proc.once("exit", (code) => resolve({ code }))
+    })
+    active.delete(keyOf(root, job.id))
+    const final = (await list({ root })).find((item) => item.id === job.id)
+    if (final?.status === "cancelled") return
+    await patch(root, job.id, {
+      status: result.code === 0 ? "succeeded" : "failed",
+      completed_at: new Date().toISOString(),
+      exit_code: result.code,
+      error: result.error,
+    })
+  }
+
+  export async function start(input: Input, options: Options = {}): Promise<Job> {
+    const parsed = Input.parse(input)
+    const root = rootOf(options.root)
+    const hostId = parsed.target.kind === "ssh" ? parsed.target.host_id : undefined
+    const host = hostId ? options.hosts?.find((item) => item.id === hostId) : undefined
+    if (parsed.target.kind === "ssh" && !host) throw new Error("The selected SSH compute profile was not found")
+    const id = crypto.randomUUID().slice(0, 12)
+    const spec = command({ id, ...parsed }, host)
+    const job = Job.parse({
+      id,
+      name: parsed.name,
+      command: parsed.command,
+      cwd: parsed.cwd || host?.workdir,
+      target: parsed.target,
+      target_label: spec.label,
+      scheduler: spec.scheduler,
+      status: "queued",
+      created_at: new Date().toISOString(),
+    })
+    await change(root, (jobs) => {
+      jobs.push(job)
+    })
+    void execute(job, host, root).catch(async (error) => {
+      await fs.mkdir(logsOf(root), { recursive: true })
+      await fs
+        .appendFile(
+          path.join(logsOf(root), `${job.id}.log`),
+          `${error instanceof Error ? error.message : String(error)}\n`,
+        )
+        .catch(() => {})
+      await patch(root, job.id, {
+        status: "failed",
+        completed_at: new Date().toISOString(),
+        exit_code: null,
+        error: error instanceof Error ? error.message : String(error),
+      }).catch(() => {})
+    })
+    return job
+  }
+
+  export async function list(options: Options = {}): Promise<Job[]> {
+    const root = rootOf(options.root)
+    await sync(root)
+    return (await read(root)).toSorted(
+      (a, b) => Date.parse(b.created_at) - Date.parse(a.created_at) || b.id.localeCompare(a.id),
+    )
+  }
+
+  export async function get(id: string, options: Options = {}): Promise<Job | undefined> {
+    return (await read(rootOf(options.root))).find((job) => job.id === id)
+  }
+
+  export async function log(id: string, options: Options & { bytes?: number } = {}): Promise<string> {
+    const job = await get(id, options)
+    if (!job) throw new Error(`Compute job ${id} was not found`)
+    const text = await Bun.file(path.join(logsOf(rootOf(options.root)), `${job.id}.log`))
+      .text()
+      .catch(() => "")
+    return text.slice(-Math.max(1, options.bytes ?? 256_000))
+  }
+
+  export async function cancel(id: string, options: Options = {}): Promise<Job> {
+    const root = rootOf(options.root)
+    const job = await get(id, { root })
+    if (!job) throw new Error(`Compute job ${id} was not found`)
+    if (terminal.has(job.status)) return job
+    const cancelled = await patch(root, id, {
+      status: "cancelled",
+      completed_at: new Date().toISOString(),
+      exit_code: null,
+    })
+    const runtime = active.get(keyOf(root, id))
+    if (runtime) {
+      await Shell.killTree(runtime.process, {
+        detached: runtime.detached,
+        exited: () => runtime.process.exitCode !== null,
+      })
+      active.delete(keyOf(root, id))
+    } else if (job.pid) {
+      try {
+        if (process.platform === "win32") process.kill(job.pid, "SIGTERM")
+        else process.kill(-job.pid, "SIGTERM")
+      } catch {}
+    }
+    const hostId = job.target.kind === "ssh" ? job.target.host_id : undefined
+    const host = hostId ? options.hosts?.find((item) => item.id === hostId) : undefined
+    if (host && host.scheduler !== "none") {
+      const action =
+        host.scheduler === "slurm"
+          ? `scancel --name ${quote(`os-${job.id}`)}`
+          : `qselect -N ${quote(name(`os-${job.id}`))} | xargs -r qdel`
+      const spec = command(
+        { id: job.id, name: job.name, command: action, cwd: host.workdir },
+        { ...host, scheduler: "none" },
+      )
+      const proc = spawn(spec.argv[0]!, spec.argv.slice(1), {
+        env: await OpenScience.subprocessEnv(process.env),
+        windowsHide: true,
+        stdio: "ignore",
+      })
+      await new Promise<void>((resolve) => {
+        proc.once("error", () => resolve())
+        proc.once("exit", () => resolve())
+      })
+    }
+    return cancelled
+  }
+
+  export async function clear(options: Options = {}): Promise<number> {
+    const root = rootOf(options.root)
+    const removed = await change(root, (jobs) => {
+      const done = jobs.filter((job) => terminal.has(job.status)).map((job) => job.id)
+      const keep = jobs.filter((job) => !terminal.has(job.status))
+      jobs.splice(0, jobs.length, ...keep)
+      return done
+    })
+    await Promise.all(
+      removed.flatMap((id) => [
+        fs.rm(path.join(logsOf(root), `${id}.log`), { force: true }),
+        fs.rm(exitOf(root, id), { force: true }),
+      ]),
+    )
+    return removed.length
+  }
+
+  export async function wait(id: string, options: Options & { timeout?: number } = {}): Promise<Job> {
+    const started = Date.now()
+    const timeout = options.timeout ?? 30_000
+    for (;;) {
+      const job = (await list(options)).find((item) => item.id === id)
+      if (!job) throw new Error(`Compute job ${id} was not found`)
+      if (terminal.has(job.status)) return job
+      if (Date.now() - started >= timeout) throw new Error(`Timed out waiting for compute job ${id}`)
+      await Bun.sleep(25)
+    }
+  }
+}
diff --git a/backend/cli/src/server/routes/settings/compute.ts b/backend/cli/src/server/routes/settings/compute.ts
index 4269586d..ef5482bb 100644
--- a/backend/cli/src/server/routes/settings/compute.ts
+++ b/backend/cli/src/server/routes/settings/compute.ts
@@ -9,6 +9,7 @@ import { Env } from "../../../env"
 import { OpenScience } from "../../../openscience"
 import { errors } from "../../error"
 import { lazy } from "../../../util/lazy"
+import { ComputeJobs } from "../../../compute/jobs"
 
 // ── Compute settings store ──────────────────────────────────────────────────
 //
@@ -96,13 +97,7 @@ export namespace ComputeSettings {
   ]
 
   // ── Schemas ──
-  export const SshHost = z.object({
-    id: z.string(),
-    label: z.string(),
-    host: z.string(),
-    user: z.string().optional(),
-    port: z.number().int().positive().optional(),
-  })
+  export const SshHost = ComputeJobs.Host
   export type SshHost = z.infer<typeof SshHost>
 
   export const Endpoint = z.object({
@@ -301,6 +296,10 @@ export namespace ComputeSettings {
     return view(stored)
   }
 
+  export async function findSshHost(target: string): Promise<SshHost | undefined> {
+    return (await read()).ssh_hosts.find((host) => host.id === target)
+  }
+
   export async function addEndpoint(input: Omit<Endpoint, "id">): Promise<Info> {
     const stored = await read()
     stored.endpoints.push({ id: id(), ...input })
@@ -385,10 +384,32 @@ export const ComputeSettingsRoutes = lazy(() =>
           host: z.string().min(1),
           user: z.string().optional(),
           port: z.number().int().positive().optional(),
+          scheduler: ComputeJobs.Scheduler.default("none"),
+          workdir: z.string().optional(),
         }),
       ),
       async (c) => c.json(await ComputeSettings.addSshHost(c.req.valid("json"))),
     )
+    .post(
+      "/ssh/:id/test",
+      describeRoute({
+        summary: "Test an SSH compute host",
+        operationId: "settings.compute.ssh.test",
+        responses: {
+          200: {
+            description: "Connection result",
+            content: { "application/json": { schema: resolver(ComputeJobs.Probe) } },
+          },
+          ...errors(404),
+        },
+      }),
+      validator("param", z.object({ id: z.string() })),
+      async (c) => {
+        const host = await ComputeSettings.findSshHost(c.req.valid("param").id)
+        if (!host) return c.json({ error: "SSH host not found" }, 404)
+        return c.json(await ComputeJobs.probe(host))
+      },
+    )
     .delete(
       "/ssh/:id",
       describeRoute({
@@ -432,5 +453,94 @@ export const ComputeSettingsRoutes = lazy(() =>
       }),
       validator("param", z.object({ id: z.string() })),
       async (c) => c.json(await ComputeSettings.removeEndpoint(c.req.valid("param").id)),
+    )
+    .get(
+      "/jobs",
+      describeRoute({
+        summary: "List local and remote compute jobs",
+        operationId: "settings.compute.jobs.list",
+        responses: {
+          200: {
+            description: "Compute jobs",
+            content: { "application/json": { schema: resolver(ComputeJobs.Job.array()) } },
+          },
+        },
+      }),
+      async (c) => c.json(await ComputeJobs.list()),
+    )
+    .post(
+      "/jobs",
+      describeRoute({
+        summary: "Start a local, SSH, Slurm, or PBS compute job",
+        operationId: "settings.compute.jobs.start",
+        responses: {
+          200: { description: "Started job", content: { "application/json": { schema: resolver(ComputeJobs.Job) } } },
+          ...errors(400),
+        },
+      }),
+      validator("json", ComputeJobs.Input),
+      async (c) => {
+        const settings = await ComputeSettings.get()
+        const input = c.req.valid("json")
+        const hostId = input.target.kind === "ssh" ? input.target.host_id : undefined
+        if (hostId && !settings.ssh_hosts.some((host) => host.id === hostId)) {
+          return c.json({ error: "The selected SSH compute profile was not found" }, 400)
+        }
+        return c.json(await ComputeJobs.start(input, { hosts: settings.ssh_hosts }))
+      },
+    )
+    .delete(
+      "/jobs/completed",
+      describeRoute({
+        summary: "Clear completed compute jobs",
+        operationId: "settings.compute.jobs.clear",
+        responses: {
+          200: {
+            description: "Number cleared",
+            content: {
+              "application/json": { schema: resolver(z.object({ cleared: z.number().int().nonnegative() })) },
+            },
+          },
+        },
+      }),
+      async (c) => c.json({ cleared: await ComputeJobs.clear() }),
+    )
+    .get(
+      "/jobs/:id/log",
+      describeRoute({
+        summary: "Read a compute job log",
+        operationId: "settings.compute.jobs.log",
+        responses: {
+          200: {
+            description: "Job output",
+            content: { "application/json": { schema: resolver(z.object({ log: z.string() })) } },
+          },
+          ...errors(404),
+        },
+      }),
+      validator("param", z.object({ id: z.string() })),
+      async (c) => {
+        const job = await ComputeJobs.get(c.req.valid("param").id)
+        if (!job) return c.json({ error: "Compute job not found" }, 404)
+        return c.json({ log: await ComputeJobs.log(job.id) })
+      },
+    )
+    .post(
+      "/jobs/:id/cancel",
+      describeRoute({
+        summary: "Cancel a compute job",
+        operationId: "settings.compute.jobs.cancel",
+        responses: {
+          200: { description: "Cancelled job", content: { "application/json": { schema: resolver(ComputeJobs.Job) } } },
+          ...errors(404),
+        },
+      }),
+      validator("param", z.object({ id: z.string() })),
+      async (c) => {
+        const settings = await ComputeSettings.get()
+        const job = await ComputeJobs.get(c.req.valid("param").id)
+        if (!job) return c.json({ error: "Compute job not found" }, 404)
+        return c.json(await ComputeJobs.cancel(job.id, { hosts: settings.ssh_hosts }))
+      },
     ),
 )
diff --git a/backend/cli/test/compute/jobs.test.ts b/backend/cli/test/compute/jobs.test.ts
new file mode 100644
index 00000000..682c9d48
--- /dev/null
+++ b/backend/cli/test/compute/jobs.test.ts
@@ -0,0 +1,109 @@
+import { describe, expect, test } from "bun:test"
+import fs from "node:fs/promises"
+import path from "node:path"
+import { ComputeJobs } from "../../src/compute/jobs"
+import { tmpdir } from "../fixture/fixture"
+
+describe("ComputeJobs command adapters", () => {
+  const host = {
+    id: "cluster",
+    label: "Lab cluster",
+    host: "hpc.example.org",
+    user: "researcher",
+    port: 2222,
+    scheduler: "slurm" as const,
+    workdir: "/scratch/team project",
+  }
+
+  test("builds a non-interactive SSH command for a Slurm job", () => {
+    const command = ComputeJobs.command(
+      {
+        id: "job-123",
+        name: "RNA benchmark",
+        command: "python train.py --label 'A B'",
+        cwd: "/scratch/team project",
+      },
+      host,
+    )
+
+    expect(command.argv.slice(0, 7)).toEqual(["ssh", "-o", "BatchMode=yes", "-o", "ConnectTimeout=8", "-p", "2222"])
+    expect(command.argv).toContain("researcher@hpc.example.org")
+    expect(command.argv.at(-1)).toContain("sbatch --wait --parsable")
+    expect(command.argv.at(-1)).toContain("os-job-123")
+    expect(command.argv.at(-1)).toContain("python train.py")
+  })
+
+  test("builds PBS and direct SSH adapters from the same profile", () => {
+    const input = { id: "job-9", name: "Variant call", command: "bash pipeline.sh", cwd: "/work" }
+    expect(ComputeJobs.command(input, { ...host, scheduler: "pbs" }).argv.at(-1)).toContain("qsub")
+    expect(ComputeJobs.command(input, { ...host, scheduler: "none" }).argv.at(-1)).toContain("exec")
+  })
+})
+
+describe("ComputeJobs local lifecycle", () => {
+  test("runs a real local job, persists status, and streams its log", async () => {
+    await using tmp = await tmpdir()
+    const root = path.join(tmp.path, "state")
+    const job = await ComputeJobs.start(
+      {
+        name: "deterministic smoke",
+        command: "printf 'alpha\\nbeta\\n'",
+        cwd: tmp.path,
+        target: { kind: "local" },
+      },
+      { root },
+    )
+
+    const finished = await ComputeJobs.wait(job.id, { root, timeout: 5_000 })
+    expect(finished.status).toBe("succeeded")
+    expect(finished.exit_code).toBe(0)
+    expect(await ComputeJobs.log(job.id, { root })).toContain("alpha\nbeta")
+  })
+
+  test("cancels a running local process tree", async () => {
+    await using tmp = await tmpdir()
+    const root = path.join(tmp.path, "state")
+    const job = await ComputeJobs.start(
+      {
+        name: "cancel smoke",
+        command: "sleep 30",
+        cwd: tmp.path,
+        target: { kind: "local" },
+      },
+      { root },
+    )
+
+    await ComputeJobs.cancel(job.id, { root })
+    const cancelled = await ComputeJobs.wait(job.id, { root, timeout: 5_000 })
+    expect(cancelled.status).toBe("cancelled")
+  })
+
+  test("recovers a completed detached job from its durable exit marker", async () => {
+    const root = await fs.mkdtemp(path.join(import.meta.dir, "jobs-recovery-"))
+    const id = "recovered-job"
+    await fs.mkdir(path.join(root, "jobs"), { recursive: true })
+    await Bun.write(
+      path.join(root, "jobs.json"),
+      JSON.stringify([
+        {
+          id,
+          name: "recovered",
+          command: "true",
+          target: { kind: "local" },
+          target_label: "This computer",
+          scheduler: "none",
+          status: "running",
+          created_at: new Date(Date.now() - 10_000).toISOString(),
+          started_at: new Date(Date.now() - 9_000).toISOString(),
+          pid: 999_999,
+        },
+      ]),
+    )
+    await Bun.write(path.join(root, "jobs", `${id}.exit`), "0")
+
+    const job = (await ComputeJobs.list({ root })).find((item) => item.id === id)
+    expect(job?.status).toBe("succeeded")
+    expect(job?.exit_code).toBe(0)
+    await fs.rm(root, { recursive: true, force: true })
+  })
+})
diff --git a/backend/cli/test/server/settings-compute.test.ts b/backend/cli/test/server/settings-compute.test.ts
index 40de845a..a5be11de 100644
--- a/backend/cli/test/server/settings-compute.test.ts
+++ b/backend/cli/test/server/settings-compute.test.ts
@@ -78,3 +78,48 @@ test("re-saving a key updates the injected value in place", async () => {
   await ComputeSettingsRoutes().request("/provider/runpod", { method: "DELETE" })
   expect(process.env["RUNPOD_API_KEY"]).toBeUndefined()
 })
+
+test("compute job routes execute a real local command and expose its log", async () => {
+  const started = await ComputeSettingsRoutes().request("/jobs", {
+    method: "POST",
+    headers: { "content-type": "application/json" },
+    body: JSON.stringify({
+      name: "route smoke test",
+      command: "printf 'compute-route-ok\\n'",
+      target: { kind: "local" },
+    }),
+  })
+  expect(started.status).toBe(200)
+  const first = (await started.json()) as { id: string }
+  const final = await (async () => {
+    for (const _ of Array.from({ length: 100 })) {
+      const response = await ComputeSettingsRoutes().request("/jobs")
+      const jobs = (await response.json()) as { id: string; status: string }[]
+      const job = jobs.find((item) => item.id === first.id)
+      if (job && ["succeeded", "failed", "cancelled"].includes(job.status)) return job
+      await Bun.sleep(20)
+    }
+    throw new Error("Timed out waiting for route compute job")
+  })()
+  expect(final.status).toBe("succeeded")
+
+  const output = await ComputeSettingsRoutes().request(`/jobs/${first.id}/log`)
+  expect(output.status).toBe(200)
+  expect(await output.json()).toEqual({ log: "compute-route-ok\n" })
+
+  const cleared = await ComputeSettingsRoutes().request("/jobs/completed", { method: "DELETE" })
+  expect(cleared.status).toBe(200)
+})
+
+test("compute job routes reject an SSH target that is not configured", async () => {
+  const response = await ComputeSettingsRoutes().request("/jobs", {
+    method: "POST",
+    headers: { "content-type": "application/json" },
+    body: JSON.stringify({
+      name: "missing host",
+      command: "true",
+      target: { kind: "ssh", host_id: "does-not-exist" },
+    }),
+  })
+  expect(response.status).toBe(400)
+})
diff --git a/frontend/workspace/e2e/compute-jobs.spec.ts b/frontend/workspace/e2e/compute-jobs.spec.ts
new file mode 100644
index 00000000..0c6db0e7
--- /dev/null
+++ b/frontend/workspace/e2e/compute-jobs.spec.ts
@@ -0,0 +1,18 @@
+import { expect, test } from "./fixtures"
+
+test("runs a local compute job and follows its output from the right pane", async ({ page, gotoSession }) => {
+  await gotoSession()
+
+  await page.getByTitle("jobs").click()
+  const pane = page.locator(".session-right-pane")
+  await expect(pane.getByText("compute jobs", { exact: true })).toBeVisible()
+
+  await pane.getByTitle("new job").click()
+  await pane.getByLabel("Job name").fill("Playwright compute smoke")
+  await pane.getByLabel("Command").fill("printf 'ui-compute-ok\\n'")
+  await pane.getByRole("button", { name: "run job" }).click()
+
+  await expect(pane.getByText("Playwright compute smoke", { exact: true }).first()).toBeVisible()
+  await expect(pane.locator("pre")).toContainText("ui-compute-ok")
+  await expect(pane.getByText(/This computer · succeeded/)).toBeVisible()
+})
diff --git a/frontend/workspace/src/atlas/ComputeJobs.tsx b/frontend/workspace/src/atlas/ComputeJobs.tsx
new file mode 100644
index 00000000..df5c7d61
--- /dev/null
+++ b/frontend/workspace/src/atlas/ComputeJobs.tsx
@@ -0,0 +1,662 @@
+import { For, Show, createEffect, createMemo, createResource, createSignal, onCleanup, type JSX } from "solid-js"
+import { Dynamic } from "solid-js/web"
+import { useGlobalSDK } from "@/context/global-sdk"
+import { usePlatform } from "@/context/platform"
+import { settingsApi } from "@/components/settings/api"
+import { FONT_MONO, FONT_SANS } from "@/styles/tokens"
+import { toast } from "@/atlas/Toast"
+import {
+  IconActivity,
+  IconAlertCircle,
+  IconCheckCircle,
+  IconClock,
+  IconCpu,
+  IconPlus,
+  IconRefresh,
+  IconStop,
+  IconTrash,
+} from "@/atlas/shared/Icon"
+
+type Status = "queued" | "running" | "succeeded" | "failed" | "cancelled" | "interrupted"
+type Target = { kind: "local" } | { kind: "ssh"; host_id: string }
+
+interface Host {
+  id: string
+  label: string
+  host: string
+  scheduler: "none" | "slurm" | "pbs"
+  workdir?: string
+}
+
+interface Settings {
+  ssh_hosts: Host[]
+}
+
+interface Job {
+  id: string
+  name: string
+  command: string
+  cwd?: string
+  target: Target
+  target_label: string
+  scheduler: "none" | "slurm" | "pbs"
+  status: Status
+  created_at: string
+  started_at?: string
+  completed_at?: string
+  exit_code?: number | null
+  error?: string
+}
+
+const terminal = new Set<Status>(["succeeded", "failed", "cancelled", "interrupted"])
+
+export function ComputeJobs(): JSX.Element {
+  const sdk = useGlobalSDK()
+  const platform = usePlatform()
+  const fetchFn = platform.fetch ?? fetch
+  const call = <T,>(path: string, init?: RequestInit) =>
+    settingsApi<T>(sdk.url, fetchFn, `/settings/compute${path}`, init)
+
+  const [jobs, jobsApi] = createResource(() => call<Job[]>("/jobs"))
+  const [settings] = createResource(() => call<Settings>(""))
+  const [selected, setSelected] = createSignal<string>()
+  const [creating, setCreating] = createSignal(false)
+  const [busy, setBusy] = createSignal(false)
+  const [name, setName] = createSignal("")
+  const [command, setCommand] = createSignal("")
+  const [cwd, setCwd] = createSignal("")
+  const [target, setTarget] = createSignal("local")
+  const current = createMemo(() => jobs()?.find((job) => job.id === selected()))
+  const active = createMemo(() => jobs()?.filter((job) => !terminal.has(job.status)).length ?? 0)
+  const [output, outputApi] = createResource(
+    selected,
+    async (id) => (await call<{ log: string }>(`/jobs/${id}/log`)).log,
+  )
+
+  createEffect(() => {
+    const list = jobs()
+    if (!list?.length) {
+      setSelected(undefined)
+      return
+    }
+    if (!selected() || !list.some((job) => job.id === selected())) setSelected(list[0].id)
+  })
+
+  const timer = setInterval(() => {
+    void jobsApi.refetch()
+    if (selected()) void outputApi.refetch()
+  }, 1_500)
+  onCleanup(() => clearInterval(timer))
+
+  const reset = () => {
+    setName("")
+    setCommand("")
+    setCwd("")
+    setTarget("local")
+    setCreating(false)
+  }
+
+  const start = async () => {
+    if (!name().trim() || !command().trim()) return
+    setBusy(true)
+    const value = target()
+    const next = await call<Job>("/jobs", {
+      method: "POST",
+      body: JSON.stringify({
+        name: name().trim(),
+        command: command().trim(),
+        cwd: cwd().trim() || undefined,
+        target: value === "local" ? { kind: "local" } : { kind: "ssh", host_id: value.slice(4) },
+      }),
+    }).catch((error) => {
+      toast.error("job did not start", error instanceof Error ? error.message : String(error))
+      return undefined
+    })
+    setBusy(false)
+    if (!next) return
+    jobsApi.mutate((list) => [next, ...(list ?? []).filter((job) => job.id !== next.id)])
+    setSelected(next.id)
+    reset()
+    void jobsApi.refetch()
+  }
+
+  const cancel = async (job: Job) => {
+    setBusy(true)
+    const next = await call<Job>(`/jobs/${job.id}/cancel`, { method: "POST" }).catch((error) => {
+      toast.error("job did not cancel", error instanceof Error ? error.message : String(error))
+      return undefined
+    })
+    setBusy(false)
+    if (!next) return
+    jobsApi.mutate((list) => list?.map((item) => (item.id === next.id ? next : item)))
+    void outputApi.refetch()
+  }
+
+  const rerun = (job: Job) => {
+    setName(job.name)
+    setCommand(job.command)
+    setCwd(job.cwd ?? "")
+    setTarget(job.target.kind === "local" ? "local" : `ssh:${job.target.host_id}`)
+    setCreating(true)
+  }
+
+  const clear = async () => {
+    setBusy(true)
+    await call<{ cleared: number }>("/jobs/completed", { method: "DELETE" }).catch((error) =>
+      toast.error("jobs were not cleared", error instanceof Error ? error.message : String(error)),
+    )
+    setBusy(false)
+    await jobsApi.refetch()
+  }
+
+  return (
+    <div style={shell}>
+      <div style={header}>
+        <div style={{ display: "flex", "align-items": "center", gap: "8px", "min-width": 0 }}>
+          <span style={mark}>
+            <IconCpu size={13} strokeWidth={1.5} />
+          </span>
+          <div style={{ display: "flex", "flex-direction": "column", "min-width": 0 }}>
+            <span style={title}>compute jobs</span>
+            <span style={subtitle}>{active() ? `${active()} active` : "local · SSH · schedulers"}</span>
+          </div>
+        </div>
+        <div style={{ display: "flex", gap: "4px" }}>
+          <Action title="refresh jobs" onClick={() => void jobsApi.refetch()}>
+            <IconRefresh size={12} />
+          </Action>
+          <Action title="new job" active={creating()} onClick={() => setCreating((value) => !value)}>
+            <IconPlus size={13} />
+          </Action>
+        </div>
+      </div>
+
+      <Show when={jobs.error}>
+        <div role="alert" style={errorBox}>
+          <span style={{ flex: 1 }}>
+            Compute jobs are unavailable. {jobs.error instanceof Error ? jobs.error.message : String(jobs.error)}
+          </span>
+          <button type="button" style={secondaryButton} onClick={() => void jobsApi.refetch()}>
+            retry
+          </button>
+        </div>
+      </Show>
+
+      <Show when={creating()}>
+        <form
+          style={form}
+          onSubmit={(event) => {
+            event.preventDefault()
+            void start()
+          }}
+        >
+          <input
+            aria-label="Job name"
+            style={input}
+            value={name()}
+            placeholder="Experiment name"
+            onInput={(event) => setName(event.currentTarget.value)}
+          />
+          <div style={{ display: "grid", "grid-template-columns": "minmax(0, 1fr) minmax(0, 1fr)", gap: "6px" }}>
+            <select
+              aria-label="Compute target"
+              style={input}
+              value={target()}
+              onChange={(event) => setTarget(event.currentTarget.value)}
+            >
+              <option value="local">This computer</option>
+              <For each={settings()?.ssh_hosts}>
+                {(host) => (
+                  <option value={`ssh:${host.id}`}>
+                    {host.label}
+                    {host.scheduler === "none" ? "" : ` · ${host.scheduler}`}
+                  </option>
+                )}
+              </For>
+            </select>
+            <input
+              aria-label="Working directory"
+              style={input}
+              value={cwd()}
+              placeholder="Working directory"
+              onInput={(event) => setCwd(event.currentTarget.value)}
+            />
+          </div>
+          <textarea
+            aria-label="Command"
+            style={{ ...input, height: "76px", resize: "vertical", "line-height": 1.45, padding: "9px 10px" }}
+            value={command()}
+            placeholder={"python train.py --config config.yaml"}
+            spellcheck={false}
+            onInput={(event) => setCommand(event.currentTarget.value)}
+          />
+          <div style={{ display: "flex", "justify-content": "flex-end", gap: "6px" }}>
+            <button type="button" style={secondaryButton} onClick={reset}>
+              cancel
+            </button>
+            <button type="submit" style={primaryButton} disabled={busy() || !name().trim() || !command().trim()}>
+              {busy() ? "starting…" : "run job"}
+            </button>
+          </div>
+        </form>
+      </Show>
+
+      <Show
+        when={(jobs()?.length ?? 0) > 0}
+        fallback={
+          <div style={empty}>
+            <span style={emptyMark}>
+              <IconActivity size={18} />
+            </span>
+            <strong style={{ color: "var(--color-text)", "font-size": "12px" }}>No compute jobs yet</strong>
+            <span>Run a script locally or send it to an SSH, Slurm, or PBS machine. Output stays attached here.</span>
+            <button style={primaryButton} onClick={() => setCreating(true)}>
+              create first job
+            </button>
+          </div>
+        }
+      >
+        <div style={listHeader}>
+          <span>recent runs</span>
+          <button disabled={busy()} style={textButton} onClick={() => void clear()}>
+            <IconTrash size={10} />
+            clear finished
+          </button>
+        </div>
+        <div style={list}>
+          <For each={jobs()}>
+            {(job) => (
+              <button
+                type="button"
+                onClick={() => setSelected(job.id)}
+                style={{
+                  ...row,
+                  background: selected() === job.id ? "var(--color-surface-solid)" : "transparent",
+                  "border-color": selected() === job.id ? "var(--color-border-strong)" : "transparent",
+                }}
+              >
+                <StatusIcon status={job.status} />
+                <span style={{ display: "flex", "flex-direction": "column", gap: "3px", "min-width": 0, flex: 1 }}>
+                  <span
+                    style={{
+                      color: "var(--color-text)",
+                      "font-weight": 600,
+                      overflow: "hidden",
+                      "text-overflow": "ellipsis",
+                      "white-space": "nowrap",
+                    }}
+                  >
+                    {job.name}
+                  </span>
+                  <span
+                    style={{
+                      color: "var(--color-text-faint)",
+                      overflow: "hidden",
+                      "text-overflow": "ellipsis",
+                      "white-space": "nowrap",
+                    }}
+                  >
+                    {job.target_label} · {job.scheduler === "none" ? job.status : `${job.scheduler} · ${job.status}`}
+                  </span>
+                </span>
+                <span style={{ color: "var(--color-text-faint)", "font-size": "9px", "white-space": "nowrap" }}>
+                  {age(job.created_at)}
+                </span>
+              </button>
+            )}
+          </For>
+        </div>
+      </Show>
+
+      <Show when={current()}>
+        {(job) => (
+          <div style={detail}>
+            <div style={{ display: "flex", "align-items": "flex-start", gap: "8px" }}>
+              <div style={{ display: "flex", "flex-direction": "column", gap: "3px", flex: 1, "min-width": 0 }}>
+                <span
+                  style={{
+                    color: "var(--color-text)",
+                    "font-family": FONT_SANS,
+                    "font-size": "12px",
+                    "font-weight": 650,
+                  }}
+                >
+                  {job().name}
+                </span>
+                <span style={{ color: "var(--color-text-faint)", "font-family": FONT_MONO, "font-size": "9px" }}>
+                  {job().id} · {duration(job())}
+                </span>
+              </div>
+              <Show when={!terminal.has(job().status)}>
+                <Action title="cancel job" onClick={() => void cancel(job())}>
+                  <IconStop size={11} />
+                </Action>
+              </Show>
+              <button style={secondaryButton} onClick={() => rerun(job())}>
+                rerun
+              </button>
+            </div>
+            <div style={commandBox}>
+              <span style={{ color: "var(--color-text-faint)", "user-select": "none" }}>$</span>
+              <span>{job().command}</span>
+            </div>
+            <Show when={job().cwd}>
+              <div style={meta}>cwd · {job().cwd}</div>
+            </Show>
+            <div style={logHeader}>
+              <span>output</span>
+              <span>{output.loading ? "syncing…" : `${output()?.length ?? 0} bytes`}</span>
+            </div>
+            <pre style={log}>
+              {output() || (terminal.has(job().status) ? "No output was captured." : "Waiting for output…")}
+            </pre>
+            <Show when={job().error}>
+              <div style={errorBox}>{job().error}</div>
+            </Show>
+          </div>
+        )}
+      </Show>
+    </div>
+  )
+}
+
+function StatusIcon(props: { status: Status }): JSX.Element {
+  const config = () => {
+    if (props.status === "succeeded") return { color: "var(--color-success)", icon: IconCheckCircle }
+    if (props.status === "failed") return { color: "var(--color-danger)", icon: IconAlertCircle }
+    if (props.status === "interrupted") return { color: "var(--color-warning)", icon: IconAlertCircle }
+    if (props.status === "cancelled") return { color: "var(--color-text-faint)", icon: IconStop }
+    if (props.status === "running") return { color: "var(--color-accent)", icon: IconActivity }
+    return { color: "var(--color-text-muted)", icon: IconClock }
+  }
+  return (
+    <span style={{ color: config().color, display: "inline-flex", "flex-shrink": 0 }}>
+      <Dynamic component={config().icon} size={13} strokeWidth={1.7} />
+    </span>
+  )
+}
+
+function Action(props: { title: string; active?: boolean; onClick: () => void; children: JSX.Element }): JSX.Element {
+  return (
+    <button
+      type="button"
+      title={props.title}
+      aria-label={props.title}
+      onClick={props.onClick}
+      style={{
+        all: "unset",
+        cursor: "pointer",
+        width: "27px",
+        height: "27px",
+        display: "inline-flex",
+        "align-items": "center",
+        "justify-content": "center",
+        "border-radius": "4px",
+        border: "1px solid var(--color-border)",
+        background: props.active ? "var(--color-accent-subtle)" : "var(--color-bg-elevated)",
+        color: props.active ? "var(--color-accent)" : "var(--color-text-muted)",
+        "box-sizing": "border-box",
+      }}
+    >
+      {props.children}
+    </button>
+  )
+}
+
+function age(value: string): string {
+  const delta = Math.max(0, Date.now() - Date.parse(value))
+  if (delta < 60_000) return "now"
+  if (delta < 3_600_000) return `${Math.floor(delta / 60_000)}m`
+  if (delta < 86_400_000) return `${Math.floor(delta / 3_600_000)}h`
+  return `${Math.floor(delta / 86_400_000)}d`
+}
+
+function duration(job: Job): string {
+  if (!job.started_at) return job.status
+  const end = job.completed_at ? Date.parse(job.completed_at) : Date.now()
+  const seconds = Math.max(0, Math.round((end - Date.parse(job.started_at)) / 1_000))
+  if (seconds < 60) return `${job.status} · ${seconds}s`
+  return `${job.status} · ${Math.floor(seconds / 60)}m ${seconds % 60}s`
+}
+
+const shell: JSX.CSSProperties = {
+  flex: 1,
+  "min-height": 0,
+  display: "flex",
+  "flex-direction": "column",
+  overflow: "hidden",
+  background: "var(--color-bg-subtle)",
+  "font-family": FONT_SANS,
+}
+
+const header: JSX.CSSProperties = {
+  display: "flex",
+  "align-items": "center",
+  "justify-content": "space-between",
+  gap: "10px",
+  padding: "10px",
+  "border-bottom": "1px solid var(--color-border)",
+  background: "var(--color-bg)",
+  "flex-shrink": 0,
+}
+
+const mark: JSX.CSSProperties = {
+  width: "27px",
+  height: "27px",
+  display: "inline-flex",
+  "align-items": "center",
+  "justify-content": "center",
+  "border-radius": "6px",
+  background: "color-mix(in srgb, var(--color-accent) 12%, transparent)",
+  color: "var(--color-accent)",
+}
+
+const title: JSX.CSSProperties = {
+  color: "var(--color-text)",
+  "font-size": "12px",
+  "font-weight": 680,
+  "letter-spacing": "-0.01em",
+}
+
+const subtitle: JSX.CSSProperties = {
+  color: "var(--color-text-faint)",
+  "font-family": FONT_MONO,
+  "font-size": "9px",
+}
+
+const form: JSX.CSSProperties = {
+  display: "flex",
+  "flex-direction": "column",
+  gap: "7px",
+  padding: "10px",
+  "border-bottom": "1px solid var(--color-border)",
+  background: "var(--color-surface-solid)",
+  "flex-shrink": 0,
+}
+
+const input: JSX.CSSProperties = {
+  width: "100%",
+  height: "32px",
+  "box-sizing": "border-box",
+  border: "1px solid var(--color-border)",
+  "border-radius": "4px",
+  background: "var(--color-bg)",
+  color: "var(--color-text)",
+  padding: "0 9px",
+  outline: "none",
+  "font-family": FONT_MONO,
+  "font-size": "10px",
+}
+
+const primaryButton: JSX.CSSProperties = {
+  cursor: "pointer",
+  border: "1px solid var(--color-accent)",
+  "border-radius": "4px",
+  background: "var(--color-accent)",
+  color: "var(--color-bg)",
+  padding: "6px 10px",
+  "font-family": FONT_MONO,
+  "font-size": "10px",
+  "font-weight": 650,
+}
+
+const secondaryButton: JSX.CSSProperties = {
+  cursor: "pointer",
+  border: "1px solid var(--color-border)",
+  "border-radius": "4px",
+  background: "var(--color-bg-elevated)",
+  color: "var(--color-text-muted)",
+  padding: "5px 8px",
+  "font-family": FONT_MONO,
+  "font-size": "10px",
+}
+
+const empty: JSX.CSSProperties = {
+  display: "flex",
+  "flex-direction": "column",
+  "align-items": "center",
+  gap: "8px",
+  padding: "36px 22px",
+  color: "var(--color-text-muted)",
+  "font-size": "11px",
+  "line-height": 1.5,
+  "text-align": "center",
+}
+
+const emptyMark: JSX.CSSProperties = {
+  width: "38px",
+  height: "38px",
+  display: "inline-flex",
+  "align-items": "center",
+  "justify-content": "center",
+  "border-radius": "10px",
+  background: "var(--color-surface-solid)",
+  border: "1px solid var(--color-border)",
+  color: "var(--color-text-faint)",
+}
+
+const listHeader: JSX.CSSProperties = {
+  display: "flex",
+  "align-items": "center",
+  "justify-content": "space-between",
+  padding: "8px 10px 4px",
+  color: "var(--color-text-faint)",
+  "font-family": FONT_MONO,
+  "font-size": "9px",
+  "text-transform": "uppercase",
+  "letter-spacing": "0.08em",
+}
+
+const textButton: JSX.CSSProperties = {
+  all: "unset",
+  cursor: "pointer",
+  display: "inline-flex",
+  "align-items": "center",
+  gap: "4px",
+  color: "var(--color-text-faint)",
+  "font-size": "9px",
+  "text-transform": "none",
+  "letter-spacing": "normal",
+}
+
+const list: JSX.CSSProperties = {
+  display: "flex",
+  "flex-direction": "column",
+  gap: "2px",
+  padding: "3px 7px 8px",
+  "max-height": "190px",
+  overflow: "auto",
+  "flex-shrink": 0,
+  "border-bottom": "1px solid var(--color-border)",
+}
+
+const row: JSX.CSSProperties = {
+  cursor: "pointer",
+  width: "100%",
+  display: "flex",
+  "align-items": "center",
+  gap: "8px",
+  padding: "8px",
+  border: "1px solid transparent",
+  "border-radius": "5px",
+  "text-align": "left",
+  "font-family": FONT_MONO,
+  "font-size": "10px",
+}
+
+const detail: JSX.CSSProperties = {
+  flex: 1,
+  "min-height": 0,
+  overflow: "auto",
+  display: "flex",
+  "flex-direction": "column",
+  gap: "8px",
+  padding: "10px",
+  background: "var(--color-bg)",
+}
+
+const commandBox: JSX.CSSProperties = {
+  display: "flex",
+  gap: "7px",
+  padding: "8px",
+  border: "1px solid var(--color-border)",
+  "border-radius": "4px",
+  background: "var(--color-bg-subtle)",
+  color: "var(--color-text-muted)",
+  "font-family": FONT_MONO,
+  "font-size": "10px",
+  "line-height": 1.45,
+  "white-space": "pre-wrap",
+  "overflow-wrap": "anywhere",
+}
+
+const meta: JSX.CSSProperties = {
+  color: "var(--color-text-faint)",
+  "font-family": FONT_MONO,
+  "font-size": "9px",
+  overflow: "hidden",
+  "text-overflow": "ellipsis",
+  "white-space": "nowrap",
+}
+
+const logHeader: JSX.CSSProperties = {
+  display: "flex",
+  "justify-content": "space-between",
+  color: "var(--color-text-faint)",
+  "font-family": FONT_MONO,
+  "font-size": "9px",
+  "text-transform": "uppercase",
+  "letter-spacing": "0.08em",
+  "margin-top": "2px",
+}
+
+const log: JSX.CSSProperties = {
+  flex: 1,
+  "min-height": "100px",
+  margin: 0,
+  padding: "10px",
+  border: "1px solid var(--color-border)",
+  "border-radius": "4px",
+  background: "#101411",
+  color: "#c9d4cc",
+  "font-family": FONT_MONO,
+  "font-size": "10px",
+  "line-height": 1.55,
+  "white-space": "pre-wrap",
+  "overflow-wrap": "anywhere",
+  overflow: "auto",
+}
+
+const errorBox: JSX.CSSProperties = {
+  display: "flex",
+  "align-items": "center",
+  gap: "8px",
+  padding: "8px",
+  "border-radius": "4px",
+  border: "1px solid color-mix(in srgb, var(--color-danger) 35%, transparent)",
+  background: "color-mix(in srgb, var(--color-danger) 8%, transparent)",
+  color: "var(--color-danger)",
+  "font-family": FONT_MONO,
+  "font-size": "9px",
+  "line-height": 1.45,
+}
diff --git a/frontend/workspace/src/atlas/RightPane.tsx b/frontend/workspace/src/atlas/RightPane.tsx
index 6a1f0a04..7dfd98fc 100644
--- a/frontend/workspace/src/atlas/RightPane.tsx
+++ b/frontend/workspace/src/atlas/RightPane.tsx
@@ -7,6 +7,7 @@ import { Terminal } from "@/components/terminal"
 import { uiStore, type RightPaneTab } from "@/atlas/store/ui"
 import { SkillLibraryDialog } from "@/atlas/SkillsBrowser"
 import { AtlasCanvas } from "@/atlas/AtlasCanvas"
+import { ComputeJobs } from "@/atlas/ComputeJobs"
 import { toast } from "@/atlas/Toast"
 import {
   IconLayoutGrid,
@@ -15,6 +16,7 @@ import {
   IconChevronLeft,
   IconSettings,
   IconTerminal,
+  IconActivity,
 } from "@/atlas/shared/Icon"
 
 const RIGHT_PANE_WIDTH_KEY = "thesis-right-pane-width-v1"
@@ -47,6 +49,7 @@ export function RightPane(): JSX.Element {
   const TABS: { k: RightPaneTab; label?: string; Icon: (p: { size?: number; strokeWidth?: number }) => JSX.Element }[] =
     [
       { k: "canvas", label: "atlas", Icon: IconLayoutGrid },
+      { k: "jobs", Icon: IconActivity },
       { k: "terminal", Icon: IconTerminal },
     ]
   const visibleTabs = createMemo(() => TABS.filter((t) => !uiStore.isTabHidden(t.k)))
@@ -221,6 +224,9 @@ export function RightPane(): JSX.Element {
           <KeepAlive show={tab() === "canvas"} mounted={visited().has("canvas")}>
             <CanvasTab />
           </KeepAlive>
+          <KeepAlive show={tab() === "jobs"} mounted={visited().has("jobs")}>
+            <ComputeJobs />
+          </KeepAlive>
           <KeepAlive show={tab() === "terminal"} mounted={visited().has("terminal")}>
             <TerminalTab />
           </KeepAlive>
diff --git a/frontend/workspace/src/atlas/store/ui.ts b/frontend/workspace/src/atlas/store/ui.ts
index f9618611..b55afac1 100644
--- a/frontend/workspace/src/atlas/store/ui.ts
+++ b/frontend/workspace/src/atlas/store/ui.ts
@@ -1,6 +1,6 @@
 import { createSignal } from "solid-js"
 
-export type RightPaneTab = "canvas" | "terminal"
+export type RightPaneTab = "canvas" | "jobs" | "terminal"
 
 const PANE_OPEN_KEY = "openscience-rightpane-open-v2"
 const HIDDEN_TABS_KEY = "thesis-rightpane-hidden-tabs-v1"
diff --git a/frontend/workspace/src/components/settings/Compute.tsx b/frontend/workspace/src/components/settings/Compute.tsx
index ea0f1148..2690f0d7 100644
--- a/frontend/workspace/src/components/settings/Compute.tsx
+++ b/frontend/workspace/src/components/settings/Compute.tsx
@@ -21,6 +21,8 @@ interface SshHost {
   host: string
   user?: string
   port?: number
+  scheduler: "none" | "slurm" | "pbs"
+  workdir?: string
 }
 interface Endpoint {
   id: string
@@ -97,11 +99,16 @@ const Compute: Component = () => {
   const [hHost, setHHost] = createSignal("")
   const [hUser, setHUser] = createSignal("")
   const [hPort, setHPort] = createSignal("")
+  const [hScheduler, setHScheduler] = createSignal<"none" | "slurm" | "pbs">("none")
+  const [hWorkdir, setHWorkdir] = createSignal("")
+  const [testingHost, setTestingHost] = createSignal<string>()
   const resetHost = () => {
     setHLabel("")
     setHHost("")
     setHUser("")
     setHPort("")
+    setHScheduler("none")
+    setHWorkdir("")
     setAddingHost(false)
   }
   const saveHost = async () => {
@@ -115,12 +122,49 @@ const Compute: Component = () => {
             host: hHost().trim(),
             user: hUser().trim() || undefined,
             port: hPort().trim() ? Number(hPort().trim()) : undefined,
+            scheduler: hScheduler(),
+            workdir: hWorkdir().trim() || undefined,
           }),
         }),
       "Failed to add SSH host",
     )
     resetHost()
   }
+  const testHost = async (host: SshHost) => {
+    setTestingHost(host.id)
+    const result = await call<{
+      ok: boolean
+      latency_ms: number
+      hostname?: string
+      python: boolean
+      gpu: boolean
+      slurm: boolean
+      pbs: boolean
+      error?: string
+    }>(`/ssh/${host.id}/test`, { method: "POST" }).catch((error) => ({
+      ok: false,
+      latency_ms: 0,
+      python: false,
+      gpu: false,
+      slurm: false,
+      pbs: false,
+      hostname: undefined,
+      error: error instanceof Error ? error.message : String(error),
+    }))
+    setTestingHost(undefined)
+    const capabilities = [
+      result.python ? "Python" : undefined,
+      result.gpu ? "NVIDIA GPU" : undefined,
+      result.slurm ? "Slurm" : undefined,
+      result.pbs ? "PBS" : undefined,
+    ].filter(Boolean)
+    showToast({
+      title: result.ok ? `Connected to ${result.hostname ?? host.label}` : `Could not connect to ${host.label}`,
+      description: result.ok
+        ? `${result.latency_ms} ms${capabilities.length ? ` · ${capabilities.join(" · ")}` : ""}`
+        : result.error || "SSH did not return a successful connection probe.",
+    })
+  }
 
   // ── Endpoint add form ──
   const [addingEp, setAddingEp] = createSignal(false)
@@ -150,6 +194,11 @@ const Compute: Component = () => {
     { value: "remote", label: "Remote" },
     { value: "local", label: "Local" },
   ]
+  const schedulerOptions: { value: "none" | "slurm" | "pbs"; label: string }[] = [
+    { value: "none", label: "Direct SSH" },
+    { value: "slurm", label: "Slurm" },
+    { value: "pbs", label: "PBS / Torque" },
+  ]
 
   return (
     <div class="flex flex-col h-full overflow-y-auto no-scrollbar">
@@ -212,13 +261,32 @@ const Compute: Component = () => {
             >
               <For each={info()?.ssh_hosts}>
                 {(h) => (
-                  <Row title={h.label} subtitle={`${h.user ? `${h.user}@` : ""}${h.host}${h.port ? `:${h.port}` : ""}`}>
-                    <RemoveButton
-                      disabled={busy()}
-                      onClick={() =>
-                        run(() => call<ComputeInfo>(`/ssh/${h.id}`, { method: "DELETE" }), "Failed to remove host")
-                      }
-                    />
+                  <Row
+                    title={h.label}
+                    subtitle={[
+                      `${h.user ? `${h.user}@` : ""}${h.host}${h.port ? `:${h.port}` : ""}`,
+                      h.scheduler === "slurm" ? "Slurm" : h.scheduler === "pbs" ? "PBS" : "direct",
+                      h.workdir,
+                    ]
+                      .filter(Boolean)
+                      .join(" · ")}
+                  >
+                    <div class="flex items-center gap-1.5">
+                      <Button
+                        size="small"
+                        variant="secondary"
+                        disabled={busy() || testingHost() === h.id}
+                        onClick={() => void testHost(h)}
+                      >
+                        {testingHost() === h.id ? "testing…" : "test"}
+                      </Button>
+                      <RemoveButton
+                        disabled={busy()}
+                        onClick={() =>
+                          run(() => call<ComputeInfo>(`/ssh/${h.id}`, { method: "DELETE" }), "Failed to remove host")
+                        }
+                      />
+                    </div>
                   </Row>
                 )}
               </For>
@@ -235,6 +303,25 @@ const Compute: Component = () => {
                   />
                   <TextField label="User (optional)" value={hUser()} onInput={setHUser} placeholder="ubuntu" />
                   <TextField label="Port (optional)" value={hPort()} onInput={setHPort} placeholder="22" />
+                  <div class="flex flex-col gap-1.5">
+                    <span class="text-12-medium text-text-weak">Scheduler</span>
+                    <Select
+                      options={schedulerOptions}
+                      current={schedulerOptions.find((option) => option.value === hScheduler())}
+                      value={(option) => option.value}
+                      label={(option) => option.label}
+                      onSelect={(option) => option && setHScheduler(option.value)}
+                      variant="secondary"
+                      size="small"
+                      triggerVariant="settings"
+                    />
+                  </div>
+                  <TextField
+                    label="Working directory (optional)"
+                    value={hWorkdir()}
+                    onInput={setHWorkdir}
+                    placeholder="/home/ubuntu/research"
+                  />
                 </div>
                 <FormActions
                   onCancel={resetHost}
diff --git a/tooling/sdk/js/src/v2/gen/sdk.gen.ts b/tooling/sdk/js/src/v2/gen/sdk.gen.ts
index b1b1056c..f6345135 100644
--- a/tooling/sdk/js/src/v2/gen/sdk.gen.ts
+++ b/tooling/sdk/js/src/v2/gen/sdk.gen.ts
@@ -171,12 +171,22 @@ import type {
   SettingsComputeEndpointAddResponses,
   SettingsComputeEndpointRemoveResponses,
   SettingsComputeGetResponses,
+  SettingsComputeJobsCancelErrors,
+  SettingsComputeJobsCancelResponses,
+  SettingsComputeJobsClearResponses,
+  SettingsComputeJobsListResponses,
+  SettingsComputeJobsLogErrors,
+  SettingsComputeJobsLogResponses,
+  SettingsComputeJobsStartErrors,
+  SettingsComputeJobsStartResponses,
   SettingsComputeProviderConnectErrors,
   SettingsComputeProviderConnectResponses,
   SettingsComputeProviderDisconnectResponses,
   SettingsComputeSshAddErrors,
   SettingsComputeSshAddResponses,
   SettingsComputeSshRemoveResponses,
+  SettingsComputeSshTestErrors,
+  SettingsComputeSshTestResponses,
   SettingsCredentialsListResponses,
   SettingsCredentialsRemoveResponses,
   SettingsCredentialsSetResponses,
@@ -742,6 +752,8 @@ export class Ssh extends HeyApiClient {
       host?: string
       user?: string
       port?: number
+      scheduler?: "none" | "slurm" | "pbs"
+      workdir?: string
     },
     options?: Options<never, ThrowOnError>,
   ) {
@@ -754,6 +766,8 @@ export class Ssh extends HeyApiClient {
             { in: "body", key: "host" },
             { in: "body", key: "user" },
             { in: "body", key: "port" },
+            { in: "body", key: "scheduler" },
+            { in: "body", key: "workdir" },
           ],
         },
       ],
@@ -774,6 +788,27 @@ export class Ssh extends HeyApiClient {
     })
   }
 
+  /**
+   * Test an SSH compute host
+   */
+  public test<ThrowOnError extends boolean = false>(
+    parameters: {
+      id: string
+    },
+    options?: Options<never, ThrowOnError>,
+  ) {
+    const params = buildClientParams([parameters], [{ args: [{ in: "path", key: "id" }] }])
+    return (options?.client ?? this.client).post<
+      SettingsComputeSshTestResponses,
+      SettingsComputeSshTestErrors,
+      ThrowOnError
+    >({
+      url: "/settings/compute/ssh/{id}/test",
+      ...options,
+      ...params,
+    })
+  }
+
   /**
    * Remove SSH host
    */
@@ -850,6 +885,118 @@ export class Endpoint extends HeyApiClient {
   }
 }
 
+export class Jobs extends HeyApiClient {
+  /**
+   * List local and remote compute jobs
+   */
+  public list<ThrowOnError extends boolean = false>(options?: Options<never, ThrowOnError>) {
+    return (options?.client ?? this.client).get<SettingsComputeJobsListResponses, unknown, ThrowOnError>({
+      url: "/settings/compute/jobs",
+      ...options,
+    })
+  }
+
+  /**
+   * Start a local, SSH, Slurm, or PBS compute job
+   */
+  public start<ThrowOnError extends boolean = false>(
+    parameters?: {
+      name?: string
+      command?: string
+      cwd?: string
+      target?:
+        | {
+            kind: "local"
+          }
+        | {
+            kind: "ssh"
+            host_id: string
+          }
+    },
+    options?: Options<never, ThrowOnError>,
+  ) {
+    const params = buildClientParams(
+      [parameters],
+      [
+        {
+          args: [
+            { in: "body", key: "name" },
+            { in: "body", key: "command" },
+            { in: "body", key: "cwd" },
+            { in: "body", key: "target" },
+          ],
+        },
+      ],
+    )
+    return (options?.client ?? this.client).post<
+      SettingsComputeJobsStartResponses,
+      SettingsComputeJobsStartErrors,
+      ThrowOnError
+    >({
+      url: "/settings/compute/jobs",
+      ...options,
+      ...params,
+      headers: {
+        "Content-Type": "application/json",
+        ...options?.headers,
+        ...params.headers,
+      },
+    })
+  }
+
+  /**
+   * Clear completed compute jobs
+   */
+  public clear<ThrowOnError extends boolean = false>(options?: Options<never, ThrowOnError>) {
+    return (options?.client ?? this.client).delete<SettingsComputeJobsClearResponses, unknown, ThrowOnError>({
+      url: "/settings/compute/jobs/completed",
+      ...options,
+    })
+  }
+
+  /**
+   * Read a compute job log
+   */
+  public log<ThrowOnError extends boolean = false>(
+    parameters: {
+      id: string
+    },
+    options?: Options<never, ThrowOnError>,
+  ) {
+    const params = buildClientParams([parameters], [{ args: [{ in: "path", key: "id" }] }])
+    return (options?.client ?? this.client).get<
+      SettingsComputeJobsLogResponses,
+      SettingsComputeJobsLogErrors,
+      ThrowOnError
+    >({
+      url: "/settings/compute/jobs/{id}/log",
+      ...options,
+      ...params,
+    })
+  }
+
+  /**
+   * Cancel a compute job
+   */
+  public cancel<ThrowOnError extends boolean = false>(
+    parameters: {
+      id: string
+    },
+    options?: Options<never, ThrowOnError>,
+  ) {
+    const params = buildClientParams([parameters], [{ args: [{ in: "path", key: "id" }] }])
+    return (options?.client ?? this.client).post<
+      SettingsComputeJobsCancelResponses,
+      SettingsComputeJobsCancelErrors,
+      ThrowOnError
+    >({
+      url: "/settings/compute/jobs/{id}/cancel",
+      ...options,
+      ...params,
+    })
+  }
+}
+
 export class Compute extends HeyApiClient {
   /**
    * Get compute settings
@@ -875,6 +1022,11 @@ export class Compute extends HeyApiClient {
   get endpoint(): Endpoint {
     return (this._endpoint ??= new Endpoint({ client: this.client }))
   }
+
+  private _jobs?: Jobs
+  get jobs(): Jobs {
+    return (this._jobs ??= new Jobs({ client: this.client }))
+  }
 }
 
 export class Permissions extends HeyApiClient {
diff --git a/tooling/sdk/js/src/v2/gen/types.gen.ts b/tooling/sdk/js/src/v2/gen/types.gen.ts
index 3879b8ab..8f2ae3e4 100644
--- a/tooling/sdk/js/src/v2/gen/types.gen.ts
+++ b/tooling/sdk/js/src/v2/gen/types.gen.ts
@@ -1885,6 +1885,13 @@ export type BadRequestError = {
   success: false
 }
 
+export type NotFoundError = {
+  name: "NotFoundError"
+  data: {
+    message: string
+  }
+}
+
 export type OAuth = {
   type: "oauth"
   refresh: string
@@ -1907,13 +1914,6 @@ export type WellKnownAuth = {
 
 export type Auth = OAuth | ApiAuth | WellKnownAuth
 
-export type NotFoundError = {
-  name: "NotFoundError"
-  data: {
-    message: string
-  }
-}
-
 export type Model = {
   id: string
   providerID: string
@@ -2836,6 +2836,8 @@ export type SettingsComputeGetResponses = {
       host: string
       user?: string
       port?: number
+      scheduler?: "none" | "slurm" | "pbs"
+      workdir?: string
     }>
     endpoints?: Array<{
       id: string
@@ -2878,6 +2880,8 @@ export type SettingsComputeProviderDisconnectResponses = {
       host: string
       user?: string
       port?: number
+      scheduler?: "none" | "slurm" | "pbs"
+      workdir?: string
     }>
     endpoints?: Array<{
       id: string
@@ -2933,6 +2937,8 @@ export type SettingsComputeProviderConnectResponses = {
       host: string
       user?: string
       port?: number
+      scheduler?: "none" | "slurm" | "pbs"
+      workdir?: string
     }>
     endpoints?: Array<{
       id: string
@@ -2952,6 +2958,8 @@ export type SettingsComputeSshAddData = {
     host: string
     user?: string
     port?: number
+    scheduler?: "none" | "slurm" | "pbs"
+    workdir?: string
   }
   path?: never
   query?: never
@@ -2988,6 +2996,8 @@ export type SettingsComputeSshAddResponses = {
       host: string
       user?: string
       port?: number
+      scheduler?: "none" | "slurm" | "pbs"
+      workdir?: string
     }>
     endpoints?: Array<{
       id: string
@@ -3000,6 +3010,43 @@ export type SettingsComputeSshAddResponses = {
 
 export type SettingsComputeSshAddResponse = SettingsComputeSshAddResponses[keyof SettingsComputeSshAddResponses]
 
+export type SettingsComputeSshTestData = {
+  body?: never
+  path: {
+    id: string
+  }
+  query?: never
+  url: "/settings/compute/ssh/{id}/test"
+}
+
+export type SettingsComputeSshTestErrors = {
+  /**
+   * Not found
+   */
+  404: NotFoundError
+}
+
+export type SettingsComputeSshTestError = SettingsComputeSshTestErrors[keyof SettingsComputeSshTestErrors]
+
+export type SettingsComputeSshTestResponses = {
+  /**
+   * Connection result
+   */
+  200: {
+    ok: boolean
+    host: string
+    latency_ms: number
+    hostname?: string
+    python: boolean
+    gpu: boolean
+    slurm: boolean
+    pbs: boolean
+    error?: string
+  }
+}
+
+export type SettingsComputeSshTestResponse = SettingsComputeSshTestResponses[keyof SettingsComputeSshTestResponses]
+
 export type SettingsComputeSshRemoveData = {
   body?: never
   path: {
@@ -3030,6 +3077,8 @@ export type SettingsComputeSshRemoveResponses = {
       host: string
       user?: string
       port?: number
+      scheduler?: "none" | "slurm" | "pbs"
+      workdir?: string
     }>
     endpoints?: Array<{
       id: string
@@ -3084,6 +3133,8 @@ export type SettingsComputeEndpointAddResponses = {
       host: string
       user?: string
       port?: number
+      scheduler?: "none" | "slurm" | "pbs"
+      workdir?: string
     }>
     endpoints?: Array<{
       id: string
@@ -3127,6 +3178,8 @@ export type SettingsComputeEndpointRemoveResponses = {
       host: string
       user?: string
       port?: number
+      scheduler?: "none" | "slurm" | "pbs"
+      workdir?: string
     }>
     endpoints?: Array<{
       id: string
@@ -3140,6 +3193,202 @@ export type SettingsComputeEndpointRemoveResponses = {
 export type SettingsComputeEndpointRemoveResponse =
   SettingsComputeEndpointRemoveResponses[keyof SettingsComputeEndpointRemoveResponses]
 
+export type SettingsComputeJobsListData = {
+  body?: never
+  path?: never
+  query?: never
+  url: "/settings/compute/jobs"
+}
+
+export type SettingsComputeJobsListResponses = {
+  /**
+   * Compute jobs
+   */
+  200: Array<{
+    id: string
+    name: string
+    command: string
+    cwd?: string
+    target:
+      | {
+          kind: "local"
+        }
+      | {
+          kind: "ssh"
+          host_id: string
+        }
+    target_label: string
+    scheduler: "none" | "slurm" | "pbs"
+    status: "queued" | "running" | "succeeded" | "failed" | "cancelled" | "interrupted"
+    created_at: string
+    started_at?: string
+    completed_at?: string
+    exit_code?: number | null
+    pid?: number
+    error?: string
+  }>
+}
+
+export type SettingsComputeJobsListResponse = SettingsComputeJobsListResponses[keyof SettingsComputeJobsListResponses]
+
+export type SettingsComputeJobsStartData = {
+  body?: {
+    name: string
+    command: string
+    cwd?: string
+    target:
+      | {
+          kind: "local"
+        }
+      | {
+          kind: "ssh"
+          host_id: string
+        }
+  }
+  path?: never
+  query?: never
+  url: "/settings/compute/jobs"
+}
+
+export type SettingsComputeJobsStartErrors = {
+  /**
+   * Bad request
+   */
+  400: BadRequestError
+}
+
+export type SettingsComputeJobsStartError = SettingsComputeJobsStartErrors[keyof SettingsComputeJobsStartErrors]
+
+export type SettingsComputeJobsStartResponses = {
+  /**
+   * Started job
+   */
+  200: {
+    id: string
+    name: string
+    command: string
+    cwd?: string
+    target:
+      | {
+          kind: "local"
+        }
+      | {
+          kind: "ssh"
+          host_id: string
+        }
+    target_label: string
+    scheduler: "none" | "slurm" | "pbs"
+    status: "queued" | "running" | "succeeded" | "failed" | "cancelled" | "interrupted"
+    created_at: string
+    started_at?: string
+    completed_at?: string
+    exit_code?: number | null
+    pid?: number
+    error?: string
+  }
+}
+
+export type SettingsComputeJobsStartResponse =
+  SettingsComputeJobsStartResponses[keyof SettingsComputeJobsStartResponses]
+
+export type SettingsComputeJobsClearData = {
+  body?: never
+  path?: never
+  query?: never
+  url: "/settings/compute/jobs/completed"
+}
+
+export type SettingsComputeJobsClearResponses = {
+  /**
+   * Number cleared
+   */
+  200: {
+    cleared: number
+  }
+}
+
+export type SettingsComputeJobsClearResponse =
+  SettingsComputeJobsClearResponses[keyof SettingsComputeJobsClearResponses]
+
+export type SettingsComputeJobsLogData = {
+  body?: never
+  path: {
+    id: string
+  }
+  query?: never
+  url: "/settings/compute/jobs/{id}/log"
+}
+
+export type SettingsComputeJobsLogErrors = {
+  /**
+   * Not found
+   */
+  404: NotFoundError
+}
+
+export type SettingsComputeJobsLogError = SettingsComputeJobsLogErrors[keyof SettingsComputeJobsLogErrors]
+
+export type SettingsComputeJobsLogResponses = {
+  /**
+   * Job output
+   */
+  200: {
+    log: string
+  }
+}
+
+export type SettingsComputeJobsLogResponse = SettingsComputeJobsLogResponses[keyof SettingsComputeJobsLogResponses]
+
+export type SettingsComputeJobsCancelData = {
+  body?: never
+  path: {
+    id: string
+  }
+  query?: never
+  url: "/settings/compute/jobs/{id}/cancel"
+}
+
+export type SettingsComputeJobsCancelErrors = {
+  /**
+   * Not found
+   */
+  404: NotFoundError
+}
+
+export type SettingsComputeJobsCancelError = SettingsComputeJobsCancelErrors[keyof SettingsComputeJobsCancelErrors]
+
+export type SettingsComputeJobsCancelResponses = {
+  /**
+   * Cancelled job
+   */
+  200: {
+    id: string
+    name: string
+    command: string
+    cwd?: string
+    target:
+      | {
+          kind: "local"
+        }
+      | {
+          kind: "ssh"
+          host_id: string
+        }
+    target_label: string
+    scheduler: "none" | "slurm" | "pbs"
+    status: "queued" | "running" | "succeeded" | "failed" | "cancelled" | "interrupted"
+    created_at: string
+    started_at?: string
+    completed_at?: string
+    exit_code?: number | null
+    pid?: number
+    error?: string
+  }
+}
+
+export type SettingsComputeJobsCancelResponse =
+  SettingsComputeJobsCancelResponses[keyof SettingsComputeJobsCancelResponses]
+
 export type SettingsPermissionsGetData = {
   body?: never
   path?: never
diff --git a/tooling/sdk/openapi.json b/tooling/sdk/openapi.json
index 1bef936a..052dc445 100644
--- a/tooling/sdk/openapi.json
+++ b/tooling/sdk/openapi.json
@@ -1445,6 +1445,18 @@
                             "type": "integer",
                             "exclusiveMinimum": 0,
                             "maximum": 9007199254740991
+                          },
+                          "scheduler": {
+                            "default": "none",
+                            "type": "string",
+                            "enum": [
+                              "none",
+                              "slurm",
+                              "pbs"
+                            ]
+                          },
+                          "workdir": {
+                            "type": "string"
                           }
                         },
                         "required": [
@@ -1590,6 +1602,18 @@
                             "type": "integer",
                             "exclusiveMinimum": 0,
                             "maximum": 9007199254740991
+                          },
+                          "scheduler": {
+                            "default": "none",
+                            "type": "string",
+                            "enum": [
+                              "none",
+                              "slurm",
+                              "pbs"
+                            ]
+                          },
+                          "workdir": {
+                            "type": "string"
                           }
                         },
                         "required": [
@@ -1771,6 +1795,18 @@
                             "type": "integer",
                             "exclusiveMinimum": 0,
                             "maximum": 9007199254740991
+                          },
+                          "scheduler": {
+                            "default": "none",
+                            "type": "string",
+                            "enum": [
+                              "none",
+                              "slurm",
+                              "pbs"
+                            ]
+                          },
+                          "workdir": {
+                            "type": "string"
                           }
                         },
                         "required": [
@@ -1926,6 +1962,18 @@
                             "type": "integer",
                             "exclusiveMinimum": 0,
                             "maximum": 9007199254740991
+                          },
+                          "scheduler": {
+                            "default": "none",
+                            "type": "string",
+                            "enum": [
+                              "none",
+                              "slurm",
+                              "pbs"
+                            ]
+                          },
+                          "workdir": {
+                            "type": "string"
                           }
                         },
                         "required": [
@@ -2003,6 +2051,18 @@
                     "type": "integer",
                     "exclusiveMinimum": 0,
                     "maximum": 9007199254740991
+                  },
+                  "scheduler": {
+                    "default": "none",
+                    "type": "string",
+                    "enum": [
+                      "none",
+                      "slurm",
+                      "pbs"
+                    ]
+                  },
+                  "workdir": {
+                    "type": "string"
                   }
                 },
                 "required": [
@@ -2021,6 +2081,89 @@
         ]
       }
     },
+    "/settings/compute/ssh/{id}/test": {
+      "post": {
+        "operationId": "settings.compute.ssh.test",
+        "summary": "Test an SSH compute host",
+        "responses": {
+          "200": {
+            "description": "Connection result",
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "object",
+                  "properties": {
+                    "ok": {
+                      "type": "boolean"
+                    },
+                    "host": {
+                      "type": "string"
+                    },
+                    "latency_ms": {
+                      "type": "number",
+                      "minimum": 0
+                    },
+                    "hostname": {
+                      "type": "string"
+                    },
+                    "python": {
+                      "type": "boolean"
+                    },
+                    "gpu": {
+                      "type": "boolean"
+                    },
+                    "slurm": {
+                      "type": "boolean"
+                    },
+                    "pbs": {
+                      "type": "boolean"
+                    },
+                    "error": {
+                      "type": "string"
+                    }
+                  },
+                  "required": [
+                    "ok",
+                    "host",
+                    "latency_ms",
+                    "python",
+                    "gpu",
+                    "slurm",
+                    "pbs"
+                  ]
+                }
+              }
+            }
+          },
+          "404": {
+            "description": "Not found",
+            "content": {
+              "application/json": {
+                "schema": {
+                  "$ref": "#/components/schemas/NotFoundError"
+                }
+              }
+            }
+          }
+        },
+        "parameters": [
+          {
+            "in": "path",
+            "name": "id",
+            "schema": {
+              "type": "string"
+            },
+            "required": true
+          }
+        ],
+        "x-codeSamples": [
+          {
+            "lang": "js",
+            "source": "import { createOpenScienceClient } from \"@synsci/sdk\"\n\nconst client = createOpenScienceClient()\nawait client.settings.compute.ssh.test({\n  ...\n})"
+          }
+        ]
+      }
+    },
     "/settings/compute/ssh/{id}": {
       "delete": {
         "operationId": "settings.compute.ssh.remove",
@@ -2112,6 +2255,18 @@
                             "type": "integer",
                             "exclusiveMinimum": 0,
                             "maximum": 9007199254740991
+                          },
+                          "scheduler": {
+                            "default": "none",
+                            "type": "string",
+                            "enum": [
+                              "none",
+                              "slurm",
+                              "pbs"
+                            ]
+                          },
+                          "workdir": {
+                            "type": "string"
                           }
                         },
                         "required": [
@@ -2267,6 +2422,18 @@
                             "type": "integer",
                             "exclusiveMinimum": 0,
                             "maximum": 9007199254740991
+                          },
+                          "scheduler": {
+                            "default": "none",
+                            "type": "string",
+                            "enum": [
+                              "none",
+                              "slurm",
+                              "pbs"
+                            ]
+                          },
+                          "workdir": {
+                            "type": "string"
                           }
                         },
                         "required": [
@@ -2357,143 +2524,726 @@
         "x-codeSamples": [
           {
             "lang": "js",
-            "source": "import { createOpenScienceClient } from \"@synsci/sdk\"\n\nconst client = createOpenScienceClient()\nawait client.settings.compute.endpoint.add({\n  ...\n})"
+            "source": "import { createOpenScienceClient } from \"@synsci/sdk\"\n\nconst client = createOpenScienceClient()\nawait client.settings.compute.endpoint.add({\n  ...\n})"
+          }
+        ]
+      }
+    },
+    "/settings/compute/endpoint/{id}": {
+      "delete": {
+        "operationId": "settings.compute.endpoint.remove",
+        "summary": "Remove model endpoint",
+        "responses": {
+          "200": {
+            "description": "Updated",
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "object",
+                  "properties": {
+                    "providers": {
+                      "default": [],
+                      "type": "array",
+                      "items": {
+                        "type": "object",
+                        "properties": {
+                          "id": {
+                            "type": "string"
+                          },
+                          "name": {
+                            "type": "string"
+                          },
+                          "verified": {
+                            "type": "boolean"
+                          },
+                          "placeholder": {
+                            "type": "string"
+                          },
+                          "hint": {
+                            "type": "string"
+                          },
+                          "connected": {
+                            "type": "boolean"
+                          },
+                          "connected_at": {
+                            "anyOf": [
+                              {
+                                "type": "string"
+                              },
+                              {
+                                "type": "null"
+                              }
+                            ]
+                          },
+                          "last_used": {
+                            "anyOf": [
+                              {
+                                "type": "string"
+                              },
+                              {
+                                "type": "null"
+                              }
+                            ]
+                          }
+                        },
+                        "required": [
+                          "id",
+                          "name",
+                          "verified",
+                          "placeholder",
+                          "hint",
+                          "connected",
+                          "connected_at",
+                          "last_used"
+                        ]
+                      }
+                    },
+                    "ssh_hosts": {
+                      "default": [],
+                      "type": "array",
+                      "items": {
+                        "type": "object",
+                        "properties": {
+                          "id": {
+                            "type": "string"
+                          },
+                          "label": {
+                            "type": "string"
+                          },
+                          "host": {
+                            "type": "string"
+                          },
+                          "user": {
+                            "type": "string"
+                          },
+                          "port": {
+                            "type": "integer",
+                            "exclusiveMinimum": 0,
+                            "maximum": 9007199254740991
+                          },
+                          "scheduler": {
+                            "default": "none",
+                            "type": "string",
+                            "enum": [
+                              "none",
+                              "slurm",
+                              "pbs"
+                            ]
+                          },
+                          "workdir": {
+                            "type": "string"
+                          }
+                        },
+                        "required": [
+                          "id",
+                          "label",
+                          "host"
+                        ]
+                      }
+                    },
+                    "endpoints": {
+                      "default": [],
+                      "type": "array",
+                      "items": {
+                        "type": "object",
+                        "properties": {
+                          "id": {
+                            "type": "string"
+                          },
+                          "label": {
+                            "type": "string"
+                          },
+                          "url": {
+                            "type": "string"
+                          },
+                          "kind": {
+                            "type": "string",
+                            "enum": [
+                              "local",
+                              "remote"
+                            ]
+                          }
+                        },
+                        "required": [
+                          "id",
+                          "label",
+                          "url",
+                          "kind"
+                        ]
+                      }
+                    }
+                  }
+                }
+              }
+            }
+          }
+        },
+        "parameters": [
+          {
+            "in": "path",
+            "name": "id",
+            "schema": {
+              "type": "string"
+            },
+            "required": true
+          }
+        ],
+        "x-codeSamples": [
+          {
+            "lang": "js",
+            "source": "import { createOpenScienceClient } from \"@synsci/sdk\"\n\nconst client = createOpenScienceClient()\nawait client.settings.compute.endpoint.remove({\n  ...\n})"
+          }
+        ]
+      }
+    },
+    "/settings/compute/jobs": {
+      "get": {
+        "operationId": "settings.compute.jobs.list",
+        "summary": "List local and remote compute jobs",
+        "responses": {
+          "200": {
+            "description": "Compute jobs",
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "type": "object",
+                    "properties": {
+                      "id": {
+                        "type": "string"
+                      },
+                      "name": {
+                        "type": "string"
+                      },
+                      "command": {
+                        "type": "string"
+                      },
+                      "cwd": {
+                        "type": "string"
+                      },
+                      "target": {
+                        "anyOf": [
+                          {
+                            "type": "object",
+                            "properties": {
+                              "kind": {
+                                "type": "string",
+                                "const": "local"
+                              }
+                            },
+                            "required": [
+                              "kind"
+                            ]
+                          },
+                          {
+                            "type": "object",
+                            "properties": {
+                              "kind": {
+                                "type": "string",
+                                "const": "ssh"
+                              },
+                              "host_id": {
+                                "type": "string"
+                              }
+                            },
+                            "required": [
+                              "kind",
+                              "host_id"
+                            ]
+                          }
+                        ]
+                      },
+                      "target_label": {
+                        "type": "string"
+                      },
+                      "scheduler": {
+                        "type": "string",
+                        "enum": [
+                          "none",
+                          "slurm",
+                          "pbs"
+                        ]
+                      },
+                      "status": {
+                        "type": "string",
+                        "enum": [
+                          "queued",
+                          "running",
+                          "succeeded",
+                          "failed",
+                          "cancelled",
+                          "interrupted"
+                        ]
+                      },
+                      "created_at": {
+                        "type": "string"
+                      },
+                      "started_at": {
+                        "type": "string"
+                      },
+                      "completed_at": {
+                        "type": "string"
+                      },
+                      "exit_code": {
+                        "anyOf": [
+                          {
+                            "type": "integer",
+                            "minimum": -9007199254740991,
+                            "maximum": 9007199254740991
+                          },
+                          {
+                            "type": "null"
+                          }
+                        ]
+                      },
+                      "pid": {
+                        "type": "integer",
+                        "exclusiveMinimum": 0,
+                        "maximum": 9007199254740991
+                      },
+                      "error": {
+                        "type": "string"
+                      }
+                    },
+                    "required": [
+                      "id",
+                      "name",
+                      "command",
+                      "target",
+                      "target_label",
+                      "scheduler",
+                      "status",
+                      "created_at"
+                    ]
+                  }
+                }
+              }
+            }
+          }
+        },
+        "x-codeSamples": [
+          {
+            "lang": "js",
+            "source": "import { createOpenScienceClient } from \"@synsci/sdk\"\n\nconst client = createOpenScienceClient()\nawait client.settings.compute.jobs.list({\n  ...\n})"
+          }
+        ]
+      },
+      "post": {
+        "operationId": "settings.compute.jobs.start",
+        "summary": "Start a local, SSH, Slurm, or PBS compute job",
+        "responses": {
+          "200": {
+            "description": "Started job",
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "object",
+                  "properties": {
+                    "id": {
+                      "type": "string"
+                    },
+                    "name": {
+                      "type": "string"
+                    },
+                    "command": {
+                      "type": "string"
+                    },
+                    "cwd": {
+                      "type": "string"
+                    },
+                    "target": {
+                      "anyOf": [
+                        {
+                          "type": "object",
+                          "properties": {
+                            "kind": {
+                              "type": "string",
+                              "const": "local"
+                            }
+                          },
+                          "required": [
+                            "kind"
+                          ]
+                        },
+                        {
+                          "type": "object",
+                          "properties": {
+                            "kind": {
+                              "type": "string",
+                              "const": "ssh"
+                            },
+                            "host_id": {
+                              "type": "string"
+                            }
+                          },
+                          "required": [
+                            "kind",
+                            "host_id"
+                          ]
+                        }
+                      ]
+                    },
+                    "target_label": {
+                      "type": "string"
+                    },
+                    "scheduler": {
+                      "type": "string",
+                      "enum": [
+                        "none",
+                        "slurm",
+                        "pbs"
+                      ]
+                    },
+                    "status": {
+                      "type": "string",
+                      "enum": [
+                        "queued",
+                        "running",
+                        "succeeded",
+                        "failed",
+                        "cancelled",
+                        "interrupted"
+                      ]
+                    },
+                    "created_at": {
+                      "type": "string"
+                    },
+                    "started_at": {
+                      "type": "string"
+                    },
+                    "completed_at": {
+                      "type": "string"
+                    },
+                    "exit_code": {
+                      "anyOf": [
+                        {
+                          "type": "integer",
+                          "minimum": -9007199254740991,
+                          "maximum": 9007199254740991
+                        },
+                        {
+                          "type": "null"
+                        }
+                      ]
+                    },
+                    "pid": {
+                      "type": "integer",
+                      "exclusiveMinimum": 0,
+                      "maximum": 9007199254740991
+                    },
+                    "error": {
+                      "type": "string"
+                    }
+                  },
+                  "required": [
+                    "id",
+                    "name",
+                    "command",
+                    "target",
+                    "target_label",
+                    "scheduler",
+                    "status",
+                    "created_at"
+                  ]
+                }
+              }
+            }
+          },
+          "400": {
+            "description": "Bad request",
+            "content": {
+              "application/json": {
+                "schema": {
+                  "$ref": "#/components/schemas/BadRequestError"
+                }
+              }
+            }
+          }
+        },
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "type": "object",
+                "properties": {
+                  "name": {
+                    "type": "string",
+                    "minLength": 1,
+                    "maxLength": 120
+                  },
+                  "command": {
+                    "type": "string",
+                    "minLength": 1,
+                    "maxLength": 100000
+                  },
+                  "cwd": {
+                    "type": "string"
+                  },
+                  "target": {
+                    "anyOf": [
+                      {
+                        "type": "object",
+                        "properties": {
+                          "kind": {
+                            "type": "string",
+                            "const": "local"
+                          }
+                        },
+                        "required": [
+                          "kind"
+                        ]
+                      },
+                      {
+                        "type": "object",
+                        "properties": {
+                          "kind": {
+                            "type": "string",
+                            "const": "ssh"
+                          },
+                          "host_id": {
+                            "type": "string"
+                          }
+                        },
+                        "required": [
+                          "kind",
+                          "host_id"
+                        ]
+                      }
+                    ]
+                  }
+                },
+                "required": [
+                  "name",
+                  "command",
+                  "target"
+                ]
+              }
+            }
+          }
+        },
+        "x-codeSamples": [
+          {
+            "lang": "js",
+            "source": "import { createOpenScienceClient } from \"@synsci/sdk\"\n\nconst client = createOpenScienceClient()\nawait client.settings.compute.jobs.start({\n  ...\n})"
+          }
+        ]
+      }
+    },
+    "/settings/compute/jobs/completed": {
+      "delete": {
+        "operationId": "settings.compute.jobs.clear",
+        "summary": "Clear completed compute jobs",
+        "responses": {
+          "200": {
+            "description": "Number cleared",
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "object",
+                  "properties": {
+                    "cleared": {
+                      "type": "integer",
+                      "minimum": 0,
+                      "maximum": 9007199254740991
+                    }
+                  },
+                  "required": [
+                    "cleared"
+                  ]
+                }
+              }
+            }
+          }
+        },
+        "x-codeSamples": [
+          {
+            "lang": "js",
+            "source": "import { createOpenScienceClient } from \"@synsci/sdk\"\n\nconst client = createOpenScienceClient()\nawait client.settings.compute.jobs.clear({\n  ...\n})"
+          }
+        ]
+      }
+    },
+    "/settings/compute/jobs/{id}/log": {
+      "get": {
+        "operationId": "settings.compute.jobs.log",
+        "summary": "Read a compute job log",
+        "responses": {
+          "200": {
+            "description": "Job output",
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "object",
+                  "properties": {
+                    "log": {
+                      "type": "string"
+                    }
+                  },
+                  "required": [
+                    "log"
+                  ]
+                }
+              }
+            }
+          },
+          "404": {
+            "description": "Not found",
+            "content": {
+              "application/json": {
+                "schema": {
+                  "$ref": "#/components/schemas/NotFoundError"
+                }
+              }
+            }
+          }
+        },
+        "parameters": [
+          {
+            "in": "path",
+            "name": "id",
+            "schema": {
+              "type": "string"
+            },
+            "required": true
+          }
+        ],
+        "x-codeSamples": [
+          {
+            "lang": "js",
+            "source": "import { createOpenScienceClient } from \"@synsci/sdk\"\n\nconst client = createOpenScienceClient()\nawait client.settings.compute.jobs.log({\n  ...\n})"
           }
         ]
       }
     },
-    "/settings/compute/endpoint/{id}": {
-      "delete": {
-        "operationId": "settings.compute.endpoint.remove",
-        "summary": "Remove model endpoint",
+    "/settings/compute/jobs/{id}/cancel": {
+      "post": {
+        "operationId": "settings.compute.jobs.cancel",
+        "summary": "Cancel a compute job",
         "responses": {
           "200": {
-            "description": "Updated",
+            "description": "Cancelled job",
             "content": {
               "application/json": {
                 "schema": {
                   "type": "object",
                   "properties": {
-                    "providers": {
-                      "default": [],
-                      "type": "array",
-                      "items": {
-                        "type": "object",
-                        "properties": {
-                          "id": {
-                            "type": "string"
-                          },
-                          "name": {
-                            "type": "string"
-                          },
-                          "verified": {
-                            "type": "boolean"
-                          },
-                          "placeholder": {
-                            "type": "string"
-                          },
-                          "hint": {
-                            "type": "string"
-                          },
-                          "connected": {
-                            "type": "boolean"
-                          },
-                          "connected_at": {
-                            "anyOf": [
-                              {
-                                "type": "string"
-                              },
-                              {
-                                "type": "null"
-                              }
-                            ]
-                          },
-                          "last_used": {
-                            "anyOf": [
-                              {
-                                "type": "string"
-                              },
-                              {
-                                "type": "null"
-                              }
-                            ]
-                          }
-                        },
-                        "required": [
-                          "id",
-                          "name",
-                          "verified",
-                          "placeholder",
-                          "hint",
-                          "connected",
-                          "connected_at",
-                          "last_used"
-                        ]
-                      }
+                    "id": {
+                      "type": "string"
                     },
-                    "ssh_hosts": {
-                      "default": [],
-                      "type": "array",
-                      "items": {
-                        "type": "object",
-                        "properties": {
-                          "id": {
-                            "type": "string"
-                          },
-                          "label": {
-                            "type": "string"
-                          },
-                          "host": {
-                            "type": "string"
-                          },
-                          "user": {
-                            "type": "string"
-                          },
-                          "port": {
-                            "type": "integer",
-                            "exclusiveMinimum": 0,
-                            "maximum": 9007199254740991
-                          }
-                        },
-                        "required": [
-                          "id",
-                          "label",
-                          "host"
-                        ]
-                      }
+                    "name": {
+                      "type": "string"
                     },
-                    "endpoints": {
-                      "default": [],
-                      "type": "array",
-                      "items": {
-                        "type": "object",
-                        "properties": {
-                          "id": {
-                            "type": "string"
-                          },
-                          "label": {
-                            "type": "string"
+                    "command": {
+                      "type": "string"
+                    },
+                    "cwd": {
+                      "type": "string"
+                    },
+                    "target": {
+                      "anyOf": [
+                        {
+                          "type": "object",
+                          "properties": {
+                            "kind": {
+                              "type": "string",
+                              "const": "local"
+                            }
                           },
-                          "url": {
-                            "type": "string"
+                          "required": [
+                            "kind"
+                          ]
+                        },
+                        {
+                          "type": "object",
+                          "properties": {
+                            "kind": {
+                              "type": "string",
+                              "const": "ssh"
+                            },
+                            "host_id": {
+                              "type": "string"
+                            }
                           },
-                          "kind": {
-                            "type": "string",
-                            "enum": [
-                              "local",
-                              "remote"
-                            ]
-                          }
+                          "required": [
+                            "kind",
+                            "host_id"
+                          ]
+                        }
+                      ]
+                    },
+                    "target_label": {
+                      "type": "string"
+                    },
+                    "scheduler": {
+                      "type": "string",
+                      "enum": [
+                        "none",
+                        "slurm",
+                        "pbs"
+                      ]
+                    },
+                    "status": {
+                      "type": "string",
+                      "enum": [
+                        "queued",
+                        "running",
+                        "succeeded",
+                        "failed",
+                        "cancelled",
+                        "interrupted"
+                      ]
+                    },
+                    "created_at": {
+                      "type": "string"
+                    },
+                    "started_at": {
+                      "type": "string"
+                    },
+                    "completed_at": {
+                      "type": "string"
+                    },
+                    "exit_code": {
+                      "anyOf": [
+                        {
+                          "type": "integer",
+                          "minimum": -9007199254740991,
+                          "maximum": 9007199254740991
                         },
-                        "required": [
-                          "id",
-                          "label",
-                          "url",
-                          "kind"
-                        ]
-                      }
+                        {
+                          "type": "null"
+                        }
+                      ]
+                    },
+                    "pid": {
+                      "type": "integer",
+                      "exclusiveMinimum": 0,
+                      "maximum": 9007199254740991
+                    },
+                    "error": {
+                      "type": "string"
                     }
-                  }
+                  },
+                  "required": [
+                    "id",
+                    "name",
+                    "command",
+                    "target",
+                    "target_label",
+                    "scheduler",
+                    "status",
+                    "created_at"
+                  ]
+                }
+              }
+            }
+          },
+          "404": {
+            "description": "Not found",
+            "content": {
+              "application/json": {
+                "schema": {
+                  "$ref": "#/components/schemas/NotFoundError"
                 }
               }
             }
@@ -2512,7 +3262,7 @@
         "x-codeSamples": [
           {
             "lang": "js",
-            "source": "import { createOpenScienceClient } from \"@synsci/sdk\"\n\nconst client = createOpenScienceClient()\nawait client.settings.compute.endpoint.remove({\n  ...\n})"
+            "source": "import { createOpenScienceClient } from \"@synsci/sdk\"\n\nconst client = createOpenScienceClient()\nawait client.settings.compute.jobs.cancel({\n  ...\n})"
           }
         ]
       }
@@ -14725,6 +15475,30 @@
           "success"
         ]
       },
+      "NotFoundError": {
+        "type": "object",
+        "properties": {
+          "name": {
+            "type": "string",
+            "const": "NotFoundError"
+          },
+          "data": {
+            "type": "object",
+            "properties": {
+              "message": {
+                "type": "string"
+              }
+            },
+            "required": [
+              "message"
+            ]
+          }
+        },
+        "required": [
+          "name",
+          "data"
+        ]
+      },
       "OAuth": {
         "type": "object",
         "properties": {
@@ -14804,30 +15578,6 @@
           }
         ]
       },
-      "NotFoundError": {
-        "type": "object",
-        "properties": {
-          "name": {
-            "type": "string",
-            "const": "NotFoundError"
-          },
-          "data": {
-            "type": "object",
-            "properties": {
-              "message": {
-                "type": "string"
-              }
-            },
-            "required": [
-              "message"
-            ]
-          }
-        },
-        "required": [
-          "name",
-          "data"
-        ]
-      },
       "Model": {
         "type": "object",
         "properties": {

From 7187e6e6ffa849f17df2736a769f146e276c7ea1 Mon Sep 17 00:00:00 2001
From: Aayam Bansal <aayambansal@gmail.com>
Date: Wed, 29 Jul 2026 07:06:36 +0800
Subject: [PATCH 12/40] feat: add resilient workspace recovery

---
 .../workspace/e2e/server-recovery.spec.ts     |  39 ++++
 .../workspace/src/atlas/DisconnectedPanel.tsx |  28 ++-
 frontend/workspace/src/context/server.tsx     |  31 ++-
 frontend/workspace/src/pages/error.tsx        | 220 ++++++++++++++----
 4 files changed, 271 insertions(+), 47 deletions(-)
 create mode 100644 frontend/workspace/e2e/server-recovery.spec.ts

diff --git a/frontend/workspace/e2e/server-recovery.spec.ts b/frontend/workspace/e2e/server-recovery.spec.ts
new file mode 100644
index 00000000..0702e13c
--- /dev/null
+++ b/frontend/workspace/e2e/server-recovery.spec.ts
@@ -0,0 +1,39 @@
+import { expect, test } from "./fixtures"
+
+test("retries a failed server health check immediately and clears the recovery banner", async ({ page, gotoSession }) => {
+  let available = false
+  await page.route("**/global/health", async (route) => {
+    if (!available) {
+      await route.abort("connectionfailed")
+      return
+    }
+    await route.fulfill({
+      status: 200,
+      contentType: "application/json",
+      body: JSON.stringify({ healthy: true, version: "e2e" }),
+    })
+  })
+
+  await gotoSession()
+  const recovery = page.getByRole("alert", { name: "Server connection lost" })
+  await expect(recovery).toBeVisible()
+
+  available = true
+  await recovery.getByRole("button", { name: "retry now" }).click()
+  await expect(recovery).toHaveCount(0)
+})
+
+test("reconnects the global event stream after the server connection drops", async ({ page, gotoSession }) => {
+  let requests = 0
+  await page.route("**/global/event", async (route) => {
+    requests += 1
+    if (requests === 1) {
+      await route.abort("connectionfailed")
+      return
+    }
+    await route.continue()
+  })
+
+  await gotoSession()
+  await expect.poll(() => requests, { timeout: 10_000 }).toBeGreaterThan(1)
+})
diff --git a/frontend/workspace/src/atlas/DisconnectedPanel.tsx b/frontend/workspace/src/atlas/DisconnectedPanel.tsx
index da284af2..4004c246 100644
--- a/frontend/workspace/src/atlas/DisconnectedPanel.tsx
+++ b/frontend/workspace/src/atlas/DisconnectedPanel.tsx
@@ -17,6 +17,8 @@ export function DisconnectedPanel(): JSX.Element {
   return (
     <Show when={server.healthy() === false}>
       <div
+        role="alert"
+        aria-label="Server connection lost"
         style={{
           display: "flex",
           "align-items": "center",
@@ -52,9 +54,33 @@ export function DisconnectedPanel(): JSX.Element {
               "white-space": "nowrap",
             }}
           >
-            {server.name} · start it with <code>openscience web</code> or switch servers · retrying…
+            {server.name} ·{" "}
+            <Show when={server.isLocal()} fallback="check the server URL or switch servers">
+              start it with <code>openscience serve</code>
+            </Show>
+            <Show when={server.failures() > 1}> · {server.failures()} failed checks</Show>
           </div>
         </div>
+        <button
+          type="button"
+          disabled={server.checking()}
+          onClick={() => void server.refresh()}
+          style={{
+            all: "unset",
+            cursor: server.checking() ? "wait" : "pointer",
+            padding: "6px 12px",
+            "border-radius": "4px",
+            border: "1px solid var(--color-error, #ef4444)",
+            background: "var(--color-error, #ef4444)",
+            "font-family": FONT_MONO,
+            "font-size": "11px",
+            color: "white",
+            opacity: server.checking() ? 0.7 : 1,
+            "flex-shrink": 0,
+          }}
+        >
+          {server.checking() ? "checking…" : "retry now"}
+        </button>
         <button
           type="button"
           onClick={() => dialog.show(() => <DialogSelectServer />)}
diff --git a/frontend/workspace/src/context/server.tsx b/frontend/workspace/src/context/server.tsx
index e3bb0ee5..36c5a8f5 100644
--- a/frontend/workspace/src/context/server.tsx
+++ b/frontend/workspace/src/context/server.tsx
@@ -43,9 +43,13 @@ export const { use: useServer, provider: ServerProvider } = createSimpleContext(
     const [state, setState] = createStore({
       active: "",
       healthy: undefined as boolean | undefined,
+      checking: false,
+      failures: 0,
     })
 
     const healthy = () => state.healthy
+    const checking = () => state.checking
+    const failures = () => state.failures
 
     function setActive(input: string) {
       const url = normalizeServerUrl(input)
@@ -107,11 +111,28 @@ export const { use: useServer, provider: ServerProvider } = createSimpleContext(
         .catch(() => false)
     }
 
+    const refresh = async (target = state.active) => {
+      if (!target) return false
+      setState("checking", true)
+      const next = await check(target)
+      if (state.active !== target) return next
+      batch(() => {
+        setState("healthy", next)
+        setState("checking", false)
+        setState("failures", next ? 0 : state.failures + 1)
+      })
+      return next
+    }
+
     createEffect(() => {
       const url = state.active
       if (!url) return
 
-      setState("healthy", undefined)
+      batch(() => {
+        setState("healthy", undefined)
+        setState("checking", false)
+        setState("failures", 0)
+      })
 
       let alive = true
       let busy = false
@@ -124,10 +145,9 @@ export const { use: useServer, provider: ServerProvider } = createSimpleContext(
         // on a health check nobody can see; we refresh immediately on refocus.
         if (busy || hidden()) return
         busy = true
-        void check(url)
-          .then((next) => {
+        void refresh(url)
+          .then(() => {
             if (!alive) return
-            setState("healthy", next)
           })
           .finally(() => {
             busy = false
@@ -171,6 +191,9 @@ export const { use: useServer, provider: ServerProvider } = createSimpleContext(
     return {
       ready: isReady,
       healthy,
+      checking,
+      failures,
+      refresh,
       isLocal,
       get url() {
         return state.active
diff --git a/frontend/workspace/src/pages/error.tsx b/frontend/workspace/src/pages/error.tsx
index 9eabd875..564765a3 100644
--- a/frontend/workspace/src/pages/error.tsx
+++ b/frontend/workspace/src/pages/error.tsx
@@ -1,11 +1,10 @@
-import { TextField } from "@synsci/ui/text-field"
 import { Button } from "@synsci/ui/button"
-import { Component, Show } from "solid-js"
+import { Component, Show, createSignal } from "solid-js"
 import { createStore } from "solid-js/store"
 import { usePlatform } from "@/context/platform"
 import { useLanguage } from "@/context/language"
-import { Icon } from "@synsci/ui/icon"
-import { FONT_SANS } from "@/styles/tokens"
+import { FONT_MONO, FONT_SANS } from "@/styles/tokens"
+import { IconAlertCircle, IconCopy, IconRefresh } from "@/atlas/shared/Icon"
 
 export type InitError = {
   name: string
@@ -209,6 +208,7 @@ interface ErrorPageProps {
 export const ErrorPage: Component<ErrorPageProps> = (props) => {
   const platform = usePlatform()
   const language = useLanguage()
+  const [copied, setCopied] = createSignal(false)
   const [store, setStore] = createStore({
     checking: false,
     version: undefined as string | undefined,
@@ -228,66 +228,202 @@ export const ErrorPage: Component<ErrorPageProps> = (props) => {
     await platform.restart()
   }
 
+  const detail = () => formatError(props.error, language.t)
+  const hint = () => {
+    const text = detail().toLowerCase()
+    if (text.includes("providerauth") || text.includes("unauthorized") || text.includes("401")) {
+      return "A model provider rejected its credentials. Reload first; if it returns, reconnect that provider in Settings."
+    }
+    if (text.includes("config") || text.includes("json")) {
+      return "OpenScience could not read part of its configuration. The technical details below identify the file to repair."
+    }
+    if (text.includes("fetch") || text.includes("network") || text.includes("connection")) {
+      return "The app lost contact with its server. Make sure the local server is running, then reload."
+    }
+    return "Reloading usually restores the workspace without losing project files or saved conversations."
+  }
+  const diagnostics = () =>
+    [
+      "OpenScience diagnostic",
+      `time: ${new Date().toISOString()}`,
+      `version: ${platform.version ?? "unknown"}`,
+      `platform: ${platform.platform}${platform.os ? `/${platform.os}` : ""}`,
+      `url: ${typeof location === "undefined" ? "unknown" : location.href}`,
+      "",
+      detail(),
+    ].join("\n")
+  const copy = async () => {
+    await navigator.clipboard?.writeText(diagnostics())
+    setCopied(true)
+  }
+
   return (
     <div
-      class="relative flex-1 h-screen w-screen min-h-0 flex flex-col items-center justify-center bg-background-base font-sans"
-      style={{ "font-family": FONT_SANS }}
+      class="relative flex-1 h-screen w-screen min-h-0 flex flex-col items-center justify-center bg-background-base"
+      style={{
+        "font-family": FONT_SANS,
+        padding: "32px",
+        background:
+          "radial-gradient(circle at 50% 25%, color-mix(in srgb, var(--color-danger) 6%, transparent), transparent 34%), var(--color-bg)",
+      }}
     >
-      <div class="w-2/3 max-w-3xl flex flex-col items-center justify-center gap-8">
-        <div class="text-24-medium text-text-strong tracking-tight opacity-50 shrink-0">OpenScience</div>
-        <div class="flex flex-col items-center gap-2 text-center">
-          <h1 class="text-lg font-medium text-text-strong">{language.t("error.page.title")}</h1>
-          <p class="text-sm text-text-weak">{language.t("error.page.description")}</p>
+      <main
+        style={{
+          width: "min(100%, 720px)",
+          display: "flex",
+          "flex-direction": "column",
+          gap: "24px",
+          padding: "30px",
+          border: "1px solid var(--color-border)",
+          "border-radius": "10px",
+          background: "var(--color-surface-solid)",
+          "box-shadow": "var(--shadow-lg)",
+        }}
+      >
+        <div style={{ display: "flex", "align-items": "flex-start", gap: "16px" }}>
+          <span
+            style={{
+              width: "40px",
+              height: "40px",
+              display: "inline-flex",
+              "align-items": "center",
+              "justify-content": "center",
+              "border-radius": "10px",
+              background: "color-mix(in srgb, var(--color-danger) 10%, transparent)",
+              color: "var(--color-danger)",
+              "flex-shrink": 0,
+            }}
+          >
+            <IconAlertCircle size={20} strokeWidth={1.6} />
+          </span>
+          <div style={{ display: "flex", "flex-direction": "column", gap: "8px", "min-width": 0 }}>
+            <span
+              style={{
+                "font-family": FONT_MONO,
+                "font-size": "10px",
+                color: "var(--color-text-faint)",
+                "letter-spacing": "0.12em",
+                "text-transform": "uppercase",
+              }}
+            >
+              workspace recovery
+            </span>
+            <h1
+              style={{
+                margin: 0,
+                color: "var(--color-text)",
+                "font-size": "24px",
+                "font-weight": 680,
+                "letter-spacing": "-0.025em",
+              }}
+            >
+              OpenScience hit a problem
+            </h1>
+            <p style={{ margin: 0, color: "var(--color-text-muted)", "font-size": "13px", "line-height": 1.6 }}>
+              {hint()}
+            </p>
+          </div>
         </div>
-        <TextField
-          value={formatError(props.error, language.t)}
-          readOnly
-          copyable
-          multiline
-          class="max-h-96 w-full font-mono text-xs no-scrollbar"
-          label={language.t("error.page.details.label")}
-          hideLabel
-        />
-        <div class="flex items-center gap-3">
-          <Button size="large" onClick={platform.restart}>
-            {language.t("error.page.action.restart")}
+
+        <div style={{ display: "flex", "align-items": "center", "flex-wrap": "wrap", gap: "8px" }}>
+          <Button size="large" onClick={() => void platform.restart()}>
+            <span style={{ display: "inline-flex", "align-items": "center", gap: "7px" }}>
+              <IconRefresh size={13} />
+              {platform.platform === "desktop" ? "restart app" : "reload app"}
+            </span>
+          </Button>
+          <Button size="large" variant="secondary" onClick={() => void copy()}>
+            <span style={{ display: "inline-flex", "align-items": "center", gap: "7px" }}>
+              <IconCopy size={13} />
+              {copied() ? "diagnostic copied" : "copy diagnostic"}
+            </span>
           </Button>
           <Show when={platform.checkUpdate}>
             <Show
               when={store.version}
               fallback={
                 <Button size="large" variant="ghost" onClick={checkForUpdates} disabled={store.checking}>
-                  {store.checking
-                    ? language.t("error.page.action.checking")
-                    : language.t("error.page.action.checkUpdates")}
+                  {store.checking ? "checking…" : "check for updates"}
                 </Button>
               }
             >
               <Button size="large" onClick={installUpdate}>
-                {language.t("error.page.action.updateTo", { version: store.version ?? "" })}
+                update to {store.version}
               </Button>
             </Show>
           </Show>
         </div>
-        <div class="flex flex-col items-center gap-2">
-          <div class="flex items-center justify-center gap-1">
-            {language.t("error.page.report.prefix")}
+
+        <details
+          style={{
+            border: "1px solid var(--color-border)",
+            "border-radius": "6px",
+            background: "var(--color-bg-subtle)",
+            overflow: "hidden",
+          }}
+        >
+          <summary
+            style={{
+              cursor: "pointer",
+              padding: "11px 13px",
+              color: "var(--color-text-muted)",
+              "font-family": FONT_MONO,
+              "font-size": "10px",
+              "user-select": "none",
+            }}
+          >
+            technical details
+          </summary>
+          <pre
+            style={{
+              margin: 0,
+              padding: "13px",
+              "max-height": "260px",
+              overflow: "auto",
+              "border-top": "1px solid var(--color-border)",
+              background: "var(--color-bg)",
+              color: "var(--color-text-muted)",
+              "font-family": FONT_MONO,
+              "font-size": "10px",
+              "line-height": 1.55,
+              "white-space": "pre-wrap",
+              "overflow-wrap": "anywhere",
+            }}
+          >
+            {detail()}
+          </pre>
+        </details>
+
+        <footer
+          style={{
+            display: "flex",
+            "align-items": "center",
+            "justify-content": "space-between",
+            gap: "16px",
+            color: "var(--color-text-faint)",
+            "font-family": FONT_MONO,
+            "font-size": "10px",
+          }}
+        >
+          <span>OpenScience {platform.version ?? "development build"}</span>
+          <span style={{ display: "inline-flex", "align-items": "center", gap: "5px" }}>
+            Still stuck?
             <button
               type="button"
-              class="flex items-center text-text-interactive-base gap-1"
-              onClick={() => platform.openLink("https://github.com/synthetic-sciences/OpenScience/issues")}
+              onClick={() => platform.openLink("https://github.com/synthetic-sciences/openscience/issues/new")}
+              style={{
+                all: "unset",
+                cursor: "pointer",
+                color: "var(--color-accent)",
+                "text-decoration": "underline",
+                "text-underline-offset": "3px",
+              }}
             >
-              <div>{language.t("error.page.report.discord")}</div>
-              <Icon name="discord" class="text-text-interactive-base" />
+              report this issue
             </button>
-          </div>
-          <Show when={platform.version}>
-            {(version) => (
-              <p class="text-xs text-text-weak">{language.t("error.page.version", { version: version() })}</p>
-            )}
-          </Show>
-        </div>
-      </div>
+          </span>
+        </footer>
+      </main>
     </div>
   )
 }

From 4d0c744ac63400b88a2afbd8f9c7dfa87d90d549 Mon Sep 17 00:00:00 2001
From: Aayam Bansal <aayambansal@gmail.com>
Date: Wed, 29 Jul 2026 07:27:41 +0800
Subject: [PATCH 13/40] feat: add reproducible research workbench

---
 backend/cli/src/compute/jobs.ts               |  276 ++++-
 backend/cli/src/file/science.ts               |   62 +
 backend/cli/src/science/provenance/review.ts  |    2 +
 backend/cli/src/science/provenance/store.ts   |   89 +-
 backend/cli/src/server/routes/provenance.ts   |  186 +++
 backend/cli/src/server/server.ts              |    2 +
 backend/cli/src/tool/provenance.ts            |   34 +-
 backend/cli/test/compute/jobs.test.ts         |   75 +-
 backend/cli/test/server/provenance.test.ts    |  139 +++
 frontend/workspace/e2e/binary-science.spec.ts |   61 +
 frontend/workspace/e2e/compute-jobs.spec.ts   |   48 +-
 frontend/workspace/e2e/evidence-graph.spec.ts |   52 +
 .../workspace/e2e/research-launchpad.spec.ts  |   10 +-
 frontend/workspace/src/atlas/ComputeJobs.tsx  |  453 +++++++-
 .../workspace/src/atlas/EvidenceGraph.tsx     |  793 +++++++++++++
 frontend/workspace/src/atlas/RightPane.tsx    |    6 +
 frontend/workspace/src/atlas/store/ui.ts      |    2 +-
 .../session/research-launchpad.test.ts        |   29 +-
 .../components/session/research-launchpad.ts  |  176 ++-
 .../components/session/session-new-view.tsx   |   41 +-
 .../src/science/formats/BinaryScienceView.tsx |  126 ++
 .../src/science/formats/binary.test.ts        |   26 +-
 .../workspace/src/science/formats/binary.ts   |   31 +
 frontend/workspace/src/styles/atlas.css       |   50 +
 tooling/sdk/js/src/v2/gen/sdk.gen.ts          |  193 ++++
 tooling/sdk/js/src/v2/gen/types.gen.ts        |  291 +++++
 tooling/sdk/openapi.json                      | 1018 ++++++++++++++++-
 27 files changed, 4206 insertions(+), 65 deletions(-)
 create mode 100644 backend/cli/src/server/routes/provenance.ts
 create mode 100644 backend/cli/test/server/provenance.test.ts
 create mode 100644 frontend/workspace/e2e/evidence-graph.spec.ts
 create mode 100644 frontend/workspace/src/atlas/EvidenceGraph.tsx

diff --git a/backend/cli/src/compute/jobs.ts b/backend/cli/src/compute/jobs.ts
index 4362a73a..e6e4b717 100644
--- a/backend/cli/src/compute/jobs.ts
+++ b/backend/cli/src/compute/jobs.ts
@@ -1,5 +1,6 @@
 import { spawn, type ChildProcess } from "node:child_process"
 import crypto from "node:crypto"
+import { createReadStream } from "node:fs"
 import fs from "node:fs/promises"
 import path from "node:path"
 import z from "zod"
@@ -41,11 +42,59 @@ export namespace ComputeJobs {
   ])
   export type Target = z.infer<typeof Target>
 
+  export const Resources = z.object({
+    cpus: z.number().int().min(1).max(1024).optional(),
+    gpus: z.number().int().min(0).max(128).optional(),
+    memory_gb: z.number().min(0.1).max(100_000).optional(),
+    time_minutes: z
+      .number()
+      .int()
+      .min(1)
+      .max(60 * 24 * 30)
+      .optional(),
+    partition: z.string().trim().min(1).max(120).optional(),
+  })
+  export type Resources = z.infer<typeof Resources>
+
+  export const Artifact = z.object({
+    path: z.string(),
+    size: z.number().int().nonnegative(),
+    sha256: z.string().regex(/^[a-f0-9]{64}$/),
+    modified_at: z.string(),
+  })
+  export type Artifact = z.infer<typeof Artifact>
+
+  export const Reproducibility = z.object({
+    captured_at: z.string(),
+    command: z.string(),
+    cwd: z.string(),
+    platform: z.string(),
+    arch: z.string(),
+    bun: z.string(),
+    node: z.string(),
+    python: z.string().optional(),
+    git: z
+      .object({
+        branch: z.string().optional(),
+        commit: z.string().optional(),
+        dirty: z.boolean(),
+      })
+      .optional(),
+    lockfiles: Artifact.array(),
+    resources: Resources.optional(),
+  })
+  export type Reproducibility = z.infer<typeof Reproducibility>
+
   export const Input = z.object({
     name: z.string().trim().min(1).max(120),
     command: z.string().trim().min(1).max(100_000),
     cwd: z.string().optional(),
     target: Target,
+    resources: Resources.optional(),
+    modules: z.array(z.string().trim().min(1).max(240)).max(64).optional(),
+    container: z.string().trim().min(1).max(2_000).optional(),
+    artifacts: z.array(z.string().trim().min(1).max(2_000)).max(100).optional(),
+    checkpoint: z.string().trim().min(1).max(2_000).optional(),
   })
   export type Input = z.infer<typeof Input>
 
@@ -67,6 +116,15 @@ export namespace ComputeJobs {
     exit_code: z.number().int().nullable().optional(),
     pid: z.number().int().positive().optional(),
     error: z.string().optional(),
+    resources: Resources.optional(),
+    modules: z.array(z.string()).optional(),
+    container: z.string().optional(),
+    artifact_patterns: z.array(z.string()).optional(),
+    artifacts: Artifact.array().optional(),
+    checkpoint_path: z.string().optional(),
+    checkpoint: Artifact.optional(),
+    reproducibility: Reproducibility.optional(),
+    capture_error: z.string().optional(),
   })
   export type Job = z.infer<typeof Job>
 
@@ -205,32 +263,100 @@ export namespace ComputeJobs {
     return clean || "job"
   }
 
-  function remote(input: { id: string; name: string; command: string; cwd?: string }, host: Host): string {
+  function clock(minutes: number): string {
+    const hours = Math.floor(minutes / 60)
+    const mins = minutes % 60
+    return `${String(hours).padStart(2, "0")}:${String(mins).padStart(2, "0")}:00`
+  }
+
+  function workload(input: { command: string; modules?: string[]; container?: string }): string {
+    const modules = input.modules?.length ? `module load ${input.modules.map(quote).join(" ")}` : undefined
+    const command = input.container
+      ? `apptainer exec ${quote(input.container)} bash -lc ${quote(input.command)}`
+      : input.command
+    return [modules, command].filter((part): part is string => !!part).join(" && ")
+  }
+
+  function slurm(input: { resources?: Resources }): string[] {
+    const resources = input.resources
+    if (!resources) return []
+    return [
+      resources.cpus ? `--cpus-per-task=${resources.cpus}` : undefined,
+      resources.gpus ? `--gres=gpu:${resources.gpus}` : undefined,
+      resources.memory_gb ? `--mem=${resources.memory_gb}G` : undefined,
+      resources.time_minutes ? `--time=${clock(resources.time_minutes)}` : undefined,
+      resources.partition ? `--partition=${quote(resources.partition)}` : undefined,
+    ].filter((part): part is string => !!part)
+  }
+
+  function pbs(input: { resources?: Resources }): string[] {
+    const resources = input.resources
+    if (!resources) return []
+    const select = [
+      "select=1",
+      resources.cpus ? `ncpus=${resources.cpus}` : undefined,
+      resources.gpus ? `ngpus=${resources.gpus}` : undefined,
+      resources.memory_gb ? `mem=${resources.memory_gb}gb` : undefined,
+    ]
+      .filter((part): part is string => !!part)
+      .join(":")
+    return [
+      select === "select=1" ? undefined : `-l ${quote(select)}`,
+      resources.time_minutes ? `-l ${quote(`walltime=${clock(resources.time_minutes)}`)}` : undefined,
+    ].filter((part): part is string => !!part)
+  }
+
+  function remote(
+    input: {
+      id: string
+      name: string
+      command: string
+      cwd?: string
+      resources?: Resources
+      modules?: string[]
+      container?: string
+    },
+    host: Host,
+  ): string {
     const cwd = input.cwd || host.workdir || "."
     const job = `os-${input.id}`
     const folder = `.openscience/jobs`
     const log = `${folder}/${input.id}.log`
     const enter = `cd ${quote(cwd)} && mkdir -p ${quote(folder)}`
+    const run = workload(input)
     if (host.scheduler === "slurm") {
       return [
         enter,
-        `sbatch --wait --parsable --job-name=${quote(job)} --output=${quote(log)} --error=${quote(log)} --wrap=${quote(input.command)}`,
+        [
+          "sbatch --wait --parsable",
+          `--job-name=${quote(job)}`,
+          `--output=${quote(log)}`,
+          `--error=${quote(log)}`,
+          ...slurm(input),
+          `--wrap=${quote(run)}`,
+        ].join(" "),
         "code=$?",
         `test -f ${quote(log)} && cat ${quote(log)}`,
         "exit $code",
       ].join("; ")
     }
     if (host.scheduler === "pbs") {
-      const script = `#!/usr/bin/env bash\nset -o pipefail\n${input.command}\n`
+      const script = `#!/usr/bin/env bash\nset -o pipefail\n${run}\n`
       return [
         enter,
-        `printf %s ${quote(script)} | qsub -W block=true -N ${quote(name(job))} -j oe -o ${quote(log)}`,
+        [
+          `printf %s ${quote(script)} | qsub -W block=true`,
+          `-N ${quote(name(job))}`,
+          "-j oe",
+          `-o ${quote(log)}`,
+          ...pbs(input),
+        ].join(" "),
         "code=$?",
         `test -f ${quote(log)} && cat ${quote(log)}`,
         "exit $code",
       ].join("; ")
     }
-    return `${enter} && exec bash -lc ${quote(input.command)}`
+    return `${enter} && exec bash -lc ${quote(run)}`
   }
 
   function ssh(host: Host, script: string): string[] {
@@ -241,7 +367,15 @@ export namespace ComputeJobs {
   }
 
   export function command(
-    input: { id: string; name: string; command: string; cwd?: string },
+    input: {
+      id: string
+      name: string
+      command: string
+      cwd?: string
+      resources?: Resources
+      modules?: string[]
+      container?: string
+    },
     host?: Host,
   ): { argv: string[]; scheduler: Scheduler; label: string } {
     if (!host) {
@@ -258,6 +392,113 @@ export namespace ComputeJobs {
     }
   }
 
+  async function output(argv: string[], cwd: string): Promise<string | undefined> {
+    const proc = Bun.spawn(argv, {
+      cwd,
+      env: await OpenScience.subprocessEnv(process.env),
+      stdin: "ignore",
+      stdout: "pipe",
+      stderr: "ignore",
+    })
+    const [code, text] = await Promise.all([proc.exited, new Response(proc.stdout).text()])
+    if (code !== 0) return
+    return text.trim() || undefined
+  }
+
+  function inside(root: string, file: string): string | undefined {
+    const target = path.resolve(root, file)
+    const relative = path.relative(root, target)
+    if (!relative || relative === ".." || relative.startsWith(`..${path.sep}`) || path.isAbsolute(relative)) return
+    return relative
+  }
+
+  async function fingerprint(root: string, file: string): Promise<Artifact | undefined> {
+    const relative = inside(root, file)
+    if (!relative) return
+    const target = path.join(root, relative)
+    const stat = await fs.stat(target).catch(() => undefined)
+    if (!stat?.isFile()) return
+    const hash = new Bun.CryptoHasher("sha256")
+    for await (const chunk of createReadStream(target)) hash.update(chunk)
+    return Artifact.parse({
+      path: relative.split(path.sep).join("/"),
+      size: stat.size,
+      sha256: hash.digest("hex"),
+      modified_at: stat.mtime.toISOString(),
+    })
+  }
+
+  async function artifacts(root: string, patterns: string[]): Promise<Artifact[]> {
+    const files = new Set<string>()
+    for (const pattern of patterns) {
+      if (!inside(root, pattern.replaceAll("*", "x"))) continue
+      const glob = new Bun.Glob(pattern)
+      for await (const file of glob.scan({ cwd: root, dot: true, onlyFiles: true })) {
+        files.add(file)
+        if (files.size >= 200) break
+      }
+      if (files.size >= 200) break
+    }
+    const values = await Promise.all([...files].toSorted().map((file) => fingerprint(root, file)))
+    return values.filter((item): item is Artifact => !!item)
+  }
+
+  const lockfiles = [
+    "bun.lock",
+    "bun.lockb",
+    "package-lock.json",
+    "pnpm-lock.yaml",
+    "yarn.lock",
+    "uv.lock",
+    "poetry.lock",
+    "Pipfile.lock",
+    "requirements.txt",
+    "environment.yml",
+    "environment.yaml",
+    "renv.lock",
+    "Manifest.toml",
+    "Cargo.lock",
+  ]
+
+  async function reproduce(job: Job): Promise<Reproducibility> {
+    const cwd = path.resolve(job.cwd ?? process.cwd())
+    const [branch, commit, status, python, capturedLocks] = await Promise.all([
+      output(["git", "rev-parse", "--abbrev-ref", "HEAD"], cwd),
+      output(["git", "rev-parse", "HEAD"], cwd),
+      output(["git", "status", "--porcelain"], cwd),
+      output(["python3", "--version"], cwd),
+      Promise.all(lockfiles.map((file) => fingerprint(cwd, file))),
+    ])
+    const git = branch || commit || status !== undefined ? { branch, commit, dirty: !!status } : undefined
+    return Reproducibility.parse({
+      captured_at: new Date().toISOString(),
+      command: job.command,
+      cwd,
+      platform: process.platform,
+      arch: process.arch,
+      bun: Bun.version,
+      node: process.version,
+      python,
+      git,
+      lockfiles: capturedLocks.filter((item): item is Artifact => !!item),
+      resources: job.resources,
+    })
+  }
+
+  async function capture(job: Job): Promise<Pick<Job, "artifacts" | "checkpoint" | "reproducibility">> {
+    const cwd = path.resolve(job.cwd ?? process.cwd())
+    const [found, checkpoint, reproducibility] = await Promise.all([
+      artifacts(cwd, job.artifact_patterns ?? []),
+      job.checkpoint_path ? fingerprint(cwd, job.checkpoint_path) : undefined,
+      reproduce(job),
+    ])
+    return {
+      artifacts: found,
+      checkpoint,
+      reproducibility,
+    }
+  }
+
   export async function probe(host: Host): Promise<Probe> {
     const parsed = Host.parse(host)
     const started = performance.now()
@@ -350,15 +591,25 @@ export namespace ComputeJobs {
       proc.once("error", (error) => resolve({ code: null, error: error.message }))
       proc.once("exit", (code) => resolve({ code }))
     })
-    active.delete(keyOf(root, job.id))
-    const final = (await list({ root })).find((item) => item.id === job.id)
-    if (final?.status === "cancelled") return
+    const final = await get(job.id, { root })
+    if (final?.status === "cancelled") {
+      active.delete(keyOf(root, job.id))
+      return
+    }
+    const captureResult = host
+      ? undefined
+      : await capture(job)
+          .then((value) => ({ ...value, capture_error: undefined }))
+          .catch((error) => ({
+            capture_error: error instanceof Error ? error.message : String(error),
+          }))
     await patch(root, job.id, {
       status: result.code === 0 ? "succeeded" : "failed",
       completed_at: new Date().toISOString(),
       exit_code: result.code,
       error: result.error,
-    })
+      ...captureResult,
+    }).finally(() => active.delete(keyOf(root, job.id)))
   }
 
   export async function start(input: Input, options: Options = {}): Promise<Job> {
@@ -379,6 +630,11 @@ export namespace ComputeJobs {
       scheduler: spec.scheduler,
       status: "queued",
       created_at: new Date().toISOString(),
+      resources: parsed.resources,
+      modules: parsed.modules,
+      container: parsed.container,
+      artifact_patterns: parsed.artifacts,
+      checkpoint_path: parsed.checkpoint,
     })
     await change(root, (jobs) => {
       jobs.push(job)
diff --git a/backend/cli/src/file/science.ts b/backend/cli/src/file/science.ts
index 2c2febdb..65dbbbcb 100644
--- a/backend/cli/src/file/science.ts
+++ b/backend/cli/src/file/science.ts
@@ -43,6 +43,25 @@ def clean(value):
         return [clean(item) for item in value[:50]]
     return str(value)
 
+def text(value):
+    value = clean(value)
+    return str(value) if value is not None else ""
+
+def labels(handle, key, indices):
+    if not key or "obs" not in handle:
+        return []
+    value = handle["obs"].get(key)
+    if value is None:
+        return []
+    try:
+        if isinstance(value, h5py.Group) and "codes" in value and "categories" in value:
+            codes = value["codes"][indices]
+            categories = value["categories"][:]
+            return [text(categories[int(code)]) if int(code) >= 0 and int(code) < len(categories) else "" for code in codes]
+        return [text(item) for item in value[indices]]
+    except Exception:
+        return []
+
 with h5py.File(target, "r") as handle:
     result["attributes"] = {str(key): clean(value) for key, value in list(handle.attrs.items())[:50]}
 
@@ -78,12 +97,55 @@ with h5py.File(target, "r") as handle:
         result["summary"].setdefault("variables", int(matrix.shape[1]))
     if "obsm" in handle:
         result["summary"]["embeddings"] = list(handle["obsm"].keys())[:100]
+        preferred = ["X_umap", "X_tsne", "X_pca", "spatial"]
+        names = list(handle["obsm"].keys())
+        selected = next((name for name in preferred if name in names), names[0] if names else None)
+        value = handle["obsm"].get(selected) if selected else None
+        if value is not None and isinstance(value, h5py.Dataset) and len(value.shape) == 2 and value.shape[1] >= 2:
+            total = int(value.shape[0])
+            count = min(total, 2500)
+            indices = [int(index * total / count) for index in range(count)] if count else []
+            coords = value[indices, :2] if indices else []
+            label_names = ["cell_type", "celltype", "leiden", "louvain", "cluster", "batch"]
+            label_key = next((name for name in label_names if "obs" in handle and name in handle["obs"]), None)
+            categories = labels(handle, label_key, indices)
+            result["embedding"] = {
+                "name": selected,
+                "label": label_key,
+                "total": total,
+                "points": [
+                    {
+                        "x": float(point[0]),
+                        "y": float(point[1]),
+                        **({"label": categories[index]} if index < len(categories) and categories[index] else {}),
+                    }
+                    for index, point in enumerate(coords)
+                ],
+            }
     if "layers" in handle:
         result["summary"]["layers"] = list(handle["layers"].keys())[:100]
     if "row_attrs" in handle:
         result["summary"]["row_attributes"] = list(handle["row_attrs"].keys())[:100]
     if "col_attrs" in handle:
         result["summary"]["column_attributes"] = list(handle["col_attrs"].keys())[:100]
+        if "embedding" not in result:
+            candidates = [
+                (name, handle["col_attrs"].get(name))
+                for name in ["X_umap", "UMAP", "Embedding", "_Embedding", "TSNE"]
+                if name in handle["col_attrs"]
+            ]
+            selected = candidates[0] if candidates else None
+            if selected and isinstance(selected[1], h5py.Dataset) and len(selected[1].shape) == 2 and selected[1].shape[1] >= 2:
+                value = selected[1]
+                total = int(value.shape[0])
+                count = min(total, 2500)
+                indices = [int(index * total / count) for index in range(count)] if count else []
+                coords = value[indices, :2] if indices else []
+                result["embedding"] = {
+                    "name": selected[0],
+                    "total": total,
+                    "points": [{"x": float(point[0]), "y": float(point[1])} for point in coords],
+                }
 
 print(json.dumps(result))
 `
diff --git a/backend/cli/src/science/provenance/review.ts b/backend/cli/src/science/provenance/review.ts
index db278744..b1bd4c22 100644
--- a/backend/cli/src/science/provenance/review.ts
+++ b/backend/cli/src/science/provenance/review.ts
@@ -49,6 +49,7 @@ export namespace Review {
     /** Who recorded it (agent name). */
     reviewer?: string
     sessionID?: string
+    directory?: string
   }): Promise<ReviewResult> {
     const relation = input.verdict ?? "refutes"
     const node = await Provenance.record({
@@ -64,6 +65,7 @@ export namespace Review {
         verdict: relation,
         reviewer: input.reviewer ?? "reviewer",
         sessionID: input.sessionID,
+        directory: input.directory,
       },
     })
     await Provenance.link({ from: node.id, to: input.target, relation })
diff --git a/backend/cli/src/science/provenance/store.ts b/backend/cli/src/science/provenance/store.ts
index 106c49be..69980216 100644
--- a/backend/cli/src/science/provenance/store.ts
+++ b/backend/cli/src/science/provenance/store.ts
@@ -72,6 +72,7 @@ interface Graph {
 }
 
 const STORE_PATH = path.join(Global.Path.data, "provenance", "graph.json")
+const lock = { current: Promise.resolve() as Promise<unknown> }
 
 async function sha256(input: string): Promise<string> {
   const digest = await crypto.subtle.digest("SHA-256", new TextEncoder().encode(input))
@@ -80,10 +81,20 @@ async function sha256(input: string): Promise<string> {
 
 /** Deterministic content id from a node's identifying payload. */
 export async function contentId(payload: unknown): Promise<string> {
-  const canonical = JSON.stringify(payload, Object.keys(payload as object).sort())
+  const canonical = JSON.stringify(stable(payload))
   return (await sha256(canonical)).slice(0, 16)
 }
 
+function stable(value: unknown): unknown {
+  if (Array.isArray(value)) return value.map(stable)
+  if (!value || typeof value !== "object") return value
+  return Object.fromEntries(
+    Object.entries(value as Record<string, unknown>)
+      .toSorted(([a], [b]) => a.localeCompare(b))
+      .map(([key, item]) => [key, stable(item)]),
+  )
+}
+
 async function load(): Promise<Graph> {
   const file = Bun.file(STORE_PATH)
   if (!(await file.exists())) return { version: 1, nodes: {}, edges: [] }
@@ -98,25 +109,49 @@ async function save(graph: Graph): Promise<void> {
   await Bun.write(STORE_PATH, JSON.stringify(graph, null, 2))
 }
 
+async function mutate<T>(fn: (graph: Graph) => Promise<T> | T): Promise<T> {
+  const task = lock.current
+    .catch(() => undefined)
+    .then(async () => {
+      const graph = await load()
+      const result = await fn(graph)
+      await save(graph)
+      return result
+    })
+  lock.current = task
+  return task
+}
+
+function belongs(node: Node, directory: string): boolean {
+  const root = path.resolve(directory)
+  const nodeDirectory = node.meta?.directory
+  if (typeof nodeDirectory === "string" && path.resolve(nodeDirectory) === root) return true
+  if (node.kind !== "artifact" || !("path" in node) || !node.path || !path.isAbsolute(node.path)) return false
+  const relative = path.relative(root, path.resolve(node.path))
+  return relative === "" || (!relative.startsWith(`..${path.sep}`) && relative !== ".." && !path.isAbsolute(relative))
+}
+
 export namespace Provenance {
   /** Record a node. If `id` is omitted it is content-addressed from the node body. */
   export async function record(node: Omit<Node, "id" | "recordedAt"> & { id?: string }): Promise<Node> {
-    const graph = await load()
-    const recordedAt = new Date().toISOString()
-    const id = node.id ?? (await contentId({ ...node }))
-    const full = { ...node, id, recordedAt } as Node
-    graph.nodes[id] = full
-    await save(graph)
-    return full
+    return mutate(async (graph) => {
+      const recordedAt = new Date().toISOString()
+      const id = node.id ?? (await contentId({ ...node }))
+      const full = { ...node, id, recordedAt } as Node
+      graph.nodes[id] = full
+      return full
+    })
   }
 
   /** Link two existing nodes with a typed edge. */
   export async function link(edge: Edge): Promise<Edge> {
-    const graph = await load()
-    const exists = graph.edges.some((e) => e.from === edge.from && e.to === edge.to && e.relation === edge.relation)
-    if (!exists) graph.edges.push(edge)
-    await save(graph)
-    return edge
+    return mutate((graph) => {
+      if (!graph.nodes[edge.from]) throw new Error(`Provenance node ${edge.from} was not found`)
+      if (!graph.nodes[edge.to]) throw new Error(`Provenance node ${edge.to} was not found`)
+      const exists = graph.edges.some((e) => e.from === edge.from && e.to === edge.to && e.relation === edge.relation)
+      if (!exists) graph.edges.push(edge)
+      return edge
+    })
   }
 
   /** Fetch a single node by id. */
@@ -160,5 +195,33 @@ export namespace Provenance {
     return Object.values(graph.nodes)
   }
 
+  /** Return only nodes belonging to a project plus their directly or transitively linked evidence. */
+  export async function project(directory: string): Promise<{ nodes: Node[]; edges: Edge[] }> {
+    const graph = await load()
+    const seen = new Set(
+      Object.values(graph.nodes)
+        .filter((node) => belongs(node, directory))
+        .map((node) => node.id),
+    )
+    const queue = [...seen]
+    while (queue.length) {
+      const id = queue.shift()!
+      for (const edge of graph.edges) {
+        if (edge.from !== id && edge.to !== id) continue
+        const next = edge.from === id ? edge.to : edge.from
+        const node = graph.nodes[next]
+        if (seen.has(next) || !node) continue
+        const owner = node.meta?.directory
+        if (typeof owner === "string" && !belongs(node, directory)) continue
+        seen.add(next)
+        queue.push(next)
+      }
+    }
+    return {
+      nodes: [...seen].map((id) => graph.nodes[id]).filter((node): node is Node => !!node),
+      edges: graph.edges.filter((edge) => seen.has(edge.from) && seen.has(edge.to)),
+    }
+  }
+
   export const path_ = STORE_PATH
 }
diff --git a/backend/cli/src/server/routes/provenance.ts b/backend/cli/src/server/routes/provenance.ts
new file mode 100644
index 00000000..45ac3ca3
--- /dev/null
+++ b/backend/cli/src/server/routes/provenance.ts
@@ -0,0 +1,186 @@
+import { Hono } from "hono"
+import { describeRoute, validator } from "hono-openapi"
+import z from "zod"
+import { Instance } from "../../project/instance"
+import { Provenance, type Edge, type Node } from "../../science/provenance/store"
+import { Review } from "../../science/provenance/review"
+import { lazy } from "../../util/lazy"
+
+const Kind = z.enum(["artifact", "run", "source", "claim"])
+const Relation = z.enum(["produced", "consumed", "derived-from", "supports", "refutes"])
+const NodeInput = z.object({
+  kind: Kind,
+  label: z.string().trim().min(1).max(240),
+  artifact_type: z.string().trim().min(1).max(120).optional(),
+  path: z.string().max(4_000).optional(),
+  content_hash: z.string().max(240).optional(),
+  size: z.number().int().nonnegative().optional(),
+  tool: z.string().trim().min(1).max(240).optional(),
+  status: z.enum(["ok", "error"]).optional(),
+  meta: z.record(z.string(), z.unknown()).optional(),
+  derived_from: z.string().optional(),
+  relation: Relation.default("derived-from"),
+})
+const ReviewInput = z.object({
+  target: z.string(),
+  claim: z.string().trim().min(1).max(10_000),
+  issue: z.string().trim().min(1).max(10_000),
+  severity: z.enum(["blocking", "major", "minor", "info"]),
+  evidence: z.string().trim().min(1).max(20_000),
+  verdict: z.enum(["refutes", "supports"]).default("refutes"),
+})
+
+function summary(nodes: Node[], edges: Edge[]) {
+  const kinds = { artifact: 0, run: 0, source: 0, claim: 0 }
+  const reviews = { supports: 0, refutes: 0, blocking: 0, major: 0, minor: 0, info: 0 }
+  for (const node of nodes) {
+    kinds[node.kind] += 1
+    if (node.meta?.review !== true) continue
+    const verdict = node.meta.verdict
+    const severity = node.meta.severity
+    if (verdict === "supports" || verdict === "refutes") reviews[verdict] += 1
+    if (severity === "blocking" || severity === "major" || severity === "minor" || severity === "info") {
+      reviews[severity] += 1
+    }
+  }
+  return {
+    total: nodes.length,
+    edges: edges.length,
+    kinds,
+    reviews,
+    orphan_edges: edges.filter(
+      (edge) => !nodes.some((node) => node.id === edge.from) || !nodes.some((node) => node.id === edge.to),
+    ).length,
+  }
+}
+
+function lineage(id: string, nodes: Node[], edges: Edge[]) {
+  const ids = new Set([id])
+  const queue = [id]
+  while (queue.length) {
+    const current = queue.shift()!
+    for (const edge of edges) {
+      if (edge.from !== current && edge.to !== current) continue
+      const next = edge.from === current ? edge.to : edge.from
+      if (ids.has(next)) continue
+      ids.add(next)
+      queue.push(next)
+    }
+  }
+  return {
+    nodes: nodes.filter((node) => ids.has(node.id)),
+    edges: edges.filter((edge) => ids.has(edge.from) && ids.has(edge.to)),
+  }
+}
+
+export const ProvenanceRoutes = lazy(() =>
+  new Hono()
+    .get(
+      "/",
+      describeRoute({
+        summary: "List the project provenance graph",
+        description: "Returns project-scoped artifacts, runs, sources, claims, reviewer findings, and typed edges.",
+        operationId: "provenance.list",
+        responses: { 200: { description: "Project provenance graph" } },
+      }),
+      async (c) => {
+        const graph = await Provenance.project(Instance.directory)
+        return c.json({ ...graph, summary: summary(graph.nodes, graph.edges) })
+      },
+    )
+    .post(
+      "/nodes",
+      describeRoute({
+        summary: "Record a project provenance node",
+        operationId: "provenance.record",
+        responses: { 200: { description: "Recorded node" }, 400: { description: "Invalid link target" } },
+      }),
+      validator("json", NodeInput),
+      async (c) => {
+        const input = c.req.valid("json")
+        const graph = input.derived_from ? await Provenance.project(Instance.directory) : undefined
+        if (input.derived_from && !graph?.nodes.some((node) => node.id === input.derived_from)) {
+          return c.json({ error: "The provenance link target was not found" }, 400)
+        }
+        const node = await Provenance.record({
+          kind: input.kind,
+          label: input.label,
+          ...(input.artifact_type ? { artifactType: input.artifact_type } : {}),
+          ...(input.path ? { path: input.path } : {}),
+          ...(input.content_hash ? { contentHash: input.content_hash } : {}),
+          ...(input.size !== undefined ? { size: input.size } : {}),
+          ...(input.tool ? { tool: input.tool } : {}),
+          ...(input.status ? { status: input.status } : {}),
+          meta: { ...input.meta, directory: Instance.directory },
+        } as Parameters<typeof Provenance.record>[0])
+        if (input.derived_from) {
+          await Provenance.link({ from: node.id, to: input.derived_from, relation: input.relation })
+        }
+        return c.json(node)
+      },
+    )
+    .post(
+      "/reviews",
+      describeRoute({
+        summary: "Record a reviewer finding",
+        operationId: "provenance.review",
+        responses: { 200: { description: "Recorded finding" }, 400: { description: "Invalid target" } },
+      }),
+      validator("json", ReviewInput),
+      async (c) => {
+        const input = c.req.valid("json")
+        const graph = await Provenance.project(Instance.directory)
+        if (!graph.nodes.some((node) => node.id === input.target)) {
+          return c.json({ error: "The review target was not found" }, 400)
+        }
+        const result = await Review.record({
+          target: input.target,
+          finding: {
+            claim: input.claim,
+            issue: input.issue,
+            severity: input.severity,
+            evidence: input.evidence,
+          },
+          verdict: input.verdict,
+          reviewer: "manual review",
+          directory: Instance.directory,
+        })
+        return c.json(result)
+      },
+    )
+    .get(
+      "/export",
+      describeRoute({
+        summary: "Export a project provenance audit",
+        operationId: "provenance.export",
+        responses: { 200: { description: "Portable JSON audit packet" } },
+      }),
+      async (c) => {
+        const graph = await Provenance.project(Instance.directory)
+        c.header("Content-Disposition", 'attachment; filename="openscience-provenance-audit.json"')
+        return c.json({
+          format: "openscience.provenance.audit.v1",
+          generated_at: new Date().toISOString(),
+          project: Instance.directory,
+          summary: summary(graph.nodes, graph.edges),
+          ...graph,
+        })
+      },
+    )
+    .get(
+      "/:id",
+      describeRoute({
+        summary: "Trace a provenance node",
+        operationId: "provenance.trace",
+        responses: { 200: { description: "Connected lineage" }, 404: { description: "Node not found" } },
+      }),
+      validator("param", z.object({ id: z.string() })),
+      async (c) => {
+        const graph = await Provenance.project(Instance.directory)
+        const id = c.req.valid("param").id
+        if (!graph.nodes.some((node) => node.id === id)) return c.json({ error: "Provenance node not found" }, 404)
+        const connected = lineage(id, graph.nodes, graph.edges)
+        return c.json({ ...connected, summary: summary(connected.nodes, connected.edges) })
+      },
+    ),
+)
diff --git a/backend/cli/src/server/server.ts b/backend/cli/src/server/server.ts
index ea076f02..33aa5ca2 100644
--- a/backend/cli/src/server/server.ts
+++ b/backend/cli/src/server/server.ts
@@ -30,6 +30,7 @@ import { PtyRoutes } from "./routes/pty"
 import { McpRoutes } from "./routes/mcp"
 import { FileRoutes } from "./routes/file"
 import { NotebookRoutes } from "./routes/notebook"
+import { ProvenanceRoutes } from "./routes/provenance"
 import { ConfigRoutes } from "./routes/config"
 import { ExperimentalRoutes } from "./routes/experimental"
 import { ProviderRoutes } from "./routes/provider"
@@ -280,6 +281,7 @@ export namespace Server {
         .route("/provider", ProviderRoutes())
         .route("/", FileRoutes())
         .route("/notebook", NotebookRoutes())
+        .route("/provenance", ProvenanceRoutes())
         .route("/mcp", McpRoutes())
         .route("/settings/skills", SettingsSkillsRoutes())
         .route("/settings/memory", MemorySettingsRoutes())
diff --git a/backend/cli/src/tool/provenance.ts b/backend/cli/src/tool/provenance.ts
index 15d90872..9fc3bd0a 100644
--- a/backend/cli/src/tool/provenance.ts
+++ b/backend/cli/src/tool/provenance.ts
@@ -2,6 +2,7 @@ import z from "zod"
 import { Tool } from "./tool"
 import { Provenance } from "../science/provenance/store"
 import { Review } from "../science/provenance/review"
+import { Instance } from "../project/instance"
 
 /**
  * Agent-facing tools over the provenance DAG. Let the model record what it
@@ -30,13 +31,19 @@ export const ProvenanceRecordTool = Tool.define("provenance_record", {
       .describe("Optional id of a parent node this was derived from (creates a 'derived-from' edge)"),
   }),
   async execute(params, ctx) {
+    if (params.derived_from) {
+      const graph = await Provenance.project(Instance.directory)
+      if (!graph.nodes.some((node) => node.id === params.derived_from)) {
+        throw new Error(`Provenance node ${params.derived_from} is not part of this project`)
+      }
+    }
     const node = await Provenance.record({
       kind: params.kind,
       label: params.label,
       ...(params.artifact_type ? { artifactType: params.artifact_type } : {}),
       ...(params.path ? { path: params.path } : {}),
       ...(params.tool ? { tool: params.tool } : {}),
-      meta: { sessionID: ctx.sessionID, ...params.meta },
+      meta: { sessionID: ctx.sessionID, directory: Instance.directory, ...params.meta },
     } as Parameters<typeof Provenance.record>[0])
 
     if (params.derived_from) {
@@ -68,8 +75,9 @@ export const ProvenanceQueryTool = Tool.define("provenance_query", {
     id: z.string().optional().describe("Node id to trace lineage for. Omit to list everything."),
   }),
   async execute(params, _ctx) {
+    const graph = await Provenance.project(Instance.directory)
     if (!params.id) {
-      const nodes = await Provenance.list()
+      const nodes = graph.nodes
       if (!nodes.length) {
         return { title: "Provenance", output: "No provenance nodes recorded yet.", metadata: { count: 0, edges: 0 } }
       }
@@ -81,10 +89,23 @@ export const ProvenanceQueryTool = Tool.define("provenance_query", {
       }
     }
 
-    const { nodes, edges } = await Provenance.query(params.id)
-    if (!nodes.length) {
+    if (!graph.nodes.some((node) => node.id === params.id)) {
       return { title: "Provenance", output: `No node "${params.id}".`, metadata: { count: 0, edges: 0 } }
     }
+    const connected = new Set([params.id])
+    const queue = [params.id]
+    while (queue.length) {
+      const current = queue.shift()!
+      for (const edge of graph.edges) {
+        if (edge.from !== current && edge.to !== current) continue
+        const next = edge.from === current ? edge.to : edge.from
+        if (connected.has(next)) continue
+        connected.add(next)
+        queue.push(next)
+      }
+    }
+    const nodes = graph.nodes.filter((node) => connected.has(node.id))
+    const edges = graph.edges.filter((edge) => connected.has(edge.from) && connected.has(edge.to))
     const nodeRows = nodes.map((n) => `- **${n.id}** [${n.kind}] ${n.label}`)
     const edgeRows = edges.map((e) => `- ${e.from} --${e.relation}--> ${e.to}`)
     return {
@@ -127,6 +148,10 @@ export const ProvenanceReviewTool = Tool.define("provenance_review", {
       .describe("'refutes' flags a defect (default); 'supports' records a verified-sound check"),
   }),
   async execute(params, ctx) {
+    const graph = await Provenance.project(Instance.directory)
+    if (!graph.nodes.some((node) => node.id === params.target)) {
+      throw new Error(`Provenance node ${params.target} is not part of this project`)
+    }
     const { node, relation } = await Review.record({
       target: params.target,
       finding: {
@@ -138,6 +163,7 @@ export const ProvenanceReviewTool = Tool.define("provenance_review", {
       verdict: params.verdict,
       reviewer: ctx.agent,
       sessionID: ctx.sessionID,
+      directory: Instance.directory,
     })
     return {
       title: `Review ${relation}: ${node.id}`,
diff --git a/backend/cli/test/compute/jobs.test.ts b/backend/cli/test/compute/jobs.test.ts
index 682c9d48..66da8ac5 100644
--- a/backend/cli/test/compute/jobs.test.ts
+++ b/backend/cli/test/compute/jobs.test.ts
@@ -22,6 +22,15 @@ describe("ComputeJobs command adapters", () => {
         name: "RNA benchmark",
         command: "python train.py --label 'A B'",
         cwd: "/scratch/team project",
+        resources: {
+          cpus: 8,
+          gpus: 2,
+          memory_gb: 48,
+          time_minutes: 95,
+          partition: "gpu-long",
+        },
+        modules: ["cuda/12.4", "python/3.12"],
+        container: "/containers/research image.sif",
       },
       host,
     )
@@ -29,13 +38,32 @@ describe("ComputeJobs command adapters", () => {
     expect(command.argv.slice(0, 7)).toEqual(["ssh", "-o", "BatchMode=yes", "-o", "ConnectTimeout=8", "-p", "2222"])
     expect(command.argv).toContain("researcher@hpc.example.org")
     expect(command.argv.at(-1)).toContain("sbatch --wait --parsable")
+    expect(command.argv.at(-1)).toContain("--cpus-per-task=8")
+    expect(command.argv.at(-1)).toContain("--gres=gpu:2")
+    expect(command.argv.at(-1)).toContain("--mem=48G")
+    expect(command.argv.at(-1)).toContain("--time=01:35:00")
+    expect(command.argv.at(-1)).toContain("--partition='gpu-long'")
+    expect(command.argv.at(-1)).toContain("module load")
+    expect(command.argv.at(-1)).toContain("cuda/12.4")
+    expect(command.argv.at(-1)).toContain("python/3.12")
+    expect(command.argv.at(-1)).toContain("apptainer exec")
+    expect(command.argv.at(-1)).toContain("/containers/research image.sif")
     expect(command.argv.at(-1)).toContain("os-job-123")
     expect(command.argv.at(-1)).toContain("python train.py")
   })
 
   test("builds PBS and direct SSH adapters from the same profile", () => {
-    const input = { id: "job-9", name: "Variant call", command: "bash pipeline.sh", cwd: "/work" }
-    expect(ComputeJobs.command(input, { ...host, scheduler: "pbs" }).argv.at(-1)).toContain("qsub")
+    const input = {
+      id: "job-9",
+      name: "Variant call",
+      command: "bash pipeline.sh",
+      cwd: "/work",
+      resources: { cpus: 4, gpus: 1, memory_gb: 16, time_minutes: 30 },
+    }
+    const pbs = ComputeJobs.command(input, { ...host, scheduler: "pbs" }).argv.at(-1)
+    expect(pbs).toContain("qsub")
+    expect(pbs).toContain("select=1:ncpus=4:ngpus=1:mem=16gb")
+    expect(pbs).toContain("walltime=00:30:00")
     expect(ComputeJobs.command(input, { ...host, scheduler: "none" }).argv.at(-1)).toContain("exec")
   })
 })
@@ -58,6 +86,49 @@ describe("ComputeJobs local lifecycle", () => {
     expect(finished.status).toBe("succeeded")
     expect(finished.exit_code).toBe(0)
     expect(await ComputeJobs.log(job.id, { root })).toContain("alpha\nbeta")
+    expect(finished.reproducibility).toMatchObject({
+      platform: process.platform,
+      arch: process.arch,
+      command: "printf 'alpha\\nbeta\\n'",
+    })
+  })
+
+  test("captures output artifacts, checksums, lockfiles, and checkpoints", async () => {
+    await using tmp = await tmpdir({ git: true })
+    const root = path.join(tmp.path, "state")
+    await Bun.write(path.join(tmp.path, "requirements.txt"), "numpy==2.2.0\n")
+    const job = await ComputeJobs.start(
+      {
+        name: "artifact capture",
+        command:
+          "mkdir -p outputs checkpoints && printf 'metric,value\\nloss,0.1\\n' > outputs/results.csv && printf model > checkpoints/latest.ckpt",
+        cwd: tmp.path,
+        target: { kind: "local" },
+        artifacts: ["outputs/**/*.csv"],
+        checkpoint: "checkpoints/latest.ckpt",
+        resources: { cpus: 2, memory_gb: 4 },
+      },
+      { root },
+    )
+
+    const finished = await ComputeJobs.wait(job.id, { root, timeout: 5_000 })
+    expect(finished.artifacts).toHaveLength(1)
+    expect(finished.artifacts?.[0]).toMatchObject({
+      path: "outputs/results.csv",
+      size: 22,
+    })
+    expect(finished.artifacts?.[0]?.sha256).toMatch(/^[a-f0-9]{64}$/)
+    expect(finished.checkpoint).toMatchObject({
+      path: "checkpoints/latest.ckpt",
+      size: 5,
+    })
+    expect(finished.reproducibility?.git?.dirty).toBe(true)
+    expect(finished.reproducibility?.lockfiles).toContainEqual(
+      expect.objectContaining({
+        path: "requirements.txt",
+        sha256: expect.stringMatching(/^[a-f0-9]{64}$/),
+      }),
+    )
   })
 
   test("cancels a running local process tree", async () => {
diff --git a/backend/cli/test/server/provenance.test.ts b/backend/cli/test/server/provenance.test.ts
new file mode 100644
index 00000000..1343ce00
--- /dev/null
+++ b/backend/cli/test/server/provenance.test.ts
@@ -0,0 +1,139 @@
+import { describe, expect, test } from "bun:test"
+import { Instance } from "../../src/project/instance"
+import { ProvenanceRoutes } from "../../src/server/routes/provenance"
+import { tmpdir } from "../fixture/fixture"
+
+describe("/provenance routes", () => {
+  test("records, reviews, scopes, traces, and exports a project audit graph", async () => {
+    await using tmp = await tmpdir({ git: true })
+    await Instance.provide({
+      directory: tmp.path,
+      fn: async () => {
+        const app = ProvenanceRoutes()
+        const source = await app.request("/nodes", {
+          method: "POST",
+          headers: { "Content-Type": "application/json" },
+          body: JSON.stringify({
+            kind: "source",
+            label: "Trial registry record",
+            meta: { doi: "10.1000/example" },
+          }),
+        })
+        expect(source.status).toBe(200)
+        const sourceNode = (await source.json()) as { id: string }
+
+        const claim = await app.request("/nodes", {
+          method: "POST",
+          headers: { "Content-Type": "application/json" },
+          body: JSON.stringify({
+            kind: "claim",
+            label: "Treatment improves response",
+            derived_from: sourceNode.id,
+          }),
+        })
+        expect(claim.status).toBe(200)
+        const claimNode = (await claim.json()) as { id: string }
+
+        const review = await app.request("/reviews", {
+          method: "POST",
+          headers: { "Content-Type": "application/json" },
+          body: JSON.stringify({
+            target: claimNode.id,
+            claim: "Treatment improves response",
+            issue: "verified",
+            severity: "info",
+            evidence: sourceNode.id,
+            verdict: "supports",
+          }),
+        })
+        expect(review.status).toBe(200)
+
+        const graph = await app.request("/")
+        const result = (await graph.json()) as {
+          nodes: Array<{ id: string; kind: string }>
+          edges: Array<{ from: string; to: string; relation: string }>
+          summary: {
+            total: number
+            edges: number
+            kinds: Record<string, number>
+            reviews: Record<string, number>
+          }
+        }
+        expect(result.summary).toMatchObject({
+          total: 3,
+          edges: 2,
+          kinds: { source: 1, claim: 2 },
+          reviews: { supports: 1, refutes: 0 },
+        })
+        expect(result.edges).toContainEqual({
+          from: claimNode.id,
+          to: sourceNode.id,
+          relation: "derived-from",
+        })
+
+        const lineage = await app.request(`/${claimNode.id}`)
+        expect(lineage.status).toBe(200)
+        expect(((await lineage.json()) as { nodes: unknown[] }).nodes).toHaveLength(3)
+
+        const audit = await app.request("/export")
+        expect(audit.status).toBe(200)
+        expect(audit.headers.get("content-disposition")).toContain("openscience-provenance-audit.json")
+        expect(((await audit.json()) as { project: string }).project).toBe(tmp.path)
+      },
+    })
+  })
+
+  test("rejects links to missing nodes", async () => {
+    await using tmp = await tmpdir()
+    await Instance.provide({
+      directory: tmp.path,
+      fn: async () => {
+        const response = await ProvenanceRoutes().request("/nodes", {
+          method: "POST",
+          headers: { "Content-Type": "application/json" },
+          body: JSON.stringify({
+            kind: "claim",
+            label: "Unsupported claim",
+            derived_from: "missing-node",
+          }),
+        })
+        expect(response.status).toBe(400)
+      },
+    })
+  })
+
+  test("does not expose or link provenance across project boundaries", async () => {
+    await using first = await tmpdir()
+    await using second = await tmpdir()
+    const source = await Instance.provide({
+      directory: first.path,
+      fn: async () => {
+        const response = await ProvenanceRoutes().request("/nodes", {
+          method: "POST",
+          headers: { "Content-Type": "application/json" },
+          body: JSON.stringify({ kind: "source", label: "Private first-project source" }),
+        })
+        return (await response.json()) as { id: string }
+      },
+    })
+
+    await Instance.provide({
+      directory: second.path,
+      fn: async () => {
+        const graph = await ProvenanceRoutes().request("/")
+        expect(((await graph.json()) as { nodes: unknown[] }).nodes).toHaveLength(0)
+
+        const link = await ProvenanceRoutes().request("/nodes", {
+          method: "POST",
+          headers: { "Content-Type": "application/json" },
+          body: JSON.stringify({
+            kind: "claim",
+            label: "Cross-project claim",
+            derived_from: source.id,
+          }),
+        })
+        expect(link.status).toBe(400)
+      },
+    })
+  })
+})
diff --git a/frontend/workspace/e2e/binary-science.spec.ts b/frontend/workspace/e2e/binary-science.spec.ts
index 4c2d15d9..76778395 100644
--- a/frontend/workspace/e2e/binary-science.spec.ts
+++ b/frontend/workspace/e2e/binary-science.spec.ts
@@ -42,3 +42,64 @@ test("inspects and streams scientific binary containers", async ({ page, gotoSes
     rmSync(directory, { recursive: true, force: true })
   }
 })
+
+test("renders an H5AD embedding with categorical cell labels", async ({ page, gotoSession }) => {
+  const directory = mkdtempSync(path.join(tmpdir(), "openscience-h5ad-embedding-e2e-"))
+  writeFileSync(
+    path.join(directory, "atlas.h5ad"),
+    Uint8Array.from([0x89, 0x48, 0x44, 0x46, 0x0d, 0x0a, 0x1a, 0x0a, 0, 0, 0, 0]),
+  )
+
+  await page.route("**/file/inspect?**", async (route) => {
+    await route.fulfill({
+      contentType: "application/json",
+      body: JSON.stringify({
+        format: "h5ad",
+        name: "atlas.h5ad",
+        size: 12,
+        modified: Date.now(),
+        signature: true,
+        tool: { name: "h5py", available: true, detail: "inspected locally" },
+        details: {
+          summary: {
+            matrix: [4, 3],
+            observations: 4,
+            variables: 3,
+            embeddings: ["X_umap"],
+          },
+          groups: ["obs", "var", "obsm"],
+          datasets: [{ path: "obsm/X_umap", shape: [4, 2], dtype: "float32", bytes: 32 }],
+          embedding: {
+            name: "X_umap",
+            label: "cell_type",
+            total: 4,
+            points: [
+              { x: -2, y: 1, label: "T cell" },
+              { x: -1, y: 2, label: "T cell" },
+              { x: 2, y: -1, label: "B cell" },
+              { x: 3, y: -2, label: "B cell" },
+            ],
+          },
+        },
+      }),
+    })
+  })
+
+  try {
+    await gotoSession()
+    await page.getByRole("tab", { name: "Files", exact: true }).click()
+    const location = page.getByPlaceholder("/absolute/path")
+    await location.fill(directory)
+    await location.press("Enter")
+    await page.getByPlaceholder("filter this folder…").fill("atlas.h5ad")
+    await page.getByRole("button", { name: /^atlas\.h5ad\b/ }).click()
+
+    const h5ad = page.locator('[data-component="binary-science"][data-format="h5ad"]')
+    await expect(h5ad.getByText("Embedding preview", { exact: true })).toBeVisible()
+    await expect(h5ad.getByRole("img", { name: "X_umap embedding scatter plot" })).toBeVisible()
+    await expect(h5ad.getByText("T cell", { exact: true })).toBeVisible()
+    await expect(h5ad.getByText("B cell", { exact: true })).toBeVisible()
+  } finally {
+    rmSync(directory, { recursive: true, force: true })
+  }
+})
diff --git a/frontend/workspace/e2e/compute-jobs.spec.ts b/frontend/workspace/e2e/compute-jobs.spec.ts
index 0c6db0e7..c53462b4 100644
--- a/frontend/workspace/e2e/compute-jobs.spec.ts
+++ b/frontend/workspace/e2e/compute-jobs.spec.ts
@@ -1,18 +1,42 @@
+import { mkdtempSync, rmSync } from "node:fs"
+import { tmpdir } from "node:os"
+import path from "node:path"
 import { expect, test } from "./fixtures"
 
-test("runs a local compute job and follows its output from the right pane", async ({ page, gotoSession }) => {
-  await gotoSession()
+test("runs a reproducible local job and captures outputs from the right pane", async ({
+  page,
+  gotoSession,
+}) => {
+  const directory = mkdtempSync(path.join(tmpdir(), "openscience-compute-e2e-"))
+  try {
+    await gotoSession()
 
-  await page.getByTitle("jobs").click()
-  const pane = page.locator(".session-right-pane")
-  await expect(pane.getByText("compute jobs", { exact: true })).toBeVisible()
+    await page.getByTitle("jobs").click()
+    const pane = page.locator(".session-right-pane")
+    await expect(pane.getByText("compute jobs", { exact: true })).toBeVisible()
 
-  await pane.getByTitle("new job").click()
-  await pane.getByLabel("Job name").fill("Playwright compute smoke")
-  await pane.getByLabel("Command").fill("printf 'ui-compute-ok\\n'")
-  await pane.getByRole("button", { name: "run job" }).click()
+    await pane.getByTitle("new job").click()
+    await pane.getByLabel("Job name").fill("Playwright compute smoke")
+    await pane.getByLabel("Working directory").fill(directory)
+    await pane
+      .getByLabel("Command")
+      .fill(
+        "mkdir -p outputs && printf 'metric,value\\nloss,0.1\\n' > outputs/ui-results.csv && printf 'ui-compute-ok\\n'",
+      )
+    await pane.getByRole("button", { name: "resources & reproducibility" }).click()
+    await pane.getByLabel("CPU cores").fill("2")
+    await pane.getByLabel("Memory in GB").fill("4")
+    await pane.getByLabel("Artifact patterns").fill("outputs/**/*.csv")
+    await pane.getByRole("button", { name: "run job" }).click()
 
-  await expect(pane.getByText("Playwright compute smoke", { exact: true }).first()).toBeVisible()
-  await expect(pane.locator("pre")).toContainText("ui-compute-ok")
-  await expect(pane.getByText(/This computer · succeeded/)).toBeVisible()
+    await expect(pane.getByText("Playwright compute smoke", { exact: true }).first()).toBeVisible()
+    await expect(pane.locator("pre")).toContainText("ui-compute-ok")
+    await expect(pane.getByText(/This computer · succeeded/)).toBeVisible()
+    await expect(pane.getByText("captured outputs", { exact: true })).toBeVisible()
+    await expect(pane.getByText("outputs/ui-results.csv", { exact: true })).toBeVisible()
+    await expect(pane.getByText("reproducibility", { exact: true })).toBeVisible()
+    await expect(pane.getByRole("button", { name: "export manifest" })).toBeVisible()
+  } finally {
+    rmSync(directory, { recursive: true, force: true })
+  }
 })
diff --git a/frontend/workspace/e2e/evidence-graph.spec.ts b/frontend/workspace/e2e/evidence-graph.spec.ts
new file mode 100644
index 00000000..ed9c2134
--- /dev/null
+++ b/frontend/workspace/e2e/evidence-graph.spec.ts
@@ -0,0 +1,52 @@
+import { expect, test } from "./fixtures"
+import { serverUrl } from "./utils"
+
+test("visualizes project lineage and reviewer findings in the evidence pane", async ({
+  page,
+  request,
+  gotoSession,
+  directory,
+}) => {
+  await gotoSession()
+
+  const post = async (path: string, data: object) => {
+    const response = await request.post(`${serverUrl}${path}`, {
+      params: { directory },
+      data,
+    })
+    expect(response.ok(), await response.text()).toBe(true)
+    return (await response.json()) as { id?: string; node?: { id: string } }
+  }
+  const source = await post("/provenance/nodes", {
+    kind: "source",
+    label: "Playwright trial registry",
+    meta: { doi: "10.1000/playwright" },
+  })
+  const claim = await post("/provenance/nodes", {
+    kind: "claim",
+    label: "Playwright response claim",
+    derived_from: source.id,
+  })
+  await post("/provenance/reviews", {
+    target: claim.id,
+    claim: "Playwright response claim",
+    issue: "verified against registry",
+    severity: "info",
+    evidence: source.id,
+    verdict: "supports",
+  })
+
+  await page.getByTitle("evidence").click()
+  const pane = page.locator(".session-right-pane")
+  await expect(pane.getByText("evidence & lineage", { exact: true })).toBeVisible()
+  await expect(pane.getByRole("img", { name: "Evidence lineage graph" })).toBeVisible()
+  const claimRow = pane.getByRole("button", { name: /Playwright response claim/ }).first()
+  await expect(claimRow).toBeVisible()
+  await claimRow.click()
+  await expect(pane.getByText("supported", { exact: true }).first()).toBeVisible()
+
+  await pane.getByRole("button", { name: "review", exact: true }).click()
+  await expect(pane.getByText("verified against registry", { exact: true })).toBeVisible()
+  await expect(pane.getByRole("button", { name: "export audit" })).toBeVisible()
+  await expect(pane.getByRole("button", { name: "run reviewer audit" })).toBeVisible()
+})
diff --git a/frontend/workspace/e2e/research-launchpad.spec.ts b/frontend/workspace/e2e/research-launchpad.spec.ts
index ca545988..7065a672 100644
--- a/frontend/workspace/e2e/research-launchpad.spec.ts
+++ b/frontend/workspace/e2e/research-launchpad.spec.ts
@@ -6,7 +6,7 @@ test("turns a scientific workflow into an editable research brief", async ({ pag
   const launchpad = page.locator('[data-component="research-launchpad"]')
   await expect(launchpad).toBeVisible()
   await expect(launchpad.getByRole("heading", { name: "What are we trying to find out?" })).toBeVisible()
-  await expect(launchpad.locator("[data-workflow]")).toHaveCount(8)
+  await expect(launchpad.locator("[data-workflow]")).toHaveCount(23)
   await expect(launchpad.getByText("Research artifacts", { exact: true })).toBeVisible()
   await expect(page.locator(".session-right-pane")).toHaveCount(0)
 
@@ -15,4 +15,12 @@ test("turns a scientific workflow into an editable research brief", async ({ pag
   const composer = page.locator('[data-component="prompt-input"]')
   await expect(composer).toBeFocused()
   await expect(composer).toContainText("Analyze the relevant dataset in this project")
+
+  await page.reload()
+  await expect(launchpad).toBeVisible()
+  await launchpad.getByRole("button", { name: /Compute 7/ }).click()
+  await expect(launchpad.locator("[data-workflow]")).toHaveCount(7)
+  await expect(launchpad.locator('[data-workflow="protein-design"]')).toBeVisible()
+  await expect(launchpad.locator('[data-workflow="molecular-docking"]')).toBeVisible()
+  await expect(launchpad.locator('[data-workflow="train-model"]')).toBeVisible()
 })
diff --git a/frontend/workspace/src/atlas/ComputeJobs.tsx b/frontend/workspace/src/atlas/ComputeJobs.tsx
index df5c7d61..934c0c14 100644
--- a/frontend/workspace/src/atlas/ComputeJobs.tsx
+++ b/frontend/workspace/src/atlas/ComputeJobs.tsx
@@ -11,6 +11,8 @@ import {
   IconCheckCircle,
   IconClock,
   IconCpu,
+  IconCopy,
+  IconDownload,
   IconPlus,
   IconRefresh,
   IconStop,
@@ -32,6 +34,39 @@ interface Settings {
   ssh_hosts: Host[]
 }
 
+interface Artifact {
+  path: string
+  size: number
+  sha256: string
+  modified_at: string
+}
+
+interface Resources {
+  cpus?: number
+  gpus?: number
+  memory_gb?: number
+  time_minutes?: number
+  partition?: string
+}
+
+interface Reproducibility {
+  captured_at: string
+  command: string
+  cwd: string
+  platform: string
+  arch: string
+  bun: string
+  node: string
+  python?: string
+  git?: {
+    branch?: string
+    commit?: string
+    dirty: boolean
+  }
+  lockfiles: Artifact[]
+  resources?: Resources
+}
+
 interface Job {
   id: string
   name: string
@@ -46,6 +81,15 @@ interface Job {
   completed_at?: string
   exit_code?: number | null
   error?: string
+  resources?: Resources
+  modules?: string[]
+  container?: string
+  artifact_patterns?: string[]
+  artifacts?: Artifact[]
+  checkpoint_path?: string
+  checkpoint?: Artifact
+  reproducibility?: Reproducibility
+  capture_error?: string
 }
 
 const terminal = new Set<Status>(["succeeded", "failed", "cancelled", "interrupted"])
@@ -66,6 +110,16 @@ export function ComputeJobs(): JSX.Element {
   const [command, setCommand] = createSignal("")
   const [cwd, setCwd] = createSignal("")
   const [target, setTarget] = createSignal("local")
+  const [advanced, setAdvanced] = createSignal(false)
+  const [cpus, setCpus] = createSignal("")
+  const [gpus, setGpus] = createSignal("")
+  const [memory, setMemory] = createSignal("")
+  const [time, setTime] = createSignal("")
+  const [partition, setPartition] = createSignal("")
+  const [modules, setModules] = createSignal("")
+  const [container, setContainer] = createSignal("")
+  const [artifacts, setArtifacts] = createSignal("")
+  const [checkpoint, setCheckpoint] = createSignal("")
   const current = createMemo(() => jobs()?.find((job) => job.id === selected()))
   const active = createMemo(() => jobs()?.filter((job) => !terminal.has(job.status)).length ?? 0)
   const [output, outputApi] = createResource(
@@ -93,6 +147,16 @@ export function ComputeJobs(): JSX.Element {
     setCommand("")
     setCwd("")
     setTarget("local")
+    setAdvanced(false)
+    setCpus("")
+    setGpus("")
+    setMemory("")
+    setTime("")
+    setPartition("")
+    setModules("")
+    setContainer("")
+    setArtifacts("")
+    setCheckpoint("")
     setCreating(false)
   }
 
@@ -100,6 +164,14 @@ export function ComputeJobs(): JSX.Element {
     if (!name().trim() || !command().trim()) return
     setBusy(true)
     const value = target()
+    const resources = {
+      cpus: number(cpus()),
+      gpus: number(gpus()),
+      memory_gb: number(memory()),
+      time_minutes: number(time()),
+      partition: partition().trim() || undefined,
+    }
+    const hasResources = Object.values(resources).some((item) => item !== undefined)
     const next = await call<Job>("/jobs", {
       method: "POST",
       body: JSON.stringify({
@@ -107,6 +179,11 @@ export function ComputeJobs(): JSX.Element {
         command: command().trim(),
         cwd: cwd().trim() || undefined,
         target: value === "local" ? { kind: "local" } : { kind: "ssh", host_id: value.slice(4) },
+        resources: hasResources ? resources : undefined,
+        modules: listValue(modules()),
+        container: container().trim() || undefined,
+        artifacts: listValue(artifacts()),
+        checkpoint: checkpoint().trim() || undefined,
       }),
     }).catch((error) => {
       toast.error("job did not start", error instanceof Error ? error.message : String(error))
@@ -137,9 +214,30 @@ export function ComputeJobs(): JSX.Element {
     setCommand(job.command)
     setCwd(job.cwd ?? "")
     setTarget(job.target.kind === "local" ? "local" : `ssh:${job.target.host_id}`)
+    setCpus(job.resources?.cpus?.toString() ?? "")
+    setGpus(job.resources?.gpus?.toString() ?? "")
+    setMemory(job.resources?.memory_gb?.toString() ?? "")
+    setTime(job.resources?.time_minutes?.toString() ?? "")
+    setPartition(job.resources?.partition ?? "")
+    setModules(job.modules?.join(", ") ?? "")
+    setContainer(job.container ?? "")
+    setArtifacts(job.artifact_patterns?.join(", ") ?? "")
+    setCheckpoint(job.checkpoint_path ?? "")
+    setAdvanced(
+      !!(job.resources || job.modules?.length || job.container || job.artifact_patterns?.length || job.checkpoint_path),
+    )
     setCreating(true)
   }
 
+  const save = (name: string, value: string, type = "text/plain") => {
+    const url = URL.createObjectURL(new Blob([value], { type }))
+    const link = document.createElement("a")
+    link.href = url
+    link.download = name
+    link.click()
+    URL.revokeObjectURL(url)
+  }
+
   const clear = async () => {
     setBusy(true)
     await call<{ cleared: number }>("/jobs/completed", { method: "DELETE" }).catch((error) =>
@@ -230,6 +328,102 @@ export function ComputeJobs(): JSX.Element {
             spellcheck={false}
             onInput={(event) => setCommand(event.currentTarget.value)}
           />
+          <button
+            type="button"
+            aria-expanded={advanced()}
+            style={advancedToggle}
+            onClick={() => setAdvanced((value) => !value)}
+          >
+            <span>resources & reproducibility</span>
+            <span>{advanced() ? "hide" : "configure"}</span>
+          </button>
+          <Show when={advanced()}>
+            <div style={advancedGrid}>
+              <Field label="CPU">
+                <input
+                  aria-label="CPU cores"
+                  style={input}
+                  type="number"
+                  min="1"
+                  placeholder="cores"
+                  value={cpus()}
+                  onInput={(event) => setCpus(event.currentTarget.value)}
+                />
+              </Field>
+              <Field label="GPU">
+                <input
+                  aria-label="GPUs"
+                  style={input}
+                  type="number"
+                  min="0"
+                  placeholder="count"
+                  value={gpus()}
+                  onInput={(event) => setGpus(event.currentTarget.value)}
+                />
+              </Field>
+              <Field label="Memory">
+                <input
+                  aria-label="Memory in GB"
+                  style={input}
+                  type="number"
+                  min="0.1"
+                  step="0.1"
+                  placeholder="GB"
+                  value={memory()}
+                  onInput={(event) => setMemory(event.currentTarget.value)}
+                />
+              </Field>
+              <Field label="Limit">
+                <input
+                  aria-label="Time limit in minutes"
+                  style={input}
+                  type="number"
+                  min="1"
+                  placeholder="minutes"
+                  value={time()}
+                  onInput={(event) => setTime(event.currentTarget.value)}
+                />
+              </Field>
+            </div>
+            <input
+              aria-label="Scheduler partition"
+              style={input}
+              value={partition()}
+              placeholder="Slurm partition (optional)"
+              onInput={(event) => setPartition(event.currentTarget.value)}
+            />
+            <input
+              aria-label="Environment modules"
+              style={input}
+              value={modules()}
+              placeholder="Modules: cuda/12.4, python/3.12"
+              onInput={(event) => setModules(event.currentTarget.value)}
+            />
+            <input
+              aria-label="Apptainer image"
+              style={input}
+              value={container()}
+              placeholder="Apptainer/Singularity image"
+              onInput={(event) => setContainer(event.currentTarget.value)}
+            />
+            <input
+              aria-label="Artifact patterns"
+              style={input}
+              value={artifacts()}
+              placeholder="Collect: outputs/**/*.csv, figures/*.png"
+              onInput={(event) => setArtifacts(event.currentTarget.value)}
+            />
+            <input
+              aria-label="Checkpoint path"
+              style={input}
+              value={checkpoint()}
+              placeholder="Checkpoint: checkpoints/latest.ckpt"
+              onInput={(event) => setCheckpoint(event.currentTarget.value)}
+            />
+            <span style={advancedHint}>
+              Local runs capture git state, lockfiles, artifact checksums, and the checkpoint automatically.
+            </span>
+          </Show>
           <div style={{ display: "flex", "justify-content": "flex-end", gap: "6px" }}>
             <button type="button" style={secondaryButton} onClick={reset}>
               cancel
@@ -343,9 +537,90 @@ export function ComputeJobs(): JSX.Element {
             <Show when={job().cwd}>
               <div style={meta}>cwd · {job().cwd}</div>
             </Show>
+            <Show when={resourceLabel(job())}>{(value) => <div style={meta}>resources · {value()}</div>}</Show>
+            <Show when={job().modules?.length}>
+              <div style={meta}>modules · {job().modules?.join(", ")}</div>
+            </Show>
+            <Show when={job().container}>
+              <div style={meta}>container · {job().container}</div>
+            </Show>
+            <Show when={job().artifacts?.length || job().checkpoint}>
+              <section style={captureCard}>
+                <div style={cardTitle}>
+                  <span>captured outputs</span>
+                  <span>{(job().artifacts?.length ?? 0) + (job().checkpoint ? 1 : 0)} verified</span>
+                </div>
+                <Show when={job().checkpoint}>{(item) => <ArtifactRow item={item()} label="checkpoint" />}</Show>
+                <For each={job().artifacts}>{(item) => <ArtifactRow item={item} />}</For>
+              </section>
+            </Show>
+            <Show when={job().reproducibility}>
+              {(manifest) => (
+                <section style={captureCard}>
+                  <div style={cardTitle}>
+                    <span>reproducibility</span>
+                    <span>{manifest().git?.dirty ? "working tree changed" : "captured"}</span>
+                  </div>
+                  <div style={manifestGrid}>
+                    <span>runtime</span>
+                    <strong>
+                      {manifest().platform} · {manifest().arch} · Bun {manifest().bun}
+                    </strong>
+                    <span>code</span>
+                    <strong>
+                      {manifest().git?.branch ?? "no git branch"}
+                      {manifest().git?.commit ? ` · ${manifest().git?.commit?.slice(0, 8)}` : ""}
+                      {manifest().git?.dirty ? " · dirty" : ""}
+                    </strong>
+                    <span>environment</span>
+                    <strong>
+                      {manifest().lockfiles.length
+                        ? manifest()
+                            .lockfiles.map((file) => file.path)
+                            .join(", ")
+                        : "no lockfile found"}
+                    </strong>
+                  </div>
+                  <button
+                    type="button"
+                    style={exportButton}
+                    onClick={() =>
+                      save(
+                        `${safeName(job().name)}-reproducibility.json`,
+                        JSON.stringify(manifest(), null, 2),
+                        "application/json",
+                      )
+                    }
+                  >
+                    <IconDownload size={11} />
+                    export manifest
+                  </button>
+                </section>
+              )}
+            </Show>
             <div style={logHeader}>
               <span>output</span>
-              <span>{output.loading ? "syncing…" : `${output()?.length ?? 0} bytes`}</span>
+              <span style={{ display: "inline-flex", "align-items": "center", gap: "7px" }}>
+                <span>{output.loading ? "syncing…" : `${output()?.length ?? 0} bytes`}</span>
+                <button
+                  type="button"
+                  title="copy command"
+                  aria-label="copy command"
+                  style={iconButton}
+                  onClick={() => void navigator.clipboard.writeText(job().command)}
+                >
+                  <IconCopy size={10} />
+                </button>
+                <button
+                  type="button"
+                  title="download log"
+                  aria-label="download log"
+                  style={iconButton}
+                  onClick={() => save(`${safeName(job().name)}.log`, output() ?? "")}
+                >
+                  <IconDownload size={10} />
+                </button>
+              </span>
             </div>
             <pre style={log}>
               {output() || (terminal.has(job().status) ? "No output was captured." : "Waiting for output…")}
@@ -353,6 +628,9 @@ export function ComputeJobs(): JSX.Element {
             <Show when={job().error}>
               <div style={errorBox}>{job().error}</div>
             </Show>
+            <Show when={job().capture_error}>
+              <div style={errorBox}>The run finished, but reproducibility capture failed: {job().capture_error}</div>
+            </Show>
           </div>
         )}
       </Show>
@@ -360,6 +638,44 @@ export function ComputeJobs(): JSX.Element {
   )
 }
 
+function Field(props: { label: string; children: JSX.Element }): JSX.Element {
+  return (
+    <label style={{ display: "flex", "flex-direction": "column", gap: "4px" }}>
+      <span style={{ color: "var(--color-text-faint)", "font-family": FONT_MONO, "font-size": "8px" }}>
+        {props.label}
+      </span>
+      {props.children}
+    </label>
+  )
+}
+
+function ArtifactRow(props: { item: Artifact; label?: string }): JSX.Element {
+  return (
+    <div style={artifactRow}>
+      <span style={{ display: "flex", "flex-direction": "column", gap: "2px", "min-width": 0, flex: 1 }}>
+        <strong
+          style={{
+            color: "var(--color-text)",
+            "font-family": FONT_MONO,
+            "font-size": "9px",
+            overflow: "hidden",
+            "text-overflow": "ellipsis",
+            "white-space": "nowrap",
+          }}
+          title={props.item.path}
+        >
+          {props.item.path}
+        </strong>
+        <span style={{ color: "var(--color-text-faint)", "font-family": FONT_MONO, "font-size": "8px" }}>
+          {props.label ? `${props.label} · ` : ""}
+          {bytes(props.item.size)} · sha256 {props.item.sha256.slice(0, 10)}
+        </span>
+      </span>
+      <IconCheckCircle size={11} strokeWidth={1.6} />
+    </div>
+  )
+}
+
 function StatusIcon(props: { status: Status }): JSX.Element {
   const config = () => {
     if (props.status === "succeeded") return { color: "var(--color-success)", icon: IconCheckCircle }
@@ -403,6 +719,49 @@ function Action(props: { title: string; active?: boolean; onClick: () => void; c
   )
 }
 
+function number(value: string): number | undefined {
+  if (!value.trim()) return
+  const parsed = Number(value)
+  return Number.isFinite(parsed) ? parsed : undefined
+}
+
+function listValue(value: string): string[] | undefined {
+  const values = value
+    .split(/[\n,]/)
+    .map((item) => item.trim())
+    .filter(Boolean)
+  return values.length ? values : undefined
+}
+
+function resourceLabel(job: Job): string | undefined {
+  const resources = job.resources
+  if (!resources) return
+  const values = [
+    resources.cpus ? `${resources.cpus} CPU` : undefined,
+    resources.gpus !== undefined ? `${resources.gpus} GPU` : undefined,
+    resources.memory_gb ? `${resources.memory_gb} GB` : undefined,
+    resources.time_minutes ? `${resources.time_minutes} min` : undefined,
+    resources.partition,
+  ].filter((value): value is string => !!value)
+  return values.length ? values.join(" · ") : undefined
+}
+
+function bytes(value: number): string {
+  if (value < 1_000) return `${value} B`
+  if (value < 1_000_000) return `${(value / 1_000).toFixed(1)} KB`
+  if (value < 1_000_000_000) return `${(value / 1_000_000).toFixed(1)} MB`
+  return `${(value / 1_000_000_000).toFixed(1)} GB`
+}
+
+function safeName(value: string): string {
+  return (
+    value
+      .trim()
+      .replace(/[^a-z0-9._-]+/gi, "-")
+      .replace(/^-+|-+$/g, "") || "compute-job"
+  )
+}
+
 function age(value: string): string {
   const delta = Math.max(0, Date.now() - Date.parse(value))
   if (delta < 60_000) return "now"
@@ -488,6 +847,31 @@ const input: JSX.CSSProperties = {
   "font-size": "10px",
 }
 
+const advancedToggle: JSX.CSSProperties = {
+  all: "unset",
+  cursor: "pointer",
+  display: "flex",
+  "align-items": "center",
+  "justify-content": "space-between",
+  color: "var(--color-text-muted)",
+  "font-family": FONT_MONO,
+  "font-size": "9px",
+  padding: "4px 1px",
+}
+
+const advancedGrid: JSX.CSSProperties = {
+  display: "grid",
+  "grid-template-columns": "repeat(4, minmax(0, 1fr))",
+  gap: "6px",
+}
+
+const advancedHint: JSX.CSSProperties = {
+  color: "var(--color-text-faint)",
+  "font-family": FONT_SANS,
+  "font-size": "9px",
+  "line-height": 1.4,
+}
+
 const primaryButton: JSX.CSSProperties = {
   cursor: "pointer",
   border: "1px solid var(--color-accent)",
@@ -619,6 +1003,64 @@ const meta: JSX.CSSProperties = {
   "white-space": "nowrap",
 }
 
+const captureCard: JSX.CSSProperties = {
+  display: "flex",
+  "flex-direction": "column",
+  gap: "6px",
+  padding: "8px",
+  border: "1px solid var(--color-border)",
+  "border-radius": "5px",
+  background: "var(--color-bg-subtle)",
+}
+
+const cardTitle: JSX.CSSProperties = {
+  display: "flex",
+  "align-items": "center",
+  "justify-content": "space-between",
+  color: "var(--color-text-faint)",
+  "font-family": FONT_MONO,
+  "font-size": "8px",
+  "text-transform": "uppercase",
+  "letter-spacing": "0.07em",
+}
+
+const artifactRow: JSX.CSSProperties = {
+  display: "flex",
+  "align-items": "center",
+  gap: "8px",
+  color: "var(--color-success)",
+  padding: "6px",
+  border: "1px solid var(--color-border)",
+  "border-radius": "4px",
+  background: "var(--color-bg)",
+}
+
+const manifestGrid: JSX.CSSProperties = {
+  display: "grid",
+  "grid-template-columns": "72px minmax(0, 1fr)",
+  gap: "5px 8px",
+  color: "var(--color-text-faint)",
+  "font-family": FONT_MONO,
+  "font-size": "8px",
+  "line-height": 1.35,
+}
+
+const exportButton: JSX.CSSProperties = {
+  all: "unset",
+  cursor: "pointer",
+  display: "inline-flex",
+  "align-items": "center",
+  "justify-content": "center",
+  gap: "5px",
+  padding: "5px 7px",
+  border: "1px solid var(--color-border)",
+  "border-radius": "4px",
+  background: "var(--color-bg)",
+  color: "var(--color-text-muted)",
+  "font-family": FONT_MONO,
+  "font-size": "8px",
+}
+
 const logHeader: JSX.CSSProperties = {
   display: "flex",
   "justify-content": "space-between",
@@ -630,6 +1072,15 @@ const logHeader: JSX.CSSProperties = {
   "margin-top": "2px",
 }
 
+const iconButton: JSX.CSSProperties = {
+  all: "unset",
+  cursor: "pointer",
+  display: "inline-flex",
+  "align-items": "center",
+  "justify-content": "center",
+  color: "var(--color-text-faint)",
+}
+
 const log: JSX.CSSProperties = {
   flex: 1,
   "min-height": "100px",
diff --git a/frontend/workspace/src/atlas/EvidenceGraph.tsx b/frontend/workspace/src/atlas/EvidenceGraph.tsx
new file mode 100644
index 00000000..85286f57
--- /dev/null
+++ b/frontend/workspace/src/atlas/EvidenceGraph.tsx
@@ -0,0 +1,793 @@
+import { For, Show, createEffect, createMemo, createResource, createSignal, onCleanup, type JSX } from "solid-js"
+import { useSDK } from "@/context/sdk"
+import { usePlatform } from "@/context/platform"
+import { FONT_MONO, FONT_SANS } from "@/styles/tokens"
+import { uiStore } from "@/atlas/store/ui"
+import {
+  IconActivity,
+  IconAlertCircle,
+  IconCheckCircle,
+  IconDownload,
+  IconFile,
+  IconNetwork,
+  IconRefresh,
+  IconSearch,
+} from "@/atlas/shared/Icon"
+
+type Kind = "artifact" | "run" | "source" | "claim"
+type Relation = "produced" | "consumed" | "derived-from" | "supports" | "refutes"
+type Filter = "all" | Kind | "review"
+
+interface Node {
+  id: string
+  kind: Kind
+  label: string
+  recordedAt: string
+  meta?: Record<string, unknown>
+  artifactType?: string
+  path?: string
+  contentHash?: string
+  size?: number
+  tool?: string
+  status?: "ok" | "error"
+}
+
+interface Edge {
+  from: string
+  to: string
+  relation: Relation
+}
+
+interface Graph {
+  nodes: Node[]
+  edges: Edge[]
+  summary: {
+    total: number
+    edges: number
+    kinds: Record<Kind, number>
+    reviews: {
+      supports: number
+      refutes: number
+      blocking: number
+      major: number
+      minor: number
+      info: number
+    }
+    orphan_edges: number
+  }
+}
+
+const colors: Record<Kind, string> = {
+  source: "#5c7cfa",
+  run: "#e6a23c",
+  artifact: "#2f9e74",
+  claim: "#9c6ade",
+}
+
+export function EvidenceGraph(): JSX.Element {
+  const sdk = useSDK()
+  const platform = usePlatform()
+  const fetchFn = platform.fetch ?? fetch
+  const endpoint = (path = "") => {
+    const url = new URL(`${sdk.url.replace(/\/+$/, "")}/provenance${path}`)
+    url.searchParams.set("directory", sdk.directory)
+    return url.toString()
+  }
+  const load = async () => {
+    const response = await fetchFn(endpoint())
+    if (!response.ok) throw new Error(await response.text())
+    return (await response.json()) as Graph
+  }
+  const [graph, graphApi] = createResource(() => sdk.directory, load)
+  const [query, setQuery] = createSignal("")
+  const [filter, setFilter] = createSignal<Filter>("all")
+  const [selected, setSelected] = createSignal<string>()
+  const nodes = createMemo(() => {
+    const value = query().trim().toLowerCase()
+    return (graph()?.nodes ?? [])
+      .filter((node) => filter() === "all" || node.kind === filter() || (filter() === "review" && node.meta?.review))
+      .filter(
+        (node) =>
+          !value ||
+          node.label.toLowerCase().includes(value) ||
+          node.id.toLowerCase().includes(value) ||
+          node.kind.includes(value),
+      )
+      .toSorted((a, b) => Date.parse(b.recordedAt) - Date.parse(a.recordedAt))
+  })
+  const current = createMemo(() => graph()?.nodes.find((node) => node.id === selected()))
+  const related = createMemo(() =>
+    (graph()?.edges ?? []).filter((edge) => edge.from === selected() || edge.to === selected()),
+  )
+  const positions = createMemo(() => layout(nodes().slice(0, 48)))
+
+  createEffect(() => {
+    const list = nodes()
+    if (!list.length) {
+      setSelected(undefined)
+      return
+    }
+    if (!selected() || !list.some((node) => node.id === selected())) setSelected(list[0].id)
+  })
+
+  const timer = setInterval(() => void graphApi.refetch(), 2_500)
+  onCleanup(() => clearInterval(timer))
+
+  const exportAudit = async () => {
+    const response = await fetchFn(endpoint("/export"))
+    if (!response.ok) return
+    const url = URL.createObjectURL(await response.blob())
+    const link = document.createElement("a")
+    link.href = url
+    link.download = "openscience-provenance-audit.json"
+    link.click()
+    URL.revokeObjectURL(url)
+  }
+
+  const audit = () => {
+    uiStore.setAgent("research")
+    uiStore.setPrefill(
+      "Audit the important claims, numbers, figures, and reports in this workspace. Use the reviewer agent and the provenance graph. Trace each claim to concrete evidence, record supported and refuted findings with provenance_review, and give me a blocking/major/minor summary.",
+    )
+    uiStore.setPrefillSend(true)
+  }
+
+  return (
+    <div style={shell}>
+      <header style={header}>
+        <div style={{ display: "flex", "align-items": "center", gap: "8px", "min-width": 0 }}>
+          <span style={mark}>
+            <IconNetwork size={13} strokeWidth={1.5} />
+          </span>
+          <div style={{ display: "flex", "flex-direction": "column", "min-width": 0 }}>
+            <span style={title}>evidence & lineage</span>
+            <span style={subtitle}>
+              {graph()?.summary.total ?? 0} nodes · {graph()?.summary.edges ?? 0} links
+            </span>
+          </div>
+        </div>
+        <div style={{ display: "flex", gap: "4px" }}>
+          <Action title="export audit" onClick={() => void exportAudit()}>
+            <IconDownload size={12} />
+          </Action>
+          <Action title="refresh evidence" onClick={() => void graphApi.refetch()}>
+            <IconRefresh size={12} />
+          </Action>
+        </div>
+      </header>
+
+      <Show when={graph.error}>
+        <div role="alert" style={errorBox}>
+          Evidence is unavailable. {graph.error instanceof Error ? graph.error.message : String(graph.error)}
+        </div>
+      </Show>
+
+      <Show
+        when={(graph()?.nodes.length ?? 0) > 0}
+        fallback={
+          <div style={empty}>
+            <span style={emptyMark}>
+              <IconNetwork size={19} />
+            </span>
+            <strong>No evidence graph yet</strong>
+            <span>
+              Notebook runs and research agents record sources, runs, artifacts, and claims here automatically.
+            </span>
+            <button type="button" style={primaryButton} onClick={audit}>
+              audit this workspace
+            </button>
+          </div>
+        }
+      >
+        <section style={scoreRow} aria-label="Evidence summary">
+          <Score label="sources" value={graph()?.summary.kinds.source ?? 0} color={colors.source} />
+          <Score label="runs" value={graph()?.summary.kinds.run ?? 0} color={colors.run} />
+          <Score label="artifacts" value={graph()?.summary.kinds.artifact ?? 0} color={colors.artifact} />
+          <Score label="claims" value={graph()?.summary.kinds.claim ?? 0} color={colors.claim} />
+        </section>
+
+        <Show when={(graph()?.summary.reviews.blocking ?? 0) + (graph()?.summary.reviews.major ?? 0) > 0}>
+          <div style={warning}>
+            <IconAlertCircle size={12} />
+            <span>
+              {graph()?.summary.reviews.blocking ?? 0} blocking · {graph()?.summary.reviews.major ?? 0} major findings
+            </span>
+          </div>
+        </Show>
+
+        <div style={controls}>
+          <label style={search}>
+            <IconSearch size={11} />
+            <input
+              aria-label="Search evidence"
+              style={{
+                all: "unset",
+                flex: 1,
+                "font-family": FONT_MONO,
+                "font-size": "9px",
+                color: "var(--color-text)",
+              }}
+              value={query()}
+              placeholder="Search evidence"
+              onInput={(event) => setQuery(event.currentTarget.value)}
+            />
+          </label>
+          <div style={filters}>
+            <For each={["all", "source", "run", "artifact", "claim", "review"] as Filter[]}>
+              {(value) => (
+                <button
+                  type="button"
+                  data-active={filter() === value ? "true" : "false"}
+                  style={filterButton(filter() === value)}
+                  onClick={() => setFilter(value)}
+                >
+                  {value}
+                </button>
+              )}
+            </For>
+          </div>
+        </div>
+
+        <div style={map}>
+          <svg
+            viewBox="0 0 360 188"
+            role="img"
+            aria-label="Evidence lineage graph"
+            style={{ width: "100%", height: "188px" }}
+          >
+            <For each={(graph()?.edges ?? []).filter((edge) => positions().has(edge.from) && positions().has(edge.to))}>
+              {(edge) => {
+                const from = () => positions().get(edge.from)!
+                const to = () => positions().get(edge.to)!
+                return (
+                  <line
+                    x1={from().x}
+                    y1={from().y}
+                    x2={to().x}
+                    y2={to().y}
+                    stroke={edge.relation === "refutes" ? "var(--color-danger)" : "var(--color-border-strong)"}
+                    stroke-width={edge.relation === "refutes" ? "1.6" : "1"}
+                    stroke-dasharray={edge.relation === "derived-from" ? "3 3" : undefined}
+                  />
+                )
+              }}
+            </For>
+            <For each={nodes().slice(0, 48)}>
+              {(node) => {
+                const point = () => positions().get(node.id)!
+                return (
+                  <g
+                    role="button"
+                    tabindex="0"
+                    aria-label={`${node.kind}: ${node.label}`}
+                    onClick={() => setSelected(node.id)}
+                    onKeyDown={(event) => {
+                      if (event.key === "Enter" || event.key === " ") setSelected(node.id)
+                    }}
+                    style={{ cursor: "pointer" }}
+                  >
+                    <circle
+                      cx={point().x}
+                      cy={point().y}
+                      r={selected() === node.id ? 7 : 5}
+                      fill={colors[node.kind]}
+                      stroke={selected() === node.id ? "var(--color-text)" : "var(--color-bg)"}
+                      stroke-width="2"
+                    />
+                    <title>{node.label}</title>
+                  </g>
+                )
+              }}
+            </For>
+          </svg>
+          <div style={legend}>
+            <span>source</span>
+            <span>run</span>
+            <span>artifact</span>
+            <span>claim / review</span>
+          </div>
+        </div>
+
+        <div style={body}>
+          <div style={nodeList}>
+            <For each={nodes()}>
+              {(node) => (
+                <button type="button" style={nodeRow(selected() === node.id)} onClick={() => setSelected(node.id)}>
+                  <span style={{ ...nodeDot, background: colors[node.kind] }} />
+                  <span style={{ display: "flex", "flex-direction": "column", gap: "2px", flex: 1, "min-width": 0 }}>
+                    <strong>{node.label}</strong>
+                    <small>
+                      {node.kind} · {status(node, graph()?.edges ?? [])}
+                    </small>
+                  </span>
+                </button>
+              )}
+            </For>
+          </div>
+
+          <Show when={current()}>
+            {(node) => (
+              <section style={detail}>
+                <div style={{ display: "flex", "align-items": "flex-start", gap: "8px" }}>
+                  <span style={{ ...detailMark, color: colors[node().kind] }}>
+                    <KindIcon node={node()} />
+                  </span>
+                  <span style={{ display: "flex", "flex-direction": "column", gap: "3px", flex: 1, "min-width": 0 }}>
+                    <strong>{node().label}</strong>
+                    <small>
+                      {node().kind} · {node().id}
+                    </small>
+                  </span>
+                  <State node={node()} edges={graph()?.edges ?? []} />
+                </div>
+                <Show when={node().path}>
+                  <div style={property}>
+                    <span>path</span>
+                    <strong>{node().path}</strong>
+                  </div>
+                </Show>
+                <Show when={node().tool}>
+                  <div style={property}>
+                    <span>tool</span>
+                    <strong>{node().tool}</strong>
+                  </div>
+                </Show>
+                <Show when={node().meta?.claim}>
+                  <div style={claimCard}>
+                    <span>claim</span>
+                    <p>{String(node().meta?.claim)}</p>
+                  </div>
+                </Show>
+                <Show when={node().meta?.issue}>
+                  <div style={finding(node().meta?.severity)}>
+                    <span>{String(node().meta?.severity ?? "review")} finding</span>
+                    <strong>{String(node().meta?.issue)}</strong>
+                    <small>{String(node().meta?.evidence ?? "")}</small>
+                  </div>
+                </Show>
+                <div style={relationList}>
+                  <For each={related()}>
+                    {(edge) => {
+                      const other = () =>
+                        graph()?.nodes.find((item) => item.id === (edge.from === node().id ? edge.to : edge.from))
+                      return (
+                        <button
+                          type="button"
+                          style={relationButton}
+                          onClick={() => other() && setSelected(other()!.id)}
+                        >
+                          <span>{edge.relation}</span>
+                          <strong>{other()?.label ?? "missing node"}</strong>
+                        </button>
+                      )
+                    }}
+                  </For>
+                </div>
+                <button type="button" style={auditButton} onClick={audit}>
+                  <IconCheckCircle size={11} />
+                  run reviewer audit
+                </button>
+              </section>
+            )}
+          </Show>
+        </div>
+      </Show>
+    </div>
+  )
+}
+
+function Score(props: { label: string; value: number; color: string }): JSX.Element {
+  return (
+    <div style={score}>
+      <strong style={{ color: props.color }}>{props.value}</strong>
+      <span>{props.label}</span>
+    </div>
+  )
+}
+
+function KindIcon(props: { node: Node }): JSX.Element {
+  if (props.node.kind === "run") return <IconActivity size={12} />
+  if (props.node.kind === "artifact") return <IconFile size={12} />
+  if (props.node.kind === "claim") return <IconCheckCircle size={12} />
+  return <IconNetwork size={12} />
+}
+
+function State(props: { node: Node; edges: Edge[] }): JSX.Element {
+  const value = () => status(props.node, props.edges)
+  const color = () => {
+    if (value() === "supported") return "var(--color-success)"
+    if (value() === "flagged") return "var(--color-danger)"
+    return "var(--color-text-faint)"
+  }
+  return <span style={{ ...state, color: color() }}>{value()}</span>
+}
+
+function status(node: Node, edges: Edge[]): string {
+  if (node.meta?.review === true) return String(node.meta.verdict ?? "reviewed")
+  if (edges.some((edge) => edge.to === node.id && edge.relation === "refutes")) return "flagged"
+  if (edges.some((edge) => edge.to === node.id && edge.relation === "supports")) return "supported"
+  if (node.kind === "run") return node.status === "error" ? "failed" : "recorded"
+  return "unchecked"
+}
+
+function layout(nodes: Node[]): Map<string, { x: number; y: number }> {
+  const columns: Record<Kind, number> = { source: 45, run: 135, artifact: 225, claim: 315 }
+  const groups = new Map<Kind, Node[]>([
+    ["source", []],
+    ["run", []],
+    ["artifact", []],
+    ["claim", []],
+  ])
+  for (const node of nodes) groups.get(node.kind)?.push(node)
+  const points = new Map<string, { x: number; y: number }>()
+  for (const [kind, values] of groups) {
+    const gap = 150 / Math.max(1, values.length)
+    values.forEach((node, index) => points.set(node.id, { x: columns[kind], y: 19 + gap * (index + 0.5) }))
+  }
+  return points
+}
+
+function Action(props: { title: string; onClick: () => void; children: JSX.Element }): JSX.Element {
+  return (
+    <button type="button" title={props.title} aria-label={props.title} onClick={props.onClick} style={action}>
+      {props.children}
+    </button>
+  )
+}
+
+const shell: JSX.CSSProperties = {
+  flex: 1,
+  "min-height": 0,
+  display: "flex",
+  "flex-direction": "column",
+  overflow: "hidden",
+  background: "var(--color-bg-subtle)",
+  "font-family": FONT_SANS,
+}
+
+const header: JSX.CSSProperties = {
+  display: "flex",
+  "align-items": "center",
+  "justify-content": "space-between",
+  gap: "10px",
+  padding: "10px",
+  border: "1px solid transparent",
+  "border-bottom-color": "var(--color-border)",
+  background: "var(--color-bg)",
+  "flex-shrink": 0,
+}
+
+const mark: JSX.CSSProperties = {
+  width: "27px",
+  height: "27px",
+  display: "inline-flex",
+  "align-items": "center",
+  "justify-content": "center",
+  "border-radius": "6px",
+  background: "color-mix(in srgb, var(--color-accent) 12%, transparent)",
+  color: "var(--color-accent)",
+}
+
+const title: JSX.CSSProperties = {
+  color: "var(--color-text)",
+  "font-size": "12px",
+  "font-weight": 680,
+  "letter-spacing": "-0.01em",
+}
+
+const subtitle: JSX.CSSProperties = {
+  color: "var(--color-text-faint)",
+  "font-family": FONT_MONO,
+  "font-size": "9px",
+}
+
+const action: JSX.CSSProperties = {
+  all: "unset",
+  cursor: "pointer",
+  width: "27px",
+  height: "27px",
+  display: "inline-flex",
+  "align-items": "center",
+  "justify-content": "center",
+  "border-radius": "4px",
+  border: "1px solid var(--color-border)",
+  background: "var(--color-bg-elevated)",
+  color: "var(--color-text-muted)",
+  "box-sizing": "border-box",
+}
+
+const scoreRow: JSX.CSSProperties = {
+  display: "grid",
+  "grid-template-columns": "repeat(4, minmax(0, 1fr))",
+  gap: "1px",
+  border: "1px solid var(--color-border)",
+  "border-width": "0 0 1px",
+  background: "var(--color-border)",
+}
+
+const score: JSX.CSSProperties = {
+  display: "flex",
+  "flex-direction": "column",
+  gap: "2px",
+  padding: "9px 8px",
+  background: "var(--color-bg)",
+  "text-align": "center",
+  "font-family": FONT_MONO,
+  "font-size": "8px",
+  color: "var(--color-text-faint)",
+}
+
+const warning: JSX.CSSProperties = {
+  display: "flex",
+  "align-items": "center",
+  gap: "6px",
+  padding: "7px 10px",
+  background: "color-mix(in srgb, var(--color-danger) 8%, transparent)",
+  color: "var(--color-danger)",
+  "font-family": FONT_MONO,
+  "font-size": "9px",
+  border: "1px solid transparent",
+  "border-bottom-color": "color-mix(in srgb, var(--color-danger) 24%, transparent)",
+}
+
+const controls: JSX.CSSProperties = {
+  display: "flex",
+  "flex-direction": "column",
+  gap: "6px",
+  padding: "8px",
+  border: "1px solid transparent",
+  "border-bottom-color": "var(--color-border)",
+  background: "var(--color-bg)",
+}
+
+const search: JSX.CSSProperties = {
+  height: "29px",
+  display: "flex",
+  "align-items": "center",
+  gap: "6px",
+  padding: "0 8px",
+  border: "1px solid var(--color-border)",
+  "border-radius": "4px",
+  color: "var(--color-text-faint)",
+  background: "var(--color-bg-subtle)",
+}
+
+const filters: JSX.CSSProperties = {
+  display: "flex",
+  gap: "3px",
+  overflow: "auto",
+}
+
+const filterButton = (active: boolean): JSX.CSSProperties => ({
+  all: "unset",
+  cursor: "pointer",
+  padding: "4px 6px",
+  border: "1px solid",
+  "border-color": active ? "var(--color-accent)" : "var(--color-border)",
+  "border-radius": "999px",
+  background: active ? "var(--color-accent-subtle)" : "transparent",
+  color: active ? "var(--color-accent)" : "var(--color-text-faint)",
+  "font-family": FONT_MONO,
+  "font-size": "8px",
+})
+
+const map: JSX.CSSProperties = {
+  position: "relative",
+  height: "210px",
+  "flex-shrink": 0,
+  background:
+    "radial-gradient(circle at 1px 1px, color-mix(in srgb, var(--color-text-faint) 18%, transparent) 1px, transparent 0)",
+  "background-size": "14px 14px",
+  border: "1px solid transparent",
+  "border-bottom-color": "var(--color-border)",
+}
+
+const legend: JSX.CSSProperties = {
+  position: "absolute",
+  left: "8px",
+  right: "8px",
+  bottom: "6px",
+  display: "flex",
+  "justify-content": "space-between",
+  color: "var(--color-text-faint)",
+  "font-family": FONT_MONO,
+  "font-size": "7px",
+  "text-transform": "uppercase",
+  "letter-spacing": "0.04em",
+}
+
+const body: JSX.CSSProperties = {
+  flex: 1,
+  "min-height": 0,
+  overflow: "auto",
+  display: "flex",
+  "flex-direction": "column",
+}
+
+const nodeList: JSX.CSSProperties = {
+  display: "flex",
+  "flex-direction": "column",
+  gap: "2px",
+  padding: "6px",
+  "max-height": "176px",
+  overflow: "auto",
+  border: "1px solid transparent",
+  "border-bottom-color": "var(--color-border)",
+}
+
+const nodeRow = (active: boolean): JSX.CSSProperties => ({
+  cursor: "pointer",
+  width: "100%",
+  display: "flex",
+  "align-items": "center",
+  gap: "7px",
+  padding: "7px",
+  border: "1px solid",
+  "border-color": active ? "var(--color-border-strong)" : "transparent",
+  "border-radius": "4px",
+  background: active ? "var(--color-surface-solid)" : "transparent",
+  "text-align": "left",
+  color: "var(--color-text)",
+  "font-family": FONT_SANS,
+  "font-size": "10px",
+})
+
+const nodeDot: JSX.CSSProperties = {
+  width: "7px",
+  height: "7px",
+  "border-radius": "50%",
+  "flex-shrink": 0,
+}
+
+const detail: JSX.CSSProperties = {
+  display: "flex",
+  "flex-direction": "column",
+  gap: "8px",
+  padding: "10px",
+  background: "var(--color-bg)",
+}
+
+const detailMark: JSX.CSSProperties = {
+  width: "25px",
+  height: "25px",
+  display: "inline-flex",
+  "align-items": "center",
+  "justify-content": "center",
+  "border-radius": "5px",
+  border: "1px solid var(--color-border)",
+  "flex-shrink": 0,
+}
+
+const state: JSX.CSSProperties = {
+  padding: "3px 5px",
+  border: "1px solid currentColor",
+  "border-radius": "999px",
+  "font-family": FONT_MONO,
+  "font-size": "7px",
+  "text-transform": "uppercase",
+}
+
+const property: JSX.CSSProperties = {
+  display: "grid",
+  "grid-template-columns": "52px minmax(0, 1fr)",
+  gap: "8px",
+  color: "var(--color-text-faint)",
+  "font-family": FONT_MONO,
+  "font-size": "8px",
+  "overflow-wrap": "anywhere",
+}
+
+const claimCard: JSX.CSSProperties = {
+  padding: "8px",
+  border: "1px solid color-mix(in srgb, #9c6ade 32%, var(--color-border))",
+  "border-radius": "5px",
+  background: "color-mix(in srgb, #9c6ade 6%, var(--color-bg))",
+  color: "var(--color-text-muted)",
+  "font-size": "10px",
+  "line-height": 1.45,
+}
+
+const finding = (severity: unknown): JSX.CSSProperties => ({
+  display: "flex",
+  "flex-direction": "column",
+  gap: "4px",
+  padding: "8px",
+  border: "1px solid",
+  "border-color":
+    severity === "blocking" || severity === "major"
+      ? "color-mix(in srgb, var(--color-danger) 38%, var(--color-border))"
+      : "var(--color-border)",
+  "border-radius": "5px",
+  background:
+    severity === "blocking" || severity === "major"
+      ? "color-mix(in srgb, var(--color-danger) 7%, var(--color-bg))"
+      : "var(--color-bg-subtle)",
+  color: "var(--color-text-muted)",
+  "font-family": FONT_MONO,
+  "font-size": "8px",
+  "line-height": 1.4,
+})
+
+const relationList: JSX.CSSProperties = {
+  display: "flex",
+  "flex-direction": "column",
+  gap: "3px",
+}
+
+const relationButton: JSX.CSSProperties = {
+  cursor: "pointer",
+  display: "grid",
+  "grid-template-columns": "72px minmax(0, 1fr)",
+  gap: "6px",
+  padding: "5px 6px",
+  border: "1px solid var(--color-border)",
+  "border-radius": "4px",
+  background: "var(--color-bg-subtle)",
+  color: "var(--color-text-faint)",
+  "font-family": FONT_MONO,
+  "font-size": "8px",
+  "text-align": "left",
+}
+
+const auditButton: JSX.CSSProperties = {
+  cursor: "pointer",
+  display: "inline-flex",
+  "align-items": "center",
+  "justify-content": "center",
+  gap: "5px",
+  padding: "6px 8px",
+  border: "1px solid var(--color-accent)",
+  "border-radius": "4px",
+  background: "var(--color-accent-subtle)",
+  color: "var(--color-accent)",
+  "font-family": FONT_MONO,
+  "font-size": "9px",
+}
+
+const errorBox: JSX.CSSProperties = {
+  margin: "8px",
+  padding: "8px",
+  border: "1px solid color-mix(in srgb, var(--color-danger) 35%, transparent)",
+  "border-radius": "4px",
+  color: "var(--color-danger)",
+  "font-family": FONT_MONO,
+  "font-size": "9px",
+}
+
+const empty: JSX.CSSProperties = {
+  flex: 1,
+  display: "flex",
+  "flex-direction": "column",
+  "align-items": "center",
+  "justify-content": "center",
+  gap: "9px",
+  padding: "30px 22px",
+  color: "var(--color-text-muted)",
+  "font-size": "11px",
+  "line-height": 1.5,
+  "text-align": "center",
+}
+
+const emptyMark: JSX.CSSProperties = {
+  width: "40px",
+  height: "40px",
+  display: "inline-flex",
+  "align-items": "center",
+  "justify-content": "center",
+  "border-radius": "10px",
+  background: "var(--color-surface-solid)",
+  border: "1px solid var(--color-border)",
+  color: "var(--color-text-faint)",
+}
+
+const primaryButton: JSX.CSSProperties = {
+  cursor: "pointer",
+  border: "1px solid var(--color-accent)",
+  "border-radius": "4px",
+  background: "var(--color-accent)",
+  color: "var(--color-bg)",
+  padding: "6px 10px",
+  "font-family": FONT_MONO,
+  "font-size": "9px",
+  "font-weight": 650,
+}
diff --git a/frontend/workspace/src/atlas/RightPane.tsx b/frontend/workspace/src/atlas/RightPane.tsx
index 7dfd98fc..bfa81019 100644
--- a/frontend/workspace/src/atlas/RightPane.tsx
+++ b/frontend/workspace/src/atlas/RightPane.tsx
@@ -8,6 +8,7 @@ import { uiStore, type RightPaneTab } from "@/atlas/store/ui"
 import { SkillLibraryDialog } from "@/atlas/SkillsBrowser"
 import { AtlasCanvas } from "@/atlas/AtlasCanvas"
 import { ComputeJobs } from "@/atlas/ComputeJobs"
+import { EvidenceGraph } from "@/atlas/EvidenceGraph"
 import { toast } from "@/atlas/Toast"
 import {
   IconLayoutGrid,
@@ -17,6 +18,7 @@ import {
   IconSettings,
   IconTerminal,
   IconActivity,
+  IconNetwork,
 } from "@/atlas/shared/Icon"
 
 const RIGHT_PANE_WIDTH_KEY = "thesis-right-pane-width-v1"
@@ -49,6 +51,7 @@ export function RightPane(): JSX.Element {
   const TABS: { k: RightPaneTab; label?: string; Icon: (p: { size?: number; strokeWidth?: number }) => JSX.Element }[] =
     [
       { k: "canvas", label: "atlas", Icon: IconLayoutGrid },
+      { k: "evidence", Icon: IconNetwork },
       { k: "jobs", Icon: IconActivity },
       { k: "terminal", Icon: IconTerminal },
     ]
@@ -227,6 +230,9 @@ export function RightPane(): JSX.Element {
           <KeepAlive show={tab() === "jobs"} mounted={visited().has("jobs")}>
             <ComputeJobs />
           </KeepAlive>
+          <KeepAlive show={tab() === "evidence"} mounted={visited().has("evidence")}>
+            <EvidenceGraph />
+          </KeepAlive>
           <KeepAlive show={tab() === "terminal"} mounted={visited().has("terminal")}>
             <TerminalTab />
           </KeepAlive>
diff --git a/frontend/workspace/src/atlas/store/ui.ts b/frontend/workspace/src/atlas/store/ui.ts
index b55afac1..0ca41cf0 100644
--- a/frontend/workspace/src/atlas/store/ui.ts
+++ b/frontend/workspace/src/atlas/store/ui.ts
@@ -1,6 +1,6 @@
 import { createSignal } from "solid-js"
 
-export type RightPaneTab = "canvas" | "jobs" | "terminal"
+export type RightPaneTab = "canvas" | "evidence" | "jobs" | "terminal"
 
 const PANE_OPEN_KEY = "openscience-rightpane-open-v2"
 const HIDDEN_TABS_KEY = "thesis-rightpane-hidden-tabs-v1"
diff --git a/frontend/workspace/src/components/session/research-launchpad.test.ts b/frontend/workspace/src/components/session/research-launchpad.test.ts
index 797fe434..9c4b5691 100644
--- a/frontend/workspace/src/components/session/research-launchpad.test.ts
+++ b/frontend/workspace/src/components/session/research-launchpad.test.ts
@@ -5,12 +5,27 @@ describe("research launchpad", () => {
   test("ships launch-ready workflows across the core scientific loop", () => {
     expect(researchWorkflows.map((workflow) => workflow.id)).toEqual([
       "analyze-data",
-      "run-notebook",
+      "single-cell",
+      "differential-expression",
       "inspect-structure",
       "sequence-qc",
+      "variant-analysis",
+      "assay-analysis",
+      "image-analysis",
+      "proteomics",
+      "run-notebook",
+      "protein-design",
+      "molecular-docking",
+      "molecular-dynamics",
+      "train-model",
+      "run-pipeline",
       "survey-literature",
+      "clinical-trials",
+      "target-prioritization",
       "reproduce-result",
       "compare-runs",
+      "verify-citations",
+      "build-figure",
       "write-report",
     ])
     expect(new Set(researchWorkflows.map((workflow) => workflow.group))).toEqual(
@@ -24,7 +39,17 @@ describe("research launchpad", () => {
       workflowGroups()
         .find((group) => group.id === "analyze")
         ?.workflows.map((workflow) => workflow.id),
-    ).toEqual(["analyze-data", "inspect-structure", "sequence-qc"])
+    ).toEqual([
+      "analyze-data",
+      "single-cell",
+      "differential-expression",
+      "inspect-structure",
+      "sequence-qc",
+      "variant-analysis",
+      "assay-analysis",
+      "image-analysis",
+      "proteomics",
+    ])
   })
 
   test("adds project context to workflow prompts when artifacts are available", () => {
diff --git a/frontend/workspace/src/components/session/research-launchpad.ts b/frontend/workspace/src/components/session/research-launchpad.ts
index 5ec8390a..0136c34a 100644
--- a/frontend/workspace/src/components/session/research-launchpad.ts
+++ b/frontend/workspace/src/components/session/research-launchpad.ts
@@ -5,7 +5,17 @@ export type ResearchWorkflow = {
   description: string
   prompt: string
   shortcut: string
-  icon: "table" | "notebook" | "atom" | "sequence" | "search" | "reproduce" | "compare" | "report"
+  icon:
+    | "table"
+    | "notebook"
+    | "atom"
+    | "sequence"
+    | "search"
+    | "reproduce"
+    | "compare"
+    | "report"
+    | "activity"
+    | "network"
 }
 
 export const researchWorkflows: ResearchWorkflow[] = [
@@ -20,14 +30,24 @@ export const researchWorkflows: ResearchWorkflow[] = [
     icon: "table",
   },
   {
-    id: "run-notebook",
-    group: "compute",
-    title: "Run a notebook",
-    description: "Open an existing notebook or build one with live Python or R outputs.",
+    id: "single-cell",
+    group: "analyze",
+    title: "Single-cell analysis",
+    description: "QC, normalize, cluster, annotate, and compare cells with traceable decisions.",
     prompt:
-      "Find the most relevant notebook in this project, inspect it before running anything, then execute or repair it cell by cell. Preserve outputs and summarize the result and environment.",
-    shortcut: "Jupyter · Python · R",
-    icon: "notebook",
+      "Run a defensible single-cell analysis on the relevant AnnData, Loom, 10x, or count-matrix data. Inspect QC before filtering, preserve raw counts, document thresholds, normalize and reduce dimensions, cluster, annotate with evidence, test differential expression, and save the executable notebook plus figures.",
+    shortcut: "Scanpy · scVI · CellTypist",
+    icon: "table",
+  },
+  {
+    id: "differential-expression",
+    group: "analyze",
+    title: "Differential expression",
+    description: "Design a statistically valid comparison with diagnostics and pathway interpretation.",
+    prompt:
+      "Analyze differential expression for the relevant count or expression data. Recover the experimental design and covariates first, check sample QC and confounding, choose an appropriate DESeq2, edgeR, limma, or nonparametric workflow, correct multiple tests, produce diagnostic plots, and separate robust signals from exploratory ones.",
+    shortcut: "DESeq2 · edgeR · limma · GSEA",
+    icon: "compare",
   },
   {
     id: "inspect-structure",
@@ -49,6 +69,106 @@ export const researchWorkflows: ResearchWorkflow[] = [
     shortcut: "FASTQ · VCF · BAM · GFF",
     icon: "sequence",
   },
+  {
+    id: "variant-analysis",
+    group: "analyze",
+    title: "Analyze variants",
+    description: "Inspect VCF/BAM evidence, annotate variants, and prioritize interpretable candidates.",
+    prompt:
+      "Analyze the relevant variant and alignment files. Validate references and sample metadata, inspect VCF and BAM quality, normalize and annotate variants with appropriate population and clinical databases, flag filtering assumptions, prioritize candidates, and produce a table whose evidence and provenance can be audited.",
+    shortcut: "VCF · BAM · ClinVar · gnomAD",
+    icon: "sequence",
+  },
+  {
+    id: "assay-analysis",
+    group: "analyze",
+    title: "Analyze an assay",
+    description: "Normalize plates, fit dose response, quantify uncertainty, and surface QC failures.",
+    prompt:
+      "Analyze the relevant assay or plate data. Identify controls and layout, check edge and batch effects, normalize with a justified method, fit dose-response or IC50 curves when appropriate, quantify uncertainty and fit quality, flag failed wells or plates, and export a clean result table and publication-ready plots.",
+    shortcut: "plates · dose response · IC50",
+    icon: "table",
+  },
+  {
+    id: "image-analysis",
+    group: "analyze",
+    title: "Analyze microscopy",
+    description: "Inspect image metadata, segment objects, extract features, and verify overlays.",
+    prompt:
+      "Build a reproducible microscopy analysis for the relevant images. Inspect channels, bit depth, scale, and acquisition metadata first; choose an appropriate Cellpose, StarDist, MONAI, or classical segmentation path; generate QC overlays; extract object-level features; and save masks, tables, figures, and parameters.",
+    shortcut: "Cellpose · StarDist · MONAI",
+    icon: "reproduce",
+  },
+  {
+    id: "proteomics",
+    group: "analyze",
+    title: "Analyze proteomics",
+    description: "QC spectra and quantification, handle missingness, and test protein-level changes.",
+    prompt:
+      "Analyze the relevant mass-spectrometry or proteomics data. Inspect mzML or result-table quality, identify the acquisition and quantification method, check contaminants and missingness, normalize without leaking groups, perform protein-level statistics with multiple-testing correction, and save diagnostic figures and traceable result tables.",
+    shortcut: "mzML · OpenMS · DIA-NN",
+    icon: "activity",
+  },
+  {
+    id: "run-notebook",
+    group: "compute",
+    title: "Run a notebook",
+    description: "Open an existing notebook or build one with live Python or R outputs.",
+    prompt:
+      "Find the most relevant notebook in this project, inspect it before running anything, then execute or repair it cell by cell. Preserve outputs and summarize the result and environment.",
+    shortcut: "Jupyter · Python · R",
+    icon: "notebook",
+  },
+  {
+    id: "protein-design",
+    group: "compute",
+    title: "Design a protein",
+    description: "Define constraints, generate candidates, score structure, and preserve model provenance.",
+    prompt:
+      "Design protein candidates for the stated objective. Recover the target, interface, motif, sequence, and developability constraints before choosing tools. Use available structure prediction, RFdiffusion, ProteinMPNN, LigandMPNN, ESM, Boltz, Chai, or related workflows only where installed or accessible. Generate a small auditable candidate set, score failure modes, render structures, and preserve every model/version/seed/config.",
+    shortcut: "ESM · Boltz · RFdiffusion · MPNN",
+    icon: "atom",
+  },
+  {
+    id: "molecular-docking",
+    group: "compute",
+    title: "Dock molecules",
+    description: "Prepare receptor and ligands, validate the box, compare poses, and inspect interactions.",
+    prompt:
+      "Run a careful molecular docking workflow on the relevant receptor and ligands. Validate chemistry, protonation, cofactors, missing residues, and the binding-site box first. Use an available DiffDock, GNINA, or AutoDock Vina path, include a control or redocking check, compare poses and scores without overstating affinity, render key interactions, and save prepared inputs and configs.",
+    shortcut: "DiffDock · GNINA · Vina",
+    icon: "atom",
+  },
+  {
+    id: "molecular-dynamics",
+    group: "compute",
+    title: "Run molecular dynamics",
+    description: "Prepare, minimize, equilibrate, simulate, and validate a molecular system.",
+    prompt:
+      "Plan and run the relevant molecular-dynamics workflow with OpenMM, GROMACS, or AMBER if available. Validate force fields, protonation, solvent, ions, restraints, timestep, and ensemble; separate minimization, equilibration, and production; checkpoint long runs; monitor stability; and report RMSD/RMSF and decision-relevant observables with exact configs.",
+    shortcut: "OpenMM · GROMACS · AMBER",
+    icon: "activity",
+  },
+  {
+    id: "train-model",
+    group: "compute",
+    title: "Train a model",
+    description: "Profile data, choose compute, track experiments, checkpoint, and compare honestly.",
+    prompt:
+      "Build a reproducible model-training run for this project. Inspect data splits and leakage risks first, establish a baseline and metric, estimate compute and memory, choose local or managed compute, capture the environment and random seeds, stream logs, save checkpoints and artifacts, evaluate on a held-out set, and run the reviewer gate before reporting results.",
+    shortcut: "PyTorch · TRL · scikit-learn",
+    icon: "activity",
+  },
+  {
+    id: "run-pipeline",
+    group: "compute",
+    title: "Run a bioinformatics pipeline",
+    description: "Detect workflow definitions, validate inputs, execute safely, and collect reports.",
+    prompt:
+      "Find and run the most appropriate workflow in this project using Nextflow, nf-core, Snakemake, WDL/Cromwell, or the repository's own runner. Validate samplesheets, references, profiles, containers, and expected outputs first. Start with a dry run or small test when possible, use managed compute for long work, stream logs, collect reports and artifacts, and record failed steps clearly.",
+    shortcut: "Nextflow · nf-core · Snakemake",
+    icon: "reproduce",
+  },
   {
     id: "survey-literature",
     group: "discover",
@@ -59,6 +179,26 @@ export const researchWorkflows: ResearchWorkflow[] = [
     shortcut: "papers · citations · claims",
     icon: "search",
   },
+  {
+    id: "clinical-trials",
+    group: "discover",
+    title: "Compare clinical trials",
+    description: "Map designs, eligibility, endpoints, status, and evidence gaps across trials.",
+    prompt:
+      "Compare clinical trials relevant to the question using real registry records. Normalize phase, population, eligibility, interventions, comparators, endpoints, enrollment, status, dates, and reported results. Distinguish planned from completed evidence, identify endpoint or population mismatches, cite registry identifiers, and produce a comparison table with explicit caveats.",
+    shortcut: "ClinicalTrials.gov · endpoints",
+    icon: "search",
+  },
+  {
+    id: "target-prioritization",
+    group: "discover",
+    title: "Prioritize a target",
+    description: "Combine genetics, expression, pathways, tractability, and safety evidence.",
+    prompt:
+      "Build a target-prioritization report for the disease or phenotype. Combine Open Targets, genetics, expression, pathways, protein structure, known drugs, tractability, and safety evidence; preserve evidence provenance; score dimensions separately before any aggregate ranking; surface contradictory evidence; and finish with the experiments that would most change the decision.",
+    shortcut: "Open Targets · genetics · pathways",
+    icon: "network",
+  },
   {
     id: "reproduce-result",
     group: "discover",
@@ -79,6 +219,26 @@ export const researchWorkflows: ResearchWorkflow[] = [
     shortcut: "metrics · configs · failures",
     icon: "compare",
   },
+  {
+    id: "verify-citations",
+    group: "communicate",
+    title: "Verify citations & claims",
+    description: "Check that sources exist, support the text, and match every quoted number.",
+    prompt:
+      "Audit the citations and scientific claims in the relevant report or manuscript. Resolve every DOI, PMID, arXiv id, URL, or bibliography key; verify that each source actually supports the attributed claim; compare quoted numbers against the source; flag missing, weak, mismatched, or contradictory citations; and record findings in the provenance graph.",
+    shortcut: "DOI · PMID · claim support",
+    icon: "reproduce",
+  },
+  {
+    id: "build-figure",
+    group: "communicate",
+    title: "Build a publication figure",
+    description: "Turn project evidence into a clear, accessible, export-ready multi-panel figure.",
+    prompt:
+      "Create a publication-quality figure from the relevant project data and results. Identify the exact claim each panel supports, choose statistically honest encodings, preserve units and uncertainty, use accessible colors and readable typography, link every panel to its source data and code, and export editable source plus SVG, PNG, and PDF versions where supported.",
+    shortcut: "SVG · PNG · PDF · provenance",
+    icon: "report",
+  },
   {
     id: "write-report",
     group: "communicate",
diff --git a/frontend/workspace/src/components/session/session-new-view.tsx b/frontend/workspace/src/components/session/session-new-view.tsx
index e63ff160..d0d93063 100644
--- a/frontend/workspace/src/components/session/session-new-view.tsx
+++ b/frontend/workspace/src/components/session/session-new-view.tsx
@@ -1,4 +1,4 @@
-import { For, Show, createMemo, createResource, type JSX } from "solid-js"
+import { For, Show, createMemo, createResource, createSignal, type JSX } from "solid-js"
 import { DateTime } from "luxon"
 import { useSync } from "@/context/sync"
 import { useModels } from "@/context/models"
@@ -40,6 +40,8 @@ const icons: Record<ResearchWorkflow["icon"], (props: { size?: number; strokeWid
   reproduce: IconRefresh,
   compare: IconNetwork,
   report: IconFile,
+  activity: IconActivity,
+  network: IconNetwork,
 }
 
 export function NewSessionView(props: NewSessionViewProps) {
@@ -62,6 +64,12 @@ export function NewSessionView(props: NewSessionViewProps) {
         .then((response) => response.data ?? [])
         .catch(() => []),
   )
+  const [workflowGroup, setWorkflowGroup] = createSignal<ResearchWorkflow["group"] | "all">("all")
+  const visibleWorkflows = createMemo(() =>
+    workflowGroup() === "all"
+      ? researchWorkflows
+      : researchWorkflows.filter((workflow) => workflow.group === workflowGroup()),
+  )
   const local = createMemo(() => {
     try {
       const host = new URL(sdk.url).hostname
@@ -173,8 +181,37 @@ export function NewSessionView(props: NewSessionViewProps) {
             </label>
           </div>
 
+          <nav class="research-launchpad__workflow-filters" aria-label="Workflow categories">
+            <For
+              each={
+                [
+                  ["all", "All workflows"],
+                  ["analyze", "Analyze"],
+                  ["compute", "Compute"],
+                  ["discover", "Discover"],
+                  ["communicate", "Communicate"],
+                ] as const
+              }
+            >
+              {(item) => (
+                <button
+                  type="button"
+                  data-active={workflowGroup() === item[0] ? "true" : "false"}
+                  onClick={() => setWorkflowGroup(item[0])}
+                >
+                  {item[1]}
+                  <span>
+                    {item[0] === "all"
+                      ? researchWorkflows.length
+                      : researchWorkflows.filter((workflow) => workflow.group === item[0]).length}
+                  </span>
+                </button>
+              )}
+            </For>
+          </nav>
+
           <div class="research-launchpad__grid">
-            <For each={researchWorkflows}>
+            <For each={visibleWorkflows()}>
               {(workflow, index) => {
                 const Icon = icons[workflow.icon]
                 return (
diff --git a/frontend/workspace/src/science/formats/BinaryScienceView.tsx b/frontend/workspace/src/science/formats/BinaryScienceView.tsx
index 80b7db64..db252e76 100644
--- a/frontend/workspace/src/science/formats/BinaryScienceView.tsx
+++ b/frontend/workspace/src/science/formats/BinaryScienceView.tsx
@@ -4,6 +4,7 @@ import { useSDK } from "@/context/sdk"
 import { FONT_CODE, FONT_MONO, FONT_SANS } from "@/styles/tokens"
 import {
   formatBytes,
+  embedding as parseEmbedding,
   normalizeInspection,
   numbers,
   object,
@@ -11,6 +12,7 @@ import {
   strings,
   type BinaryInspection,
   type BinaryScienceFormat,
+  type Embedding,
 } from "./binary"
 
 export function BinaryScienceView(props: {
@@ -222,6 +224,7 @@ function Hdf5(props: { file: BinaryInspection }): JSX.Element {
   const layers = () => strings(summary().layers)
   const row = () => strings(summary().row_attributes)
   const column = () => strings(summary().column_attributes)
+  const embedding = () => parseEmbedding(props.file.details.embedding)
   return (
     <>
       <Show when={props.file.tool.available}>
@@ -249,6 +252,7 @@ function Hdf5(props: { file: BinaryInspection }): JSX.Element {
           />
           <Metric label="datasets" value={String(datasets().length)} detail={`${groups().length} groups`} />
         </div>
+        <Show when={embedding()}>{(value) => <EmbeddingPlot value={value()} />}</Show>
         <Show when={embeddings().length || layers().length || row().length || column().length}>
           <Panel title="Scientific schema" note="Analysis-ready structures">
             <div style={{ display: "grid", gap: "10px" }}>
@@ -296,6 +300,128 @@ function Hdf5(props: { file: BinaryInspection }): JSX.Element {
   )
 }
 
+function EmbeddingPlot(props: { value: Embedding }): JSX.Element {
+  const extent = () => {
+    const xs = props.value.points.map((point) => point.x)
+    const ys = props.value.points.map((point) => point.y)
+    return {
+      minX: Math.min(...xs),
+      maxX: Math.max(...xs),
+      minY: Math.min(...ys),
+      maxY: Math.max(...ys),
+    }
+  }
+  const point = (value: number, min: number, max: number, start: number, span: number) =>
+    start + ((value - min) / Math.max(Number.EPSILON, max - min)) * span
+  const labels = () => {
+    const counts = new Map<string, number>()
+    for (const item of props.value.points) {
+      if (!item.label) continue
+      counts.set(item.label, (counts.get(item.label) ?? 0) + 1)
+    }
+    return [...counts.entries()].toSorted((a, b) => b[1] - a[1])
+  }
+  return (
+    <Panel
+      title="Embedding preview"
+      note={`${props.value.name} · ${props.value.points.length.toLocaleString()} of ${props.value.total.toLocaleString()} observations`}
+    >
+      <div
+        style={{
+          display: "grid",
+          "grid-template-columns": labels().length ? "minmax(0, 1fr) 150px" : "1fr",
+          gap: "12px",
+        }}
+      >
+        <svg
+          viewBox="0 0 720 360"
+          role="img"
+          aria-label={`${props.value.name} embedding scatter plot`}
+          style={{
+            width: "100%",
+            "min-height": "260px",
+            border: "1px solid var(--color-border)",
+            "border-radius": "6px",
+            background:
+              "radial-gradient(circle at 1px 1px, color-mix(in srgb, var(--color-text-faint) 16%, transparent) 1px, transparent 0)",
+            "background-size": "18px 18px",
+          }}
+        >
+          <line x1="32" y1="330" x2="700" y2="330" stroke="var(--color-border-strong)" stroke-width="1" />
+          <line x1="32" y1="18" x2="32" y2="330" stroke="var(--color-border-strong)" stroke-width="1" />
+          <For each={props.value.points}>
+            {(item) => (
+              <circle
+                cx={point(item.x, extent().minX, extent().maxX, 40, 650)}
+                cy={point(item.y, extent().maxY, extent().minY, 24, 296)}
+                r={props.value.points.length > 1_500 ? 1.65 : 2.15}
+                fill={item.label ? color(item.label) : "var(--color-accent)"}
+                fill-opacity="0.72"
+              >
+                <title>
+                  {item.label ? `${item.label} · ` : ""}
+                  {item.x.toFixed(3)}, {item.y.toFixed(3)}
+                </title>
+              </circle>
+            )}
+          </For>
+          <text x="690" y="350" fill="var(--color-text-faint)" font-size="10" font-family={FONT_MONO}>
+            {props.value.name} 1
+          </text>
+          <text
+            x="12"
+            y="28"
+            fill="var(--color-text-faint)"
+            font-size="10"
+            font-family={FONT_MONO}
+            transform="rotate(-90 12 28)"
+          >
+            {props.value.name} 2
+          </text>
+        </svg>
+        <Show when={labels().length}>
+          <div style={{ display: "flex", "flex-direction": "column", gap: "7px", "min-width": 0 }}>
+            <span style={{ ...muted(), "font-size": "9px", "text-transform": "uppercase", "letter-spacing": "0.06em" }}>
+              {props.value.label ?? "groups"}
+            </span>
+            <For each={labels().slice(0, 14)}>
+              {(item) => (
+                <div
+                  style={{
+                    display: "grid",
+                    "grid-template-columns": "7px minmax(0, 1fr) auto",
+                    gap: "6px",
+                    "align-items": "center",
+                    "font-family": FONT_MONO,
+                    "font-size": "9px",
+                    color: "var(--color-text-muted)",
+                  }}
+                >
+                  <span style={{ width: "7px", height: "7px", "border-radius": "50%", background: color(item[0]) }} />
+                  <span style={{ overflow: "hidden", "text-overflow": "ellipsis", "white-space": "nowrap" }}>
+                    {item[0]}
+                  </span>
+                  <span style={{ color: "var(--color-text-faint)" }}>{item[1].toLocaleString()}</span>
+                </div>
+              )}
+            </For>
+            <Show when={labels().length > 14}>
+              <span style={muted()}>+{labels().length - 14} more groups</span>
+            </Show>
+          </div>
+        </Show>
+      </div>
+    </Panel>
+  )
+}
+
+const palette = ["#5c7cfa", "#2f9e74", "#e6a23c", "#9c6ade", "#e8590c", "#0ca678", "#d6336c", "#1098ad"]
+
+function color(value: string): string {
+  const hash = [...value].reduce((total, char) => (total * 31 + char.charCodeAt(0)) >>> 0, 0)
+  return palette[hash % palette.length]!
+}
+
 function Alignment(props: { file: BinaryInspection }): JSX.Element {
   const header = () => object(props.file.details.header)
   const references = () => objects(props.file.details.references)
diff --git a/frontend/workspace/src/science/formats/binary.test.ts b/frontend/workspace/src/science/formats/binary.test.ts
index d68da263..adab2a24 100644
--- a/frontend/workspace/src/science/formats/binary.test.ts
+++ b/frontend/workspace/src/science/formats/binary.test.ts
@@ -1,7 +1,7 @@
 import { describe, expect, test } from "bun:test"
 import { readFileSync } from "node:fs"
 import { fileURLToPath } from "node:url"
-import { detectBinaryScienceFormat, formatBytes, normalizeInspection } from "./binary"
+import { detectBinaryScienceFormat, embedding, formatBytes, normalizeInspection } from "./binary"
 
 const read = (path: string) => readFileSync(fileURLToPath(new URL(path, import.meta.url)), "utf8")
 
@@ -36,6 +36,29 @@ describe("binary scientific format helpers", () => {
       tool: { name: "samtools", available: false },
     })
   })
+
+  test("normalizes finite embedding previews and preserves categorical labels", () => {
+    expect(
+      embedding({
+        name: "X_umap",
+        label: "cell_type",
+        total: 10_000,
+        points: [
+          { x: 1, y: 2, label: "T cell" },
+          { x: Number.NaN, y: 3, label: "invalid" },
+          { x: -4, y: 5, label: "B cell" },
+        ],
+      }),
+    ).toEqual({
+      name: "X_umap",
+      label: "cell_type",
+      total: 10_000,
+      points: [
+        { x: 1, y: 2, label: "T cell" },
+        { x: -4, y: 5, label: "B cell" },
+      ],
+    })
+  })
 })
 
 describe("binary scientific workbench integration", () => {
@@ -49,5 +72,6 @@ describe("binary scientific workbench integration", () => {
     expect(view).toContain("/file/inspect?")
     expect(view).toContain("Dataset inventory")
     expect(view).toContain("Reference coverage")
+    expect(view).toContain("Embedding preview")
   })
 })
diff --git a/frontend/workspace/src/science/formats/binary.ts b/frontend/workspace/src/science/formats/binary.ts
index 1295bba9..99fe3eb1 100644
--- a/frontend/workspace/src/science/formats/binary.ts
+++ b/frontend/workspace/src/science/formats/binary.ts
@@ -15,6 +15,19 @@ export interface BinaryInspection {
   details: Record<string, unknown>
 }
 
+export interface EmbeddingPoint {
+  x: number
+  y: number
+  label?: string
+}
+
+export interface Embedding {
+  name: string
+  label?: string
+  total: number
+  points: EmbeddingPoint[]
+}
+
 const formats = new Set<BinaryScienceFormat>(["bam", "cram", "h5ad", "loom"])
 
 export function detectBinaryScienceFormat(extension: string): BinaryScienceFormat | undefined {
@@ -69,3 +82,21 @@ export function object(value: unknown): Record<string, unknown> {
   if (!value || typeof value !== "object" || Array.isArray(value)) return {}
   return value as Record<string, unknown>
 }
+
+export function embedding(value: unknown): Embedding | undefined {
+  const data = object(value)
+  const points = objects(data.points)
+    .map((point) => ({
+      x: typeof point.x === "number" ? point.x : Number.NaN,
+      y: typeof point.y === "number" ? point.y : Number.NaN,
+      label: typeof point.label === "string" ? point.label : undefined,
+    }))
+    .filter((point) => Number.isFinite(point.x) && Number.isFinite(point.y))
+  if (!points.length) return
+  return {
+    name: typeof data.name === "string" ? data.name : "embedding",
+    label: typeof data.label === "string" ? data.label : undefined,
+    total: typeof data.total === "number" ? data.total : points.length,
+    points,
+  }
+}
diff --git a/frontend/workspace/src/styles/atlas.css b/frontend/workspace/src/styles/atlas.css
index d4bb50e2..c0f3c920 100644
--- a/frontend/workspace/src/styles/atlas.css
+++ b/frontend/workspace/src/styles/atlas.css
@@ -1434,6 +1434,56 @@ button.research-launchpad__status-item:hover {
   color: var(--color-text);
 }
 
+.research-launchpad__workflow-filters {
+  display: flex;
+  align-items: center;
+  gap: 5px;
+  overflow-x: auto;
+  padding-bottom: 1px;
+}
+
+.research-launchpad__workflow-filters button {
+  all: unset;
+  box-sizing: border-box;
+  flex: 0 0 auto;
+  display: inline-flex;
+  align-items: center;
+  gap: 7px;
+  padding: 6px 9px;
+  border: 1px solid var(--color-border);
+  border-radius: 999px;
+  background: color-mix(in srgb, var(--color-surface-solid) 68%, transparent);
+  color: var(--color-text-muted);
+  font-family: var(--font-family-sans);
+  font-size: 10px;
+  cursor: pointer;
+  transition:
+    border-color 140ms ease,
+    background 140ms ease,
+    color 140ms ease;
+}
+
+.research-launchpad__workflow-filters button:hover {
+  border-color: var(--color-border-strong);
+  color: var(--color-text);
+}
+
+.research-launchpad__workflow-filters button[data-active="true"] {
+  border-color: color-mix(in srgb, var(--color-accent) 46%, var(--color-border));
+  background: var(--color-accent-subtle);
+  color: var(--color-accent);
+}
+
+.research-launchpad__workflow-filters button span {
+  min-width: 16px;
+  padding: 1px 4px;
+  border-radius: 999px;
+  background: color-mix(in srgb, currentColor 9%, transparent);
+  font-family: var(--font-family-mono);
+  font-size: 8px;
+  text-align: center;
+}
+
 .research-launchpad__grid {
   display: grid;
   grid-template-columns: repeat(2, minmax(0, 1fr));
diff --git a/tooling/sdk/js/src/v2/gen/sdk.gen.ts b/tooling/sdk/js/src/v2/gen/sdk.gen.ts
index f6345135..9e4dab4b 100644
--- a/tooling/sdk/js/src/v2/gen/sdk.gen.ts
+++ b/tooling/sdk/js/src/v2/gen/sdk.gen.ts
@@ -102,6 +102,14 @@ import type {
   ProjectListResponses,
   ProjectUpdateErrors,
   ProjectUpdateResponses,
+  ProvenanceExportResponses,
+  ProvenanceListResponses,
+  ProvenanceRecordErrors,
+  ProvenanceRecordResponses,
+  ProvenanceReviewErrors,
+  ProvenanceReviewResponses,
+  ProvenanceTraceErrors,
+  ProvenanceTraceResponses,
   ProviderAuthResponses,
   ProviderListResponses,
   ProviderOauthAuthorizeErrors,
@@ -912,6 +920,17 @@ export class Jobs extends HeyApiClient {
             kind: "ssh"
             host_id: string
           }
+      resources?: {
+        cpus?: number
+        gpus?: number
+        memory_gb?: number
+        time_minutes?: number
+        partition?: string
+      }
+      modules?: Array<string>
+      container?: string
+      artifacts?: Array<string>
+      checkpoint?: string
     },
     options?: Options<never, ThrowOnError>,
   ) {
@@ -924,6 +943,11 @@ export class Jobs extends HeyApiClient {
             { in: "body", key: "command" },
             { in: "body", key: "cwd" },
             { in: "body", key: "target" },
+            { in: "body", key: "resources" },
+            { in: "body", key: "modules" },
+            { in: "body", key: "container" },
+            { in: "body", key: "artifacts" },
+            { in: "body", key: "checkpoint" },
           ],
         },
       ],
@@ -3744,6 +3768,170 @@ export class Notebook extends HeyApiClient {
   }
 }
 
+export class Provenance extends HeyApiClient {
+  /**
+   * List the project provenance graph
+   *
+   * Returns project-scoped artifacts, runs, sources, claims, reviewer findings, and typed edges.
+   */
+  public list<ThrowOnError extends boolean = false>(
+    parameters?: {
+      directory?: string
+    },
+    options?: Options<never, ThrowOnError>,
+  ) {
+    const params = buildClientParams([parameters], [{ args: [{ in: "query", key: "directory" }] }])
+    return (options?.client ?? this.client).get<ProvenanceListResponses, unknown, ThrowOnError>({
+      url: "/provenance",
+      ...options,
+      ...params,
+    })
+  }
+
+  /**
+   * Record a project provenance node
+   */
+  public record<ThrowOnError extends boolean = false>(
+    parameters?: {
+      directory?: string
+      kind?: "artifact" | "run" | "source" | "claim"
+      label?: string
+      artifact_type?: string
+      path?: string
+      content_hash?: string
+      size?: number
+      tool?: string
+      status?: "ok" | "error"
+      meta?: {
+        [key: string]: unknown
+      }
+      derived_from?: string
+      relation?: "produced" | "consumed" | "derived-from" | "supports" | "refutes"
+    },
+    options?: Options<never, ThrowOnError>,
+  ) {
+    const params = buildClientParams(
+      [parameters],
+      [
+        {
+          args: [
+            { in: "query", key: "directory" },
+            { in: "body", key: "kind" },
+            { in: "body", key: "label" },
+            { in: "body", key: "artifact_type" },
+            { in: "body", key: "path" },
+            { in: "body", key: "content_hash" },
+            { in: "body", key: "size" },
+            { in: "body", key: "tool" },
+            { in: "body", key: "status" },
+            { in: "body", key: "meta" },
+            { in: "body", key: "derived_from" },
+            { in: "body", key: "relation" },
+          ],
+        },
+      ],
+    )
+    return (options?.client ?? this.client).post<ProvenanceRecordResponses, ProvenanceRecordErrors, ThrowOnError>({
+      url: "/provenance/nodes",
+      ...options,
+      ...params,
+      headers: {
+        "Content-Type": "application/json",
+        ...options?.headers,
+        ...params.headers,
+      },
+    })
+  }
+
+  /**
+   * Record a reviewer finding
+   */
+  public review<ThrowOnError extends boolean = false>(
+    parameters?: {
+      directory?: string
+      target?: string
+      claim?: string
+      issue?: string
+      severity?: "blocking" | "major" | "minor" | "info"
+      evidence?: string
+      verdict?: "refutes" | "supports"
+    },
+    options?: Options<never, ThrowOnError>,
+  ) {
+    const params = buildClientParams(
+      [parameters],
+      [
+        {
+          args: [
+            { in: "query", key: "directory" },
+            { in: "body", key: "target" },
+            { in: "body", key: "claim" },
+            { in: "body", key: "issue" },
+            { in: "body", key: "severity" },
+            { in: "body", key: "evidence" },
+            { in: "body", key: "verdict" },
+          ],
+        },
+      ],
+    )
+    return (options?.client ?? this.client).post<ProvenanceReviewResponses, ProvenanceReviewErrors, ThrowOnError>({
+      url: "/provenance/reviews",
+      ...options,
+      ...params,
+      headers: {
+        "Content-Type": "application/json",
+        ...options?.headers,
+        ...params.headers,
+      },
+    })
+  }
+
+  /**
+   * Export a project provenance audit
+   */
+  public export<ThrowOnError extends boolean = false>(
+    parameters?: {
+      directory?: string
+    },
+    options?: Options<never, ThrowOnError>,
+  ) {
+    const params = buildClientParams([parameters], [{ args: [{ in: "query", key: "directory" }] }])
+    return (options?.client ?? this.client).get<ProvenanceExportResponses, unknown, ThrowOnError>({
+      url: "/provenance/export",
+      ...options,
+      ...params,
+    })
+  }
+
+  /**
+   * Trace a provenance node
+   */
+  public trace<ThrowOnError extends boolean = false>(
+    parameters: {
+      id: string
+      directory?: string
+    },
+    options?: Options<never, ThrowOnError>,
+  ) {
+    const params = buildClientParams(
+      [parameters],
+      [
+        {
+          args: [
+            { in: "path", key: "id" },
+            { in: "query", key: "directory" },
+          ],
+        },
+      ],
+    )
+    return (options?.client ?? this.client).get<ProvenanceTraceResponses, ProvenanceTraceErrors, ThrowOnError>({
+      url: "/provenance/{id}",
+      ...options,
+      ...params,
+    })
+  }
+}
+
 export class Config3 extends HeyApiClient {
   /**
    * Remove MCP server
@@ -4595,6 +4783,11 @@ export class OpenScienceClient extends HeyApiClient {
     return (this._notebook ??= new Notebook({ client: this.client }))
   }
 
+  private _provenance?: Provenance
+  get provenance(): Provenance {
+    return (this._provenance ??= new Provenance({ client: this.client }))
+  }
+
   private _mcp?: Mcp
   get mcp(): Mcp {
     return (this._mcp ??= new Mcp({ client: this.client }))
diff --git a/tooling/sdk/js/src/v2/gen/types.gen.ts b/tooling/sdk/js/src/v2/gen/types.gen.ts
index 8f2ae3e4..8e5efef0 100644
--- a/tooling/sdk/js/src/v2/gen/types.gen.ts
+++ b/tooling/sdk/js/src/v2/gen/types.gen.ts
@@ -3226,6 +3226,58 @@ export type SettingsComputeJobsListResponses = {
     exit_code?: number | null
     pid?: number
     error?: string
+    resources?: {
+      cpus?: number
+      gpus?: number
+      memory_gb?: number
+      time_minutes?: number
+      partition?: string
+    }
+    modules?: Array<string>
+    container?: string
+    artifact_patterns?: Array<string>
+    artifacts?: Array<{
+      path: string
+      size: number
+      sha256: string
+      modified_at: string
+    }>
+    checkpoint_path?: string
+    checkpoint?: {
+      path: string
+      size: number
+      sha256: string
+      modified_at: string
+    }
+    reproducibility?: {
+      captured_at: string
+      command: string
+      cwd: string
+      platform: string
+      arch: string
+      bun: string
+      node: string
+      python?: string
+      git?: {
+        branch?: string
+        commit?: string
+        dirty: boolean
+      }
+      lockfiles: Array<{
+        path: string
+        size: number
+        sha256: string
+        modified_at: string
+      }>
+      resources?: {
+        cpus?: number
+        gpus?: number
+        memory_gb?: number
+        time_minutes?: number
+        partition?: string
+      }
+    }
+    capture_error?: string
   }>
 }
 
@@ -3244,6 +3296,17 @@ export type SettingsComputeJobsStartData = {
           kind: "ssh"
           host_id: string
         }
+    resources?: {
+      cpus?: number
+      gpus?: number
+      memory_gb?: number
+      time_minutes?: number
+      partition?: string
+    }
+    modules?: Array<string>
+    container?: string
+    artifacts?: Array<string>
+    checkpoint?: string
   }
   path?: never
   query?: never
@@ -3285,6 +3348,58 @@ export type SettingsComputeJobsStartResponses = {
     exit_code?: number | null
     pid?: number
     error?: string
+    resources?: {
+      cpus?: number
+      gpus?: number
+      memory_gb?: number
+      time_minutes?: number
+      partition?: string
+    }
+    modules?: Array<string>
+    container?: string
+    artifact_patterns?: Array<string>
+    artifacts?: Array<{
+      path: string
+      size: number
+      sha256: string
+      modified_at: string
+    }>
+    checkpoint_path?: string
+    checkpoint?: {
+      path: string
+      size: number
+      sha256: string
+      modified_at: string
+    }
+    reproducibility?: {
+      captured_at: string
+      command: string
+      cwd: string
+      platform: string
+      arch: string
+      bun: string
+      node: string
+      python?: string
+      git?: {
+        branch?: string
+        commit?: string
+        dirty: boolean
+      }
+      lockfiles: Array<{
+        path: string
+        size: number
+        sha256: string
+        modified_at: string
+      }>
+      resources?: {
+        cpus?: number
+        gpus?: number
+        memory_gb?: number
+        time_minutes?: number
+        partition?: string
+      }
+    }
+    capture_error?: string
   }
 }
 
@@ -3383,6 +3498,58 @@ export type SettingsComputeJobsCancelResponses = {
     exit_code?: number | null
     pid?: number
     error?: string
+    resources?: {
+      cpus?: number
+      gpus?: number
+      memory_gb?: number
+      time_minutes?: number
+      partition?: string
+    }
+    modules?: Array<string>
+    container?: string
+    artifact_patterns?: Array<string>
+    artifacts?: Array<{
+      path: string
+      size: number
+      sha256: string
+      modified_at: string
+    }>
+    checkpoint_path?: string
+    checkpoint?: {
+      path: string
+      size: number
+      sha256: string
+      modified_at: string
+    }
+    reproducibility?: {
+      captured_at: string
+      command: string
+      cwd: string
+      platform: string
+      arch: string
+      bun: string
+      node: string
+      python?: string
+      git?: {
+        branch?: string
+        commit?: string
+        dirty: boolean
+      }
+      lockfiles: Array<{
+        path: string
+        size: number
+        sha256: string
+        modified_at: string
+      }>
+      resources?: {
+        cpus?: number
+        gpus?: number
+        memory_gb?: number
+        time_minutes?: number
+        partition?: string
+      }
+    }
+    capture_error?: string
   }
 }
 
@@ -5753,6 +5920,130 @@ export type NotebookInterruptResponses = {
   200: unknown
 }
 
+export type ProvenanceListData = {
+  body?: never
+  path?: never
+  query?: {
+    directory?: string
+  }
+  url: "/provenance"
+}
+
+export type ProvenanceListResponses = {
+  /**
+   * Project provenance graph
+   */
+  200: unknown
+}
+
+export type ProvenanceRecordData = {
+  body?: {
+    kind: "artifact" | "run" | "source" | "claim"
+    label: string
+    artifact_type?: string
+    path?: string
+    content_hash?: string
+    size?: number
+    tool?: string
+    status?: "ok" | "error"
+    meta?: {
+      [key: string]: unknown
+    }
+    derived_from?: string
+    relation?: "produced" | "consumed" | "derived-from" | "supports" | "refutes"
+  }
+  path?: never
+  query?: {
+    directory?: string
+  }
+  url: "/provenance/nodes"
+}
+
+export type ProvenanceRecordErrors = {
+  /**
+   * Invalid link target
+   */
+  400: unknown
+}
+
+export type ProvenanceRecordResponses = {
+  /**
+   * Recorded node
+   */
+  200: unknown
+}
+
+export type ProvenanceReviewData = {
+  body?: {
+    target: string
+    claim: string
+    issue: string
+    severity: "blocking" | "major" | "minor" | "info"
+    evidence: string
+    verdict?: "refutes" | "supports"
+  }
+  path?: never
+  query?: {
+    directory?: string
+  }
+  url: "/provenance/reviews"
+}
+
+export type ProvenanceReviewErrors = {
+  /**
+   * Invalid target
+   */
+  400: unknown
+}
+
+export type ProvenanceReviewResponses = {
+  /**
+   * Recorded finding
+   */
+  200: unknown
+}
+
+export type ProvenanceExportData = {
+  body?: never
+  path?: never
+  query?: {
+    directory?: string
+  }
+  url: "/provenance/export"
+}
+
+export type ProvenanceExportResponses = {
+  /**
+   * Portable JSON audit packet
+   */
+  200: unknown
+}
+
+export type ProvenanceTraceData = {
+  body?: never
+  path: {
+    id: string
+  }
+  query?: {
+    directory?: string
+  }
+  url: "/provenance/{id}"
+}
+
+export type ProvenanceTraceErrors = {
+  /**
+   * Node not found
+   */
+  404: unknown
+}
+
+export type ProvenanceTraceResponses = {
+  /**
+   * Connected lineage
+   */
+  200: unknown
+}
+
 export type McpStatusData = {
   body?: never
   path?: never
diff --git a/tooling/sdk/openapi.json b/tooling/sdk/openapi.json
index 052dc445..d475606f 100644
--- a/tooling/sdk/openapi.json
+++ b/tooling/sdk/openapi.json
@@ -2804,6 +2804,227 @@
                       },
                       "error": {
                         "type": "string"
+                      },
+                      "resources": {
+                        "type": "object",
+                        "properties": {
+                          "cpus": {
+                            "type": "integer",
+                            "minimum": 1,
+                            "maximum": 1024
+                          },
+                          "gpus": {
+                            "type": "integer",
+                            "minimum": 0,
+                            "maximum": 128
+                          },
+                          "memory_gb": {
+                            "type": "number",
+                            "minimum": 0.1,
+                            "maximum": 100000
+                          },
+                          "time_minutes": {
+                            "type": "integer",
+                            "minimum": 1,
+                            "maximum": 43200
+                          },
+                          "partition": {
+                            "type": "string",
+                            "minLength": 1,
+                            "maxLength": 120
+                          }
+                        }
+                      },
+                      "modules": {
+                        "type": "array",
+                        "items": {
+                          "type": "string"
+                        }
+                      },
+                      "container": {
+                        "type": "string"
+                      },
+                      "artifact_patterns": {
+                        "type": "array",
+                        "items": {
+                          "type": "string"
+                        }
+                      },
+                      "artifacts": {
+                        "type": "array",
+                        "items": {
+                          "type": "object",
+                          "properties": {
+                            "path": {
+                              "type": "string"
+                            },
+                            "size": {
+                              "type": "integer",
+                              "minimum": 0,
+                              "maximum": 9007199254740991
+                            },
+                            "sha256": {
+                              "type": "string",
+                              "pattern": "^[a-f0-9]{64}$"
+                            },
+                            "modified_at": {
+                              "type": "string"
+                            }
+                          },
+                          "required": [
+                            "path",
+                            "size",
+                            "sha256",
+                            "modified_at"
+                          ]
+                        }
+                      },
+                      "checkpoint_path": {
+                        "type": "string"
+                      },
+                      "checkpoint": {
+                        "type": "object",
+                        "properties": {
+                          "path": {
+                            "type": "string"
+                          },
+                          "size": {
+                            "type": "integer",
+                            "minimum": 0,
+                            "maximum": 9007199254740991
+                          },
+                          "sha256": {
+                            "type": "string",
+                            "pattern": "^[a-f0-9]{64}$"
+                          },
+                          "modified_at": {
+                            "type": "string"
+                          }
+                        },
+                        "required": [
+                          "path",
+                          "size",
+                          "sha256",
+                          "modified_at"
+                        ]
+                      },
+                      "reproducibility": {
+                        "type": "object",
+                        "properties": {
+                          "captured_at": {
+                            "type": "string"
+                          },
+                          "command": {
+                            "type": "string"
+                          },
+                          "cwd": {
+                            "type": "string"
+                          },
+                          "platform": {
+                            "type": "string"
+                          },
+                          "arch": {
+                            "type": "string"
+                          },
+                          "bun": {
+                            "type": "string"
+                          },
+                          "node": {
+                            "type": "string"
+                          },
+                          "python": {
+                            "type": "string"
+                          },
+                          "git": {
+                            "type": "object",
+                            "properties": {
+                              "branch": {
+                                "type": "string"
+                              },
+                              "commit": {
+                                "type": "string"
+                              },
+                              "dirty": {
+                                "type": "boolean"
+                              }
+                            },
+                            "required": [
+                              "dirty"
+                            ]
+                          },
+                          "lockfiles": {
+                            "type": "array",
+                            "items": {
+                              "type": "object",
+                              "properties": {
+                                "path": {
+                                  "type": "string"
+                                },
+                                "size": {
+                                  "type": "integer",
+                                  "minimum": 0,
+                                  "maximum": 9007199254740991
+                                },
+                                "sha256": {
+                                  "type": "string",
+                                  "pattern": "^[a-f0-9]{64}$"
+                                },
+                                "modified_at": {
+                                  "type": "string"
+                                }
+                              },
+                              "required": [
+                                "path",
+                                "size",
+                                "sha256",
+                                "modified_at"
+                              ]
+                            }
+                          },
+                          "resources": {
+                            "type": "object",
+                            "properties": {
+                              "cpus": {
+                                "type": "integer",
+                                "minimum": 1,
+                                "maximum": 1024
+                              },
+                              "gpus": {
+                                "type": "integer",
+                                "minimum": 0,
+                                "maximum": 128
+                              },
+                              "memory_gb": {
+                                "type": "number",
+                                "minimum": 0.1,
+                                "maximum": 100000
+                              },
+                              "time_minutes": {
+                                "type": "integer",
+                                "minimum": 1,
+                                "maximum": 43200
+                              },
+                              "partition": {
+                                "type": "string",
+                                "minLength": 1,
+                                "maxLength": 120
+                              }
+                            }
+                          }
+                        },
+                        "required": [
+                          "captured_at",
+                          "command",
+                          "cwd",
+                          "platform",
+                          "arch",
+                          "bun",
+                          "node",
+                          "lockfiles"
+                        ]
+                      },
+                      "capture_error": {
+                        "type": "string"
                       }
                     },
                     "required": [
@@ -2934,6 +3155,227 @@
                     },
                     "error": {
                       "type": "string"
+                    },
+                    "resources": {
+                      "type": "object",
+                      "properties": {
+                        "cpus": {
+                          "type": "integer",
+                          "minimum": 1,
+                          "maximum": 1024
+                        },
+                        "gpus": {
+                          "type": "integer",
+                          "minimum": 0,
+                          "maximum": 128
+                        },
+                        "memory_gb": {
+                          "type": "number",
+                          "minimum": 0.1,
+                          "maximum": 100000
+                        },
+                        "time_minutes": {
+                          "type": "integer",
+                          "minimum": 1,
+                          "maximum": 43200
+                        },
+                        "partition": {
+                          "type": "string",
+                          "minLength": 1,
+                          "maxLength": 120
+                        }
+                      }
+                    },
+                    "modules": {
+                      "type": "array",
+                      "items": {
+                        "type": "string"
+                      }
+                    },
+                    "container": {
+                      "type": "string"
+                    },
+                    "artifact_patterns": {
+                      "type": "array",
+                      "items": {
+                        "type": "string"
+                      }
+                    },
+                    "artifacts": {
+                      "type": "array",
+                      "items": {
+                        "type": "object",
+                        "properties": {
+                          "path": {
+                            "type": "string"
+                          },
+                          "size": {
+                            "type": "integer",
+                            "minimum": 0,
+                            "maximum": 9007199254740991
+                          },
+                          "sha256": {
+                            "type": "string",
+                            "pattern": "^[a-f0-9]{64}$"
+                          },
+                          "modified_at": {
+                            "type": "string"
+                          }
+                        },
+                        "required": [
+                          "path",
+                          "size",
+                          "sha256",
+                          "modified_at"
+                        ]
+                      }
+                    },
+                    "checkpoint_path": {
+                      "type": "string"
+                    },
+                    "checkpoint": {
+                      "type": "object",
+                      "properties": {
+                        "path": {
+                          "type": "string"
+                        },
+                        "size": {
+                          "type": "integer",
+                          "minimum": 0,
+                          "maximum": 9007199254740991
+                        },
+                        "sha256": {
+                          "type": "string",
+                          "pattern": "^[a-f0-9]{64}$"
+                        },
+                        "modified_at": {
+                          "type": "string"
+                        }
+                      },
+                      "required": [
+                        "path",
+                        "size",
+                        "sha256",
+                        "modified_at"
+                      ]
+                    },
+                    "reproducibility": {
+                      "type": "object",
+                      "properties": {
+                        "captured_at": {
+                          "type": "string"
+                        },
+                        "command": {
+                          "type": "string"
+                        },
+                        "cwd": {
+                          "type": "string"
+                        },
+                        "platform": {
+                          "type": "string"
+                        },
+                        "arch": {
+                          "type": "string"
+                        },
+                        "bun": {
+                          "type": "string"
+                        },
+                        "node": {
+                          "type": "string"
+                        },
+                        "python": {
+                          "type": "string"
+                        },
+                        "git": {
+                          "type": "object",
+                          "properties": {
+                            "branch": {
+                              "type": "string"
+                            },
+                            "commit": {
+                              "type": "string"
+                            },
+                            "dirty": {
+                              "type": "boolean"
+                            }
+                          },
+                          "required": [
+                            "dirty"
+                          ]
+                        },
+                        "lockfiles": {
+                          "type": "array",
+                          "items": {
+                            "type": "object",
+                            "properties": {
+                              "path": {
+                                "type": "string"
+                              },
+                              "size": {
+                                "type": "integer",
+                                "minimum": 0,
+                                "maximum": 9007199254740991
+                              },
+                              "sha256": {
+                                "type": "string",
+                                "pattern": "^[a-f0-9]{64}$"
+                              },
+                              "modified_at": {
+                                "type": "string"
+                              }
+                            },
+                            "required": [
+                              "path",
+                              "size",
+                              "sha256",
+                              "modified_at"
+                            ]
+                          }
+                        },
+                        "resources": {
+                          "type": "object",
+                          "properties": {
+                            "cpus": {
+                              "type": "integer",
+                              "minimum": 1,
+                              "maximum": 1024
+                            },
+                            "gpus": {
+                              "type": "integer",
+                              "minimum": 0,
+                              "maximum": 128
+                            },
+                            "memory_gb": {
+                              "type": "number",
+                              "minimum": 0.1,
+                              "maximum": 100000
+                            },
+                            "time_minutes": {
+                              "type": "integer",
+                              "minimum": 1,
+                              "maximum": 43200
+                            },
+                            "partition": {
+                              "type": "string",
+                              "minLength": 1,
+                              "maxLength": 120
+                            }
+                          }
+                        }
+                      },
+                      "required": [
+                        "captured_at",
+                        "command",
+                        "cwd",
+                        "platform",
+                        "arch",
+                        "bun",
+                        "node",
+                        "lockfiles"
+                      ]
+                    },
+                    "capture_error": {
+                      "type": "string"
                     }
                   },
                   "required": [
@@ -3011,6 +3453,64 @@
                         ]
                       }
                     ]
+                  },
+                  "resources": {
+                    "type": "object",
+                    "properties": {
+                      "cpus": {
+                        "type": "integer",
+                        "minimum": 1,
+                        "maximum": 1024
+                      },
+                      "gpus": {
+                        "type": "integer",
+                        "minimum": 0,
+                        "maximum": 128
+                      },
+                      "memory_gb": {
+                        "type": "number",
+                        "minimum": 0.1,
+                        "maximum": 100000
+                      },
+                      "time_minutes": {
+                        "type": "integer",
+                        "minimum": 1,
+                        "maximum": 43200
+                      },
+                      "partition": {
+                        "type": "string",
+                        "minLength": 1,
+                        "maxLength": 120
+                      }
+                    }
+                  },
+                  "modules": {
+                    "maxItems": 64,
+                    "type": "array",
+                    "items": {
+                      "type": "string",
+                      "minLength": 1,
+                      "maxLength": 240
+                    }
+                  },
+                  "container": {
+                    "type": "string",
+                    "minLength": 1,
+                    "maxLength": 2000
+                  },
+                  "artifacts": {
+                    "maxItems": 100,
+                    "type": "array",
+                    "items": {
+                      "type": "string",
+                      "minLength": 1,
+                      "maxLength": 2000
+                    }
+                  },
+                  "checkpoint": {
+                    "type": "string",
+                    "minLength": 1,
+                    "maxLength": 2000
                   }
                 },
                 "required": [
@@ -3210,17 +3710,238 @@
                           "minimum": -9007199254740991,
                           "maximum": 9007199254740991
                         },
-                        {
-                          "type": "null"
+                        {
+                          "type": "null"
+                        }
+                      ]
+                    },
+                    "pid": {
+                      "type": "integer",
+                      "exclusiveMinimum": 0,
+                      "maximum": 9007199254740991
+                    },
+                    "error": {
+                      "type": "string"
+                    },
+                    "resources": {
+                      "type": "object",
+                      "properties": {
+                        "cpus": {
+                          "type": "integer",
+                          "minimum": 1,
+                          "maximum": 1024
+                        },
+                        "gpus": {
+                          "type": "integer",
+                          "minimum": 0,
+                          "maximum": 128
+                        },
+                        "memory_gb": {
+                          "type": "number",
+                          "minimum": 0.1,
+                          "maximum": 100000
+                        },
+                        "time_minutes": {
+                          "type": "integer",
+                          "minimum": 1,
+                          "maximum": 43200
+                        },
+                        "partition": {
+                          "type": "string",
+                          "minLength": 1,
+                          "maxLength": 120
+                        }
+                      }
+                    },
+                    "modules": {
+                      "type": "array",
+                      "items": {
+                        "type": "string"
+                      }
+                    },
+                    "container": {
+                      "type": "string"
+                    },
+                    "artifact_patterns": {
+                      "type": "array",
+                      "items": {
+                        "type": "string"
+                      }
+                    },
+                    "artifacts": {
+                      "type": "array",
+                      "items": {
+                        "type": "object",
+                        "properties": {
+                          "path": {
+                            "type": "string"
+                          },
+                          "size": {
+                            "type": "integer",
+                            "minimum": 0,
+                            "maximum": 9007199254740991
+                          },
+                          "sha256": {
+                            "type": "string",
+                            "pattern": "^[a-f0-9]{64}$"
+                          },
+                          "modified_at": {
+                            "type": "string"
+                          }
+                        },
+                        "required": [
+                          "path",
+                          "size",
+                          "sha256",
+                          "modified_at"
+                        ]
+                      }
+                    },
+                    "checkpoint_path": {
+                      "type": "string"
+                    },
+                    "checkpoint": {
+                      "type": "object",
+                      "properties": {
+                        "path": {
+                          "type": "string"
+                        },
+                        "size": {
+                          "type": "integer",
+                          "minimum": 0,
+                          "maximum": 9007199254740991
+                        },
+                        "sha256": {
+                          "type": "string",
+                          "pattern": "^[a-f0-9]{64}$"
+                        },
+                        "modified_at": {
+                          "type": "string"
+                        }
+                      },
+                      "required": [
+                        "path",
+                        "size",
+                        "sha256",
+                        "modified_at"
+                      ]
+                    },
+                    "reproducibility": {
+                      "type": "object",
+                      "properties": {
+                        "captured_at": {
+                          "type": "string"
+                        },
+                        "command": {
+                          "type": "string"
+                        },
+                        "cwd": {
+                          "type": "string"
+                        },
+                        "platform": {
+                          "type": "string"
+                        },
+                        "arch": {
+                          "type": "string"
+                        },
+                        "bun": {
+                          "type": "string"
+                        },
+                        "node": {
+                          "type": "string"
+                        },
+                        "python": {
+                          "type": "string"
+                        },
+                        "git": {
+                          "type": "object",
+                          "properties": {
+                            "branch": {
+                              "type": "string"
+                            },
+                            "commit": {
+                              "type": "string"
+                            },
+                            "dirty": {
+                              "type": "boolean"
+                            }
+                          },
+                          "required": [
+                            "dirty"
+                          ]
+                        },
+                        "lockfiles": {
+                          "type": "array",
+                          "items": {
+                            "type": "object",
+                            "properties": {
+                              "path": {
+                                "type": "string"
+                              },
+                              "size": {
+                                "type": "integer",
+                                "minimum": 0,
+                                "maximum": 9007199254740991
+                              },
+                              "sha256": {
+                                "type": "string",
+                                "pattern": "^[a-f0-9]{64}$"
+                              },
+                              "modified_at": {
+                                "type": "string"
+                              }
+                            },
+                            "required": [
+                              "path",
+                              "size",
+                              "sha256",
+                              "modified_at"
+                            ]
+                          }
+                        },
+                        "resources": {
+                          "type": "object",
+                          "properties": {
+                            "cpus": {
+                              "type": "integer",
+                              "minimum": 1,
+                              "maximum": 1024
+                            },
+                            "gpus": {
+                              "type": "integer",
+                              "minimum": 0,
+                              "maximum": 128
+                            },
+                            "memory_gb": {
+                              "type": "number",
+                              "minimum": 0.1,
+                              "maximum": 100000
+                            },
+                            "time_minutes": {
+                              "type": "integer",
+                              "minimum": 1,
+                              "maximum": 43200
+                            },
+                            "partition": {
+                              "type": "string",
+                              "minLength": 1,
+                              "maxLength": 120
+                            }
+                          }
                         }
+                      },
+                      "required": [
+                        "captured_at",
+                        "command",
+                        "cwd",
+                        "platform",
+                        "arch",
+                        "bun",
+                        "node",
+                        "lockfiles"
                       ]
                     },
-                    "pid": {
-                      "type": "integer",
-                      "exclusiveMinimum": 0,
-                      "maximum": 9007199254740991
-                    },
-                    "error": {
+                    "capture_error": {
                       "type": "string"
                     }
                   },
@@ -8601,6 +9322,287 @@
         ]
       }
     },
+    "/provenance": {
+      "get": {
+        "operationId": "provenance.list",
+        "parameters": [
+          {
+            "in": "query",
+            "name": "directory",
+            "schema": {
+              "type": "string"
+            }
+          }
+        ],
+        "summary": "List the project provenance graph",
+        "description": "Returns project-scoped artifacts, runs, sources, claims, reviewer findings, and typed edges.",
+        "responses": {
+          "200": {
+            "description": "Project provenance graph"
+          }
+        },
+        "x-codeSamples": [
+          {
+            "lang": "js",
+            "source": "import { createOpenScienceClient } from \"@synsci/sdk\"\n\nconst client = createOpenScienceClient()\nawait client.provenance.list({\n  ...\n})"
+          }
+        ]
+      }
+    },
+    "/provenance/nodes": {
+      "post": {
+        "operationId": "provenance.record",
+        "parameters": [
+          {
+            "in": "query",
+            "name": "directory",
+            "schema": {
+              "type": "string"
+            }
+          }
+        ],
+        "summary": "Record a project provenance node",
+        "responses": {
+          "200": {
+            "description": "Recorded node"
+          },
+          "400": {
+            "description": "Invalid link target"
+          }
+        },
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "type": "object",
+                "properties": {
+                  "kind": {
+                    "type": "string",
+                    "enum": [
+                      "artifact",
+                      "run",
+                      "source",
+                      "claim"
+                    ]
+                  },
+                  "label": {
+                    "type": "string",
+                    "minLength": 1,
+                    "maxLength": 240
+                  },
+                  "artifact_type": {
+                    "type": "string",
+                    "minLength": 1,
+                    "maxLength": 120
+                  },
+                  "path": {
+                    "type": "string",
+                    "maxLength": 4000
+                  },
+                  "content_hash": {
+                    "type": "string",
+                    "maxLength": 240
+                  },
+                  "size": {
+                    "type": "integer",
+                    "minimum": 0,
+                    "maximum": 9007199254740991
+                  },
+                  "tool": {
+                    "type": "string",
+                    "minLength": 1,
+                    "maxLength": 240
+                  },
+                  "status": {
+                    "type": "string",
+                    "enum": [
+                      "ok",
+                      "error"
+                    ]
+                  },
+                  "meta": {
+                    "type": "object",
+                    "propertyNames": {
+                      "type": "string"
+                    },
+                    "additionalProperties": {}
+                  },
+                  "derived_from": {
+                    "type": "string"
+                  },
+                  "relation": {
+                    "default": "derived-from",
+                    "type": "string",
+                    "enum": [
+                      "produced",
+                      "consumed",
+                      "derived-from",
+                      "supports",
+                      "refutes"
+                    ]
+                  }
+                },
+                "required": [
+                  "kind",
+                  "label"
+                ]
+              }
+            }
+          }
+        },
+        "x-codeSamples": [
+          {
+            "lang": "js",
+            "source": "import { createOpenScienceClient } from \"@synsci/sdk\"\n\nconst client = createOpenScienceClient()\nawait client.provenance.record({\n  ...\n})"
+          }
+        ]
+      }
+    },
+    "/provenance/reviews": {
+      "post": {
+        "operationId": "provenance.review",
+        "parameters": [
+          {
+            "in": "query",
+            "name": "directory",
+            "schema": {
+              "type": "string"
+            }
+          }
+        ],
+        "summary": "Record a reviewer finding",
+        "responses": {
+          "200": {
+            "description": "Recorded finding"
+          },
+          "400": {
+            "description": "Invalid target"
+          }
+        },
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "type": "object",
+                "properties": {
+                  "target": {
+                    "type": "string"
+                  },
+                  "claim": {
+                    "type": "string",
+                    "minLength": 1,
+                    "maxLength": 10000
+                  },
+                  "issue": {
+                    "type": "string",
+                    "minLength": 1,
+                    "maxLength": 10000
+                  },
+                  "severity": {
+                    "type": "string",
+                    "enum": [
+                      "blocking",
+                      "major",
+                      "minor",
+                      "info"
+                    ]
+                  },
+                  "evidence": {
+                    "type": "string",
+                    "minLength": 1,
+                    "maxLength": 20000
+                  },
+                  "verdict": {
+                    "default": "refutes",
+                    "type": "string",
+                    "enum": [
+                      "refutes",
+                      "supports"
+                    ]
+                  }
+                },
+                "required": [
+                  "target",
+                  "claim",
+                  "issue",
+                  "severity",
+                  "evidence"
+                ]
+              }
+            }
+          }
+        },
+        "x-codeSamples": [
+          {
+            "lang": "js",
+            "source": "import { createOpenScienceClient } from \"@synsci/sdk\"\n\nconst client = createOpenScienceClient()\nawait client.provenance.review({\n  ...\n})"
+          }
+        ]
+      }
+    },
+    "/provenance/export": {
+      "get": {
+        "operationId": "provenance.export",
+        "parameters": [
+          {
+            "in": "query",
+            "name": "directory",
+            "schema": {
+              "type": "string"
+            }
+          }
+        ],
+        "summary": "Export a project provenance audit",
+        "responses": {
+          "200": {
+            "description": "Portable JSON audit packet"
+          }
+        },
+        "x-codeSamples": [
+          {
+            "lang": "js",
+            "source": "import { createOpenScienceClient } from \"@synsci/sdk\"\n\nconst client = createOpenScienceClient()\nawait client.provenance.export({\n  ...\n})"
+          }
+        ]
+      }
+    },
+    "/provenance/{id}": {
+      "get": {
+        "operationId": "provenance.trace",
+        "parameters": [
+          {
+            "in": "query",
+            "name": "directory",
+            "schema": {
+              "type": "string"
+            }
+          },
+          {
+            "in": "path",
+            "name": "id",
+            "schema": {
+              "type": "string"
+            },
+            "required": true
+          }
+        ],
+        "summary": "Trace a provenance node",
+        "responses": {
+          "200": {
+            "description": "Connected lineage"
+          },
+          "404": {
+            "description": "Node not found"
+          }
+        },
+        "x-codeSamples": [
+          {
+            "lang": "js",
+            "source": "import { createOpenScienceClient } from \"@synsci/sdk\"\n\nconst client = createOpenScienceClient()\nawait client.provenance.trace({\n  ...\n})"
+          }
+        ]
+      }
+    },
     "/mcp": {
       "get": {
         "operationId": "mcp.status",

From c9d273114655f56a19f2a0a9ad48a912363e45df Mon Sep 17 00:00:00 2001
From: Aayam Bansal <aayambansal@gmail.com>
Date: Wed, 29 Jul 2026 07:55:29 +0800
Subject: [PATCH 14/40] feat: add reproducibility and publication workflows

---
 backend/cli/src/file/artifacts.ts             | 244 ++++++++
 backend/cli/src/file/index.ts                 |  22 +
 backend/cli/src/file/publication.ts           | 129 +++++
 backend/cli/src/file/starters.ts              | 138 +++++
 backend/cli/src/server/routes/file.ts         |  83 +++
 backend/cli/test/file/publication.test.ts     |  59 ++
 backend/cli/test/file/reproducibility.test.ts |  79 +++
 backend/cli/test/file/starters.test.ts        |  27 +
 backend/cli/test/server/file-research.test.ts |  70 +++
 .../workspace/e2e/artifact-gallery.spec.ts    |  25 +-
 frontend/workspace/e2e/atlas-bridge.spec.ts   |   2 +-
 .../workspace/e2e/research-launchpad.spec.ts  |  32 ++
 frontend/workspace/e2e/terminal-init.spec.ts  |   4 +-
 .../src/artifacts/ArtifactGallery.tsx         | 369 +++++++++++-
 .../workspace/src/artifacts/model.test.ts     |  17 +-
 frontend/workspace/src/artifacts/model.ts     | 234 ++++++++
 frontend/workspace/src/atlas/RightPane.tsx    |  11 +-
 .../session/research-launchpad.test.ts        |   7 +-
 .../components/session/research-launchpad.ts  |  32 ++
 .../components/session/session-new-view.tsx   |  78 ++-
 frontend/workspace/src/styles/atlas.css       | 130 +++++
 tooling/sdk/js/src/v2/gen/sdk.gen.ts          | 134 +++++
 tooling/sdk/js/src/v2/gen/types.gen.ts        | 165 ++++++
 tooling/sdk/openapi.json                      | 529 ++++++++++++++++++
 24 files changed, 2592 insertions(+), 28 deletions(-)
 create mode 100644 backend/cli/src/file/publication.ts
 create mode 100644 backend/cli/src/file/starters.ts
 create mode 100644 backend/cli/test/file/publication.test.ts
 create mode 100644 backend/cli/test/file/reproducibility.test.ts
 create mode 100644 backend/cli/test/file/starters.test.ts
 create mode 100644 backend/cli/test/server/file-research.test.ts

diff --git a/backend/cli/src/file/artifacts.ts b/backend/cli/src/file/artifacts.ts
index beb4ad96..12d2358a 100644
--- a/backend/cli/src/file/artifacts.ts
+++ b/backend/cli/src/file/artifacts.ts
@@ -46,6 +46,55 @@ export namespace ArtifactFile {
   })
   export type Provenance = z.infer<typeof Provenance>
 
+  export const AuditCheck = z.object({
+    id: z.string(),
+    label: z.string(),
+    status: z.enum(["pass", "warn", "fail"]),
+    detail: z.string(),
+    weight: z.number().positive(),
+  })
+  export type AuditCheck = z.infer<typeof AuditCheck>
+
+  export const Audit = z.object({
+    generated_at: z.string(),
+    score: z.number().int().min(0).max(100),
+    status: z.enum(["ready", "warnings", "blocked"]),
+    git: z
+      .object({
+        branch: z.string().optional(),
+        commit: z.string().optional(),
+        dirty: z.boolean(),
+      })
+      .optional(),
+    lockfiles: z.string().array(),
+    environments: z.string().array(),
+    notebooks: z.object({
+      total: z.number().int().nonnegative(),
+      valid: z.number().int().nonnegative(),
+      invalid: z.string().array(),
+    }),
+    artifacts: z.object({
+      total: z.number().int().nonnegative(),
+      nonempty: z.number().int().nonnegative(),
+      bytes: z.number().int().nonnegative(),
+    }),
+    checks: AuditCheck.array(),
+  })
+  export type Audit = z.infer<typeof Audit>
+
+  export const ManifestArtifact = Info.extend({
+    sha256: z.string().regex(/^[a-f0-9]{64}$/),
+  })
+  export type ManifestArtifact = z.infer<typeof ManifestArtifact>
+
+  export const Manifest = z.object({
+    format: z.literal("openscience.artifact-manifest.v1"),
+    generated_at: z.string(),
+    digest: z.string().regex(/^[a-f0-9]{64}$/),
+    artifacts: ManifestArtifact.array(),
+  })
+  export type Manifest = z.infer<typeof Manifest>
+
   const kinds: Record<Kind, string[]> = {
     notebook: ["ipynb"],
     dataset: ["csv", "tsv", "jsonl", "parquet", "feather", "arrow", "xls", "xlsx", "h5", "hdf5", "h5ad", "loom"],
@@ -78,6 +127,31 @@ export namespace ArtifactFile {
   ])
   const LIMIT = 5_000
   const DEPTH = 16
+  const lockfiles = [
+    "bun.lock",
+    "bun.lockb",
+    "package-lock.json",
+    "pnpm-lock.yaml",
+    "yarn.lock",
+    "uv.lock",
+    "poetry.lock",
+    "Pipfile.lock",
+    "renv.lock",
+    "Cargo.lock",
+    "Manifest.toml",
+  ]
+  const environments = [
+    "pyproject.toml",
+    "requirements.txt",
+    "environment.yml",
+    "environment.yaml",
+    "Dockerfile",
+    "compose.yml",
+    "docker-compose.yml",
+    "package.json",
+    "renv.lock",
+    "Project.toml",
+  ]
 
   export function classify(file: string): { kind: Kind; format: string } | undefined {
     const format = path.extname(file).slice(1).toLowerCase()
@@ -153,6 +227,176 @@ export namespace ArtifactFile {
     }
   }
 
+  export async function audit(root: string): Promise<Audit> {
+    const artifacts = await scan(root)
+    const notebooks = artifacts.filter((artifact) => artifact.kind === "notebook")
+    const invalid = (
+      await Promise.all(
+        notebooks.map(async (notebook) => {
+          const value = await Bun.file(path.join(root, notebook.path))
+            .json()
+            .catch(() => undefined)
+          if (!value || typeof value !== "object") return notebook.path
+          const record = value as Record<string, unknown>
+          if (typeof record.nbformat !== "number" || !Array.isArray(record.cells)) return notebook.path
+          return undefined
+        }),
+      )
+    ).filter((file): file is string => !!file)
+    const [branch, commit, status, presentLocks, presentEnvironments, readme] = await Promise.all([
+      $`git branch --show-current`.cwd(root).quiet().nothrow().text(),
+      $`git rev-parse HEAD`.cwd(root).quiet().nothrow().text(),
+      $`git status --porcelain`.cwd(root).quiet().nothrow().text(),
+      Promise.all(lockfiles.map(async (file) => ((await Bun.file(path.join(root, file)).exists()) ? file : undefined))),
+      Promise.all(
+        environments.map(async (file) => ((await Bun.file(path.join(root, file)).exists()) ? file : undefined)),
+      ),
+      Promise.all(["README.md", "README.rst", "README.txt"].map((file) => Bun.file(path.join(root, file)).exists())),
+    ])
+    const locks = presentLocks.filter((file): file is string => !!file)
+    const envs = presentEnvironments.filter((file): file is string => !!file)
+    const git = commit.trim()
+      ? {
+          branch: branch.trim() || undefined,
+          commit: commit.trim(),
+          dirty: Boolean(status.trim()),
+        }
+      : undefined
+    const checks = [
+      check(
+        "git-repository",
+        "Version-controlled project",
+        git ? "pass" : "fail",
+        git ? "Git repository detected." : "Initialize Git so every result can point to exact code.",
+        10,
+      ),
+      check(
+        "git-clean",
+        "Clean working tree",
+        !git ? "fail" : git.dirty ? "warn" : "pass",
+        !git
+          ? "No Git state is available."
+          : git.dirty
+            ? "Commit or stash local changes before a definitive run."
+            : "Working tree matches the captured commit.",
+        15,
+      ),
+      check(
+        "git-commit",
+        "Reachable code snapshot",
+        git?.commit ? "pass" : "fail",
+        git?.commit ? `Current commit ${git.commit.slice(0, 12)}.` : "Create a commit before recording results.",
+        10,
+      ),
+      check(
+        "environment-lock",
+        "Locked dependencies",
+        locks.length ? "pass" : "fail",
+        locks.length ? locks.join(", ") : "Add a lockfile such as uv.lock, renv.lock, bun.lock, or package-lock.json.",
+        15,
+      ),
+      check(
+        "environment-spec",
+        "Environment specification",
+        envs.length ? "pass" : "warn",
+        envs.length
+          ? envs.join(", ")
+          : "Add pyproject.toml, environment.yml, requirements.txt, Dockerfile, or an equivalent spec.",
+        10,
+      ),
+      check(
+        "notebooks",
+        "Executable notebook structure",
+        invalid.length ? "fail" : "pass",
+        invalid.length
+          ? `Invalid notebooks: ${invalid.join(", ")}`
+          : notebooks.length
+            ? `${notebooks.length} notebook${notebooks.length === 1 ? "" : "s"} passed structural validation.`
+            : "No notebooks need validation.",
+        15,
+      ),
+      check(
+        "artifacts",
+        "Non-empty research artifacts",
+        !artifacts.length || artifacts.some((artifact) => artifact.size === 0) ? "warn" : "pass",
+        artifacts.length
+          ? `${artifacts.filter((artifact) => artifact.size > 0).length}/${artifacts.length} artifacts are non-empty.`
+          : "No generated research artifacts yet.",
+        10,
+      ),
+      check(
+        "readme",
+        "Project instructions",
+        readme.some(Boolean) ? "pass" : "warn",
+        readme.some(Boolean) ? "README found." : "Add a README with setup, data, and execution instructions.",
+        5,
+      ),
+    ] satisfies AuditCheck[]
+    const total = checks.reduce((sum, item) => sum + item.weight, 0)
+    const earned = checks.reduce(
+      (sum, item) => sum + (item.status === "pass" ? item.weight : item.status === "warn" ? item.weight / 2 : 0),
+      0,
+    )
+    const score = Math.round((earned / total) * 100)
+    return Audit.parse({
+      generated_at: new Date().toISOString(),
+      score,
+      status: checks.some((item) => item.status === "fail") ? "blocked" : score >= 85 ? "ready" : "warnings",
+      git,
+      lockfiles: locks,
+      environments: envs,
+      notebooks: {
+        total: notebooks.length,
+        valid: notebooks.length - invalid.length,
+        invalid,
+      },
+      artifacts: {
+        total: artifacts.length,
+        nonempty: artifacts.filter((artifact) => artifact.size > 0).length,
+        bytes: artifacts.reduce((sum, artifact) => sum + artifact.size, 0),
+      },
+      checks,
+    })
+  }
+
+  export async function manifest(root: string): Promise<Manifest> {
+    const artifacts = await scan(root)
+    const sorted = artifacts.toSorted((a, b) => a.path.localeCompare(b.path))
+    const batches = Array.from({ length: Math.ceil(sorted.length / 16) }, (_, index) =>
+      sorted.slice(index * 16, (index + 1) * 16),
+    )
+    const hashed: ManifestArtifact[] = []
+    for (const batch of batches) {
+      hashed.push(
+        ...(await Promise.all(
+          batch.map(async (artifact) =>
+            ManifestArtifact.parse({ ...artifact, sha256: await hash(path.join(root, artifact.path)) }),
+          ),
+        )),
+      )
+    }
+    const digest = await crypto.subtle.digest(
+      "SHA-256",
+      new TextEncoder().encode(hashed.map((artifact) => `${artifact.sha256}  ${artifact.path}`).join("\n")),
+    )
+    return Manifest.parse({
+      format: "openscience.artifact-manifest.v1",
+      generated_at: new Date().toISOString(),
+      digest: [...new Uint8Array(digest)].map((byte) => byte.toString(16).padStart(2, "0")).join(""),
+      artifacts: hashed,
+    })
+  }
+
+  function check(id: string, label: string, status: AuditCheck["status"], detail: string, weight: number): AuditCheck {
+    return { id, label, status, detail, weight }
+  }
+
+  async function hash(file: string): Promise<string> {
+    const digest = new Bun.CryptoHasher("sha256")
+    for await (const chunk of fs.createReadStream(file)) digest.update(chunk)
+    return digest.digest("hex")
+  }
+
   function statusOf(code: string, tracked: boolean): Provenance["status"] {
     if (code === "??") return "untracked"
     if (code.includes("D")) return "deleted"
diff --git a/backend/cli/src/file/index.ts b/backend/cli/src/file/index.ts
index 40f266bf..c839d2aa 100644
--- a/backend/cli/src/file/index.ts
+++ b/backend/cli/src/file/index.ts
@@ -17,6 +17,8 @@ import { FileWatcher } from "./watcher"
 import { createSearchCache } from "./search-cache"
 import { ScienceFile } from "./science"
 import { ArtifactFile } from "./artifacts"
+import { StarterFile } from "./starters"
+import { PublicationFile } from "./publication"
 
 export namespace File {
   const log = Log.create({ service: "file" })
@@ -377,6 +379,26 @@ export namespace File {
     return ArtifactFile.provenance(Instance.directory, file)
   }
 
+  export async function reproducibility(): Promise<ArtifactFile.Audit> {
+    return ArtifactFile.audit(Instance.directory)
+  }
+
+  export async function manifest(): Promise<ArtifactFile.Manifest> {
+    return ArtifactFile.manifest(Instance.directory)
+  }
+
+  export async function starter(template: StarterFile.Template): Promise<StarterFile.Result> {
+    return StarterFile.create(Instance.directory, template)
+  }
+
+  export async function publicationCapabilities(): Promise<PublicationFile.Capabilities> {
+    return PublicationFile.capabilities()
+  }
+
+  export async function publication(input: PublicationFile.Input): Promise<PublicationFile.Result> {
+    return PublicationFile.render(Instance.directory, input)
+  }
+
   export async function write(file: string, content: string): Promise<Content> {
     using _ = log.time("write", { file })
     const full = path.join(Instance.directory, file)
diff --git a/backend/cli/src/file/publication.ts b/backend/cli/src/file/publication.ts
new file mode 100644
index 00000000..685170bd
--- /dev/null
+++ b/backend/cli/src/file/publication.ts
@@ -0,0 +1,129 @@
+import fs from "node:fs/promises"
+import path from "node:path"
+import z from "zod"
+import { OpenScience } from "../openscience"
+
+export namespace PublicationFile {
+  export const Format = z.enum(["html", "pdf", "docx", "latex", "pptx"])
+  export type Format = z.infer<typeof Format>
+
+  export const Input = z.object({
+    path: z.string().trim().min(1).max(4_000),
+    format: Format,
+  })
+  export type Input = z.infer<typeof Input>
+
+  export const Capabilities = z.object({
+    pandoc: z.boolean(),
+    pdf_engine: z.string().optional(),
+    formats: z.record(Format, z.boolean()),
+  })
+  export type Capabilities = z.infer<typeof Capabilities>
+
+  export const Result = z.object({
+    path: z.string(),
+    format: Format,
+    size: z.number().int().nonnegative(),
+    created_at: z.string(),
+    engine: z.string(),
+  })
+  export type Result = z.infer<typeof Result>
+
+  const extensions: Record<Format, string> = {
+    html: "html",
+    pdf: "pdf",
+    docx: "docx",
+    latex: "tex",
+    pptx: "pptx",
+  }
+
+  export async function capabilities(): Promise<Capabilities> {
+    const pandoc = Boolean(Bun.which("pandoc"))
+    const pdf = Bun.which("xelatex") ?? Bun.which("pdflatex") ?? Bun.which("typst") ?? undefined
+    return Capabilities.parse({
+      pandoc,
+      pdf_engine: pdf ? path.basename(pdf) : undefined,
+      formats: {
+        html: pandoc,
+        pdf: pandoc && Boolean(pdf),
+        docx: pandoc,
+        latex: pandoc,
+        pptx: pandoc,
+      },
+    })
+  }
+
+  export async function render(root: string, input: Input): Promise<Result> {
+    const parsed = Input.parse(input)
+    const source = resolve(root, parsed.path)
+    if (![".md", ".markdown"].includes(path.extname(source).toLowerCase())) {
+      throw new Error("Publication export currently requires a Markdown report")
+    }
+    if (!(await Bun.file(source).exists())) throw new Error(`Report not found: ${parsed.path}`)
+    const support = await capabilities()
+    if (!support.formats[parsed.format]) {
+      throw new Error(
+        parsed.format === "pdf"
+          ? "PDF export requires Pandoc and a local TeX or Typst engine"
+          : `${parsed.format.toUpperCase()} export requires Pandoc`,
+      )
+    }
+    const folder = path.join(root, "exports")
+    await fs.mkdir(folder, { recursive: true })
+    const stamp = new Date().toISOString().replace(/\D/g, "").slice(0, 17)
+    const nonce = crypto.randomUUID().slice(0, 8)
+    const stem =
+      path
+        .basename(source, path.extname(source))
+        .toLowerCase()
+        .replace(/[^a-z0-9_-]+/g, "-")
+        .replace(/^-+|-+$/g, "") || "report"
+    const relative = path.join(
+      "exports",
+      `${stem}-${stamp.slice(0, 8)}-${stamp.slice(8)}-${nonce}.${extensions[parsed.format]}`,
+    )
+    const target = path.join(root, relative)
+    const args = [
+      "pandoc",
+      source,
+      "--standalone",
+      `--resource-path=${path.dirname(source)}${path.delimiter}${root}`,
+      "--output",
+      target,
+      ...(parsed.format === "pdf" && support.pdf_engine ? [`--pdf-engine=${support.pdf_engine}`] : []),
+    ]
+    const proc = Bun.spawn(args, {
+      cwd: root,
+      env: await OpenScience.subprocessEnv(process.env),
+      stdin: "ignore",
+      stdout: "pipe",
+      stderr: "pipe",
+    })
+    const [code, stdout, stderr] = await Promise.all([
+      proc.exited,
+      new Response(proc.stdout).text(),
+      new Response(proc.stderr).text(),
+    ])
+    if (code !== 0) {
+      await fs.rm(target, { force: true })
+      throw new Error(stderr.trim() || stdout.trim() || `Pandoc exited with code ${code}`)
+    }
+    const stat = await fs.stat(target)
+    return Result.parse({
+      path: relative.split(path.sep).join("/"),
+      format: parsed.format,
+      size: stat.size,
+      created_at: new Date().toISOString(),
+      engine: parsed.format === "pdf" ? `pandoc + ${support.pdf_engine}` : "pandoc",
+    })
+  }
+
+  function resolve(root: string, file: string): string {
+    const target = path.resolve(root, file)
+    const relative = path.relative(root, target)
+    if (relative === ".." || relative.startsWith(`..${path.sep}`) || path.isAbsolute(relative)) {
+      throw new Error("Publication path escapes the project directory")
+    }
+    return target
+  }
+}
diff --git a/backend/cli/src/file/starters.ts b/backend/cli/src/file/starters.ts
new file mode 100644
index 00000000..ce32a937
--- /dev/null
+++ b/backend/cli/src/file/starters.ts
@@ -0,0 +1,138 @@
+import fs from "node:fs/promises"
+import path from "node:path"
+import z from "zod"
+
+export namespace StarterFile {
+  export const Template = z.enum(["single-cell", "dose-response", "protein-structure"])
+  export type Template = z.infer<typeof Template>
+
+  export const Result = z.object({
+    template: Template,
+    directory: z.string(),
+    files: z.string().array(),
+    notebook: z.string(),
+    readme: z.string(),
+  })
+  export type Result = z.infer<typeof Result>
+
+  export async function create(root: string, template: Template): Promise<Result> {
+    const parsed = Template.parse(template)
+    const directory = path.join("openscience-starters", parsed)
+    const target = path.join(root, directory)
+    await fs.mkdir(path.dirname(target), { recursive: true })
+    const created = await fs
+      .mkdir(target)
+      .then(() => true)
+      .catch((error) => {
+        if ((error as NodeJS.ErrnoException).code === "EEXIST") return false
+        throw error
+      })
+    if (!created) throw new Error(`The ${parsed} starter already exists at ${directory}`)
+    const content = files(parsed)
+    const names = Object.keys(content).toSorted()
+    await Promise.all(
+      names.map(async (name) => {
+        const file = path.join(target, name)
+        await fs.mkdir(path.dirname(file), { recursive: true })
+        await Bun.write(file, content[name]!)
+      }),
+    )
+    return Result.parse({
+      template: parsed,
+      directory,
+      files: names.map((name) => path.join(directory, name).split(path.sep).join("/")),
+      notebook: path.join(directory, "analysis.ipynb").split(path.sep).join("/"),
+      readme: path.join(directory, "README.md").split(path.sep).join("/"),
+    })
+  }
+
+  function files(template: Template): Record<string, string> {
+    if (template === "single-cell") return singleCell()
+    if (template === "dose-response") return doseResponse()
+    return proteinStructure()
+  }
+
+  function notebook(title: string, intro: string, cells: string[]): string {
+    return JSON.stringify(
+      {
+        cells: [
+          {
+            cell_type: "markdown",
+            metadata: {},
+            source: [`# ${title}\n`, `${intro}\n`],
+          },
+          ...cells.map((source) => ({
+            cell_type: "code",
+            execution_count: null,
+            metadata: {},
+            outputs: [],
+            source: source.split("\n").map((line) => `${line}\n`),
+          })),
+        ],
+        metadata: {
+          kernelspec: { display_name: "Python 3", language: "python", name: "python3" },
+          language_info: { name: "python", version: "3" },
+          openscience: { starter: true },
+        },
+        nbformat: 4,
+        nbformat_minor: 5,
+      },
+      null,
+      2,
+    )
+  }
+
+  function singleCell(): Record<string, string> {
+    return {
+      "README.md":
+        "# Single-cell starter\n\nA small, local-first expression matrix for exploring QC, normalization, clustering, and cell-type annotation. Open `analysis.ipynb` in OpenScience and run each cell. Replace `data/cells.csv` with your own matrix when ready.\n",
+      "data/cells.csv":
+        "cell,cell_type,CD3D,MS4A1,LYZ,NKG7,MKI67\ncell_001,T cell,9,0,1,6,0\ncell_002,T cell,8,0,0,7,1\ncell_003,B cell,0,10,1,0,0\ncell_004,B cell,0,8,0,1,0\ncell_005,Monocyte,1,0,11,2,0\ncell_006,Monocyte,0,0,9,1,1\ncell_007,NK cell,2,0,0,12,0\ncell_008,NK cell,1,0,1,10,0\ncell_009,Cycling,4,1,2,3,13\ncell_010,Cycling,3,2,1,4,11\n",
+      "analysis.ipynb": notebook(
+        "Single-cell expression starter",
+        "Inspect a tiny expression matrix, calculate per-cell QC, and visualize marker structure without external downloads.",
+        [
+          "import csv\nfrom pathlib import Path\nrows = list(csv.DictReader(Path('data/cells.csv').open()))\ngenes = ['CD3D', 'MS4A1', 'LYZ', 'NKG7', 'MKI67']\nlen(rows), genes",
+          "qc = [{'cell': row['cell'], 'type': row['cell_type'], 'total': sum(int(row[g]) for g in genes), 'detected': sum(int(row[g]) > 0 for g in genes)} for row in rows]\nqc",
+          "from collections import defaultdict\nmeans = defaultdict(lambda: defaultdict(list))\nfor row in rows:\n    for gene in genes:\n        means[row['cell_type']][gene].append(int(row[gene]))\nsummary = {kind: {gene: round(sum(values[gene]) / len(values[gene]), 2) for gene in genes} for kind, values in means.items()}\nsummary",
+        ],
+      ),
+    }
+  }
+
+  function doseResponse(): Record<string, string> {
+    return {
+      "README.md":
+        "# Dose-response starter\n\nA compact plate-style dose-response dataset with vehicle controls and replicates. Use `analysis.ipynb` to aggregate response, estimate the half-maximal crossing, and review assay quality before replacing the sample CSV.\n",
+      "data/dose_response.csv":
+        "compound,dose_uM,replicate,response_pct\nVehicle,0,1,100\nVehicle,0,2,98\nCompound-A,0.001,1,96\nCompound-A,0.001,2,94\nCompound-A,0.01,1,87\nCompound-A,0.01,2,84\nCompound-A,0.1,1,62\nCompound-A,0.1,2,58\nCompound-A,1,1,31\nCompound-A,1,2,28\nCompound-A,10,1,9\nCompound-A,10,2,11\n",
+      "analysis.ipynb": notebook(
+        "Dose-response assay starter",
+        "Aggregate technical replicates and estimate the observed half-response crossing using only the Python standard library.",
+        [
+          "import csv\nfrom pathlib import Path\nrows = list(csv.DictReader(Path('data/dose_response.csv').open()))\nrows[:3]",
+          "from collections import defaultdict\nseries = defaultdict(list)\nfor row in rows:\n    if row['compound'] != 'Vehicle':\n        series[float(row['dose_uM'])].append(float(row['response_pct']))\nmeans = {dose: round(sum(values) / len(values), 2) for dose, values in sorted(series.items())}\nmeans",
+          "crossing = min(means, key=lambda dose: abs(means[dose] - 50))\n{'nearest_half_max_dose_uM': crossing, 'response_pct': means[crossing], 'replicates_per_dose': {dose: len(values) for dose, values in series.items()}}",
+        ],
+      ),
+    }
+  }
+
+  function proteinStructure(): Record<string, string> {
+    return {
+      "README.md":
+        "# Protein-structure starter\n\nA tiny alanine peptide structure for learning the native PDB viewer, measuring geometry, and preparing downstream docking or molecular-dynamics work. Open `data/alanine.pdb` for the 3D view and `analysis.ipynb` for a dependency-free inspection.\n",
+      "data/alanine.pdb":
+        "HEADER    OPENSCIENCE ALANINE STARTER\nATOM      1  N   ALA A   1      -1.458   0.000   0.000  1.00 20.00           N\nATOM      2  CA  ALA A   1       0.000   0.000   0.000  1.00 20.00           C\nATOM      3  C   ALA A   1       0.540   1.430   0.000  1.00 20.00           C\nATOM      4  O   ALA A   1      -0.160   2.390   0.000  1.00 20.00           O\nATOM      5  CB  ALA A   1       0.510  -0.770  -1.220  1.00 20.00           C\nTER\nEND\n",
+      "analysis.ipynb": notebook(
+        "Protein structure starter",
+        "Parse atoms and calculate the structure centroid before moving to docking or molecular dynamics.",
+        [
+          "from pathlib import Path\nlines = Path('data/alanine.pdb').read_text().splitlines()\natoms = [line for line in lines if line.startswith(('ATOM  ', 'HETATM'))]\nlen(atoms)",
+          "coords = [(float(line[30:38]), float(line[38:46]), float(line[46:54])) for line in atoms]\ncentroid = tuple(round(sum(axis) / len(coords), 3) for axis in zip(*coords))\n{'atoms': len(atoms), 'centroid_angstrom': centroid}",
+          "elements = {}\nfor line in atoms:\n    element = line[76:78].strip() or line[12:16].strip()[0]\n    elements[element] = elements.get(element, 0) + 1\nelements",
+        ],
+      ),
+    }
+  }
+}
diff --git a/backend/cli/src/server/routes/file.ts b/backend/cli/src/server/routes/file.ts
index 8a15b774..c8fa2f6f 100644
--- a/backend/cli/src/server/routes/file.ts
+++ b/backend/cli/src/server/routes/file.ts
@@ -8,6 +8,8 @@ import { Instance } from "../../project/instance"
 import { lazy } from "../../util/lazy"
 import { ScienceFile } from "../../file/science"
 import { ArtifactFile } from "../../file/artifacts"
+import { StarterFile } from "../../file/starters"
+import { PublicationFile } from "../../file/publication"
 
 export const FileRoutes = lazy(() =>
   new Hono()
@@ -306,6 +308,87 @@ export const FileRoutes = lazy(() =>
       ),
       async (c) => c.json(await File.provenance(c.req.valid("query").path)),
     )
+    .get(
+      "/file/reproducibility",
+      describeRoute({
+        summary: "Audit project reproducibility",
+        description:
+          "Check Git state, locked dependencies, environment specifications, notebook structure, and research artifacts.",
+        operationId: "file.reproducibility",
+        responses: {
+          200: {
+            description: "Project reproducibility audit",
+            content: { "application/json": { schema: resolver(ArtifactFile.Audit) } },
+          },
+        },
+      }),
+      async (c) => c.json(await File.reproducibility()),
+    )
+    .get(
+      "/file/manifest",
+      describeRoute({
+        summary: "Create an artifact integrity manifest",
+        description: "Hash every discovered research artifact and return a portable, deterministic manifest.",
+        operationId: "file.manifest",
+        responses: {
+          200: {
+            description: "Artifact checksum manifest",
+            content: { "application/json": { schema: resolver(ArtifactFile.Manifest) } },
+          },
+        },
+      }),
+      async (c) => {
+        c.header("Content-Disposition", 'attachment; filename="openscience-artifact-manifest.json"')
+        return c.json(await File.manifest())
+      },
+    )
+    .post(
+      "/file/starters",
+      describeRoute({
+        summary: "Create a local scientific starter project",
+        description: "Materialize a valid notebook, sample data, and README without external downloads.",
+        operationId: "file.starter",
+        responses: {
+          200: {
+            description: "Created starter files",
+            content: { "application/json": { schema: resolver(StarterFile.Result) } },
+          },
+        },
+      }),
+      validator("json", z.object({ template: StarterFile.Template })),
+      async (c) => c.json(await File.starter(c.req.valid("json").template)),
+    )
+    .get(
+      "/file/publication/capabilities",
+      describeRoute({
+        summary: "Inspect local publication export support",
+        description: "Detect Pandoc and a PDF engine before offering report export formats.",
+        operationId: "file.publicationCapabilities",
+        responses: {
+          200: {
+            description: "Available local publication formats",
+            content: { "application/json": { schema: resolver(PublicationFile.Capabilities) } },
+          },
+        },
+      }),
+      async (c) => c.json(await File.publicationCapabilities()),
+    )
+    .post(
+      "/file/publication",
+      describeRoute({
+        summary: "Export a Markdown research report",
+        description: "Create a timestamped HTML, PDF, DOCX, LaTeX, or PowerPoint publication artifact locally.",
+        operationId: "file.publication",
+        responses: {
+          200: {
+            description: "Created publication artifact",
+            content: { "application/json": { schema: resolver(PublicationFile.Result) } },
+          },
+        },
+      }),
+      validator("json", PublicationFile.Input),
+      async (c) => c.json(await File.publication(c.req.valid("json"))),
+    )
     .get(
       "/file/status",
       describeRoute({
diff --git a/backend/cli/test/file/publication.test.ts b/backend/cli/test/file/publication.test.ts
new file mode 100644
index 00000000..2f7b5d2c
--- /dev/null
+++ b/backend/cli/test/file/publication.test.ts
@@ -0,0 +1,59 @@
+import { describe, expect, test } from "bun:test"
+import path from "node:path"
+import { PublicationFile } from "../../src/file/publication"
+import { tmpdir } from "../fixture/fixture"
+
+describe("PublicationFile", () => {
+  test("detects real local publication export capabilities", async () => {
+    const capabilities = await PublicationFile.capabilities()
+    expect(capabilities.formats.html).toBe(capabilities.pandoc)
+    expect(capabilities.formats.docx).toBe(capabilities.pandoc)
+    expect(capabilities.formats.pptx).toBe(capabilities.pandoc)
+    expect(capabilities.formats.pdf).toBe(capabilities.pandoc && Boolean(capabilities.pdf_engine))
+  })
+
+  test("exports a real standalone publication when pandoc is available", async () => {
+    const capabilities = await PublicationFile.capabilities()
+    if (!capabilities.formats.html) return
+    await using tmp = await tmpdir({
+      init: async (directory) => {
+        await Bun.write(
+          path.join(directory, "report.md"),
+          "# Treatment response\n\nThe observed response was **42%**.\n",
+        )
+      },
+    })
+    const result = await PublicationFile.render(tmp.path, { path: "report.md", format: "html" })
+    expect(result.path).toMatch(/^exports\/report-\d{8}-\d{9}-[a-f0-9]{8}\.html$/)
+    expect(result.size).toBeGreaterThan(100)
+    expect(await Bun.file(path.join(tmp.path, result.path)).text()).toContain("Treatment response")
+  })
+
+  test("never overwrites a rapid repeated export", async () => {
+    const capabilities = await PublicationFile.capabilities()
+    if (!capabilities.formats.html) return
+    await using tmp = await tmpdir({
+      init: async (directory) => {
+        await Bun.write(path.join(directory, "report.md"), "# Stable export\n")
+      },
+    })
+
+    const [first, second] = await Promise.all([
+      PublicationFile.render(tmp.path, { path: "report.md", format: "html" }),
+      PublicationFile.render(tmp.path, { path: "report.md", format: "html" }),
+    ])
+    expect(first.path).not.toBe(second.path)
+    expect(await Bun.file(path.join(tmp.path, first.path)).exists()).toBe(true)
+    expect(await Bun.file(path.join(tmp.path, second.path)).exists()).toBe(true)
+  })
+
+  test("rejects non-report inputs and project traversal", async () => {
+    await using tmp = await tmpdir({
+      init: async (directory) => {
+        await Bun.write(path.join(directory, "data.csv"), "a,b\n1,2\n")
+      },
+    })
+    await expect(PublicationFile.render(tmp.path, { path: "data.csv", format: "html" })).rejects.toThrow("Markdown")
+    await expect(PublicationFile.render(tmp.path, { path: "../report.md", format: "html" })).rejects.toThrow("escapes")
+  })
+})
diff --git a/backend/cli/test/file/reproducibility.test.ts b/backend/cli/test/file/reproducibility.test.ts
new file mode 100644
index 00000000..dda962d7
--- /dev/null
+++ b/backend/cli/test/file/reproducibility.test.ts
@@ -0,0 +1,79 @@
+import { describe, expect, test } from "bun:test"
+import { $ } from "bun"
+import path from "node:path"
+import { ArtifactFile } from "../../src/file/artifacts"
+import { tmpdir } from "../fixture/fixture"
+
+describe("ArtifactFile reproducibility", () => {
+  test("audits git, environment locks, notebooks, and local artifacts", async () => {
+    await using tmp = await tmpdir({
+      git: true,
+      init: async (directory) => {
+        await Bun.write(path.join(directory, "README.md"), "# Reproducible study\n")
+        await Bun.write(path.join(directory, "uv.lock"), "version = 1\n")
+        await Bun.write(path.join(directory, "pyproject.toml"), '[project]\nname = "study"\n')
+        await Bun.write(
+          path.join(directory, "analysis.ipynb"),
+          JSON.stringify({
+            nbformat: 4,
+            nbformat_minor: 5,
+            metadata: {},
+            cells: [{ cell_type: "code", metadata: {}, source: ["print('ok')"], outputs: [], execution_count: null }],
+          }),
+        )
+        await Bun.write(path.join(directory, "results.csv"), "metric,value\naccuracy,0.95\n")
+        await $`git add README.md uv.lock pyproject.toml analysis.ipynb results.csv`.cwd(directory).quiet()
+        await $`git -c user.name=OpenScience -c user.email=test@openscience.local commit -m "reproducible baseline"`
+          .cwd(directory)
+          .quiet()
+      },
+    })
+
+    const audit = await ArtifactFile.audit(tmp.path)
+    expect(audit.status).toBe("ready")
+    expect(audit.score).toBeGreaterThanOrEqual(90)
+    expect(audit.git).toMatchObject({ dirty: false, branch: "master" })
+    expect(audit.lockfiles).toContain("uv.lock")
+    expect(audit.environments).toContain("pyproject.toml")
+    expect(audit.notebooks).toEqual({ total: 1, valid: 1, invalid: [] })
+    expect(audit.artifacts).toMatchObject({ total: 3, nonempty: 3 })
+  })
+
+  test("reports actionable blockers for an unlocked invalid project", async () => {
+    await using tmp = await tmpdir({
+      init: async (directory) => {
+        await Bun.write(path.join(directory, "broken.ipynb"), "{")
+        await Bun.write(path.join(directory, "empty.csv"), "")
+      },
+    })
+
+    const audit = await ArtifactFile.audit(tmp.path)
+    expect(audit.status).toBe("blocked")
+    expect(audit.notebooks.invalid).toEqual(["broken.ipynb"])
+    expect(audit.checks.find((check) => check.id === "environment-lock")?.status).toBe("fail")
+    expect(audit.checks.find((check) => check.id === "notebooks")?.status).toBe("fail")
+  })
+
+  test("does not mark an empty project as having complete artifacts", async () => {
+    await using tmp = await tmpdir()
+
+    const audit = await ArtifactFile.audit(tmp.path)
+    expect(audit.artifacts).toMatchObject({ total: 0, nonempty: 0, bytes: 0 })
+    expect(audit.checks.find((check) => check.id === "artifacts")?.status).toBe("warn")
+  })
+
+  test("creates a deterministic checksum manifest without escaping the project", async () => {
+    await using tmp = await tmpdir({
+      init: async (directory) => {
+        await Bun.write(path.join(directory, "results", "table.csv"), "a,b\n1,2\n")
+        await Bun.write(path.join(directory, "figure.svg"), "<svg></svg>")
+      },
+    })
+
+    const manifest = await ArtifactFile.manifest(tmp.path)
+    expect(manifest.format).toBe("openscience.artifact-manifest.v1")
+    expect(manifest.artifacts.map((item) => item.path)).toEqual(["figure.svg", "results/table.csv"])
+    expect(manifest.artifacts.every((item) => /^[a-f0-9]{64}$/.test(item.sha256))).toBe(true)
+    expect(manifest.digest).toMatch(/^[a-f0-9]{64}$/)
+  })
+})
diff --git a/backend/cli/test/file/starters.test.ts b/backend/cli/test/file/starters.test.ts
new file mode 100644
index 00000000..e6cba5ec
--- /dev/null
+++ b/backend/cli/test/file/starters.test.ts
@@ -0,0 +1,27 @@
+import { describe, expect, test } from "bun:test"
+import path from "node:path"
+import { StarterFile } from "../../src/file/starters"
+import { tmpdir } from "../fixture/fixture"
+
+describe("StarterFile", () => {
+  test.each(["single-cell", "dose-response", "protein-structure"] as const)(
+    "creates a complete %s starter without external downloads",
+    async (template) => {
+      await using tmp = await tmpdir()
+      const created = await StarterFile.create(tmp.path, template)
+      expect(created.template).toBe(template)
+      expect(created.files.length).toBeGreaterThanOrEqual(3)
+      expect(created.notebook).toEndWith(".ipynb")
+      const notebook = await Bun.file(path.join(tmp.path, created.notebook)).json()
+      expect(notebook.nbformat).toBe(4)
+      expect(notebook.cells.some((cell: { cell_type?: string }) => cell.cell_type === "code")).toBe(true)
+      expect(await Bun.file(path.join(tmp.path, created.readme)).exists()).toBe(true)
+    },
+  )
+
+  test("refuses to overwrite an existing starter", async () => {
+    await using tmp = await tmpdir()
+    await StarterFile.create(tmp.path, "single-cell")
+    await expect(StarterFile.create(tmp.path, "single-cell")).rejects.toThrow("already exists")
+  })
+})
diff --git a/backend/cli/test/server/file-research.test.ts b/backend/cli/test/server/file-research.test.ts
new file mode 100644
index 00000000..3013c6f8
--- /dev/null
+++ b/backend/cli/test/server/file-research.test.ts
@@ -0,0 +1,70 @@
+import { describe, expect, test } from "bun:test"
+import path from "node:path"
+import { Instance } from "../../src/project/instance"
+import { FileRoutes } from "../../src/server/routes/file"
+import { tmpdir } from "../fixture/fixture"
+
+describe("/file research routes", () => {
+  test("returns a project audit and downloadable integrity manifest", async () => {
+    await using tmp = await tmpdir({
+      init: async (directory) => {
+        await Bun.write(path.join(directory, "results.csv"), "metric,value\naccuracy,0.9\n")
+      },
+    })
+    await Instance.provide({
+      directory: tmp.path,
+      fn: async () => {
+        const audit = await FileRoutes().request("/file/reproducibility")
+        expect(audit.status).toBe(200)
+        expect(((await audit.json()) as { checks: unknown[] }).checks.length).toBeGreaterThan(5)
+
+        const manifest = await FileRoutes().request("/file/manifest")
+        expect(manifest.status).toBe(200)
+        expect(manifest.headers.get("content-disposition")).toContain("openscience-artifact-manifest.json")
+        expect(((await manifest.json()) as { artifacts: unknown[] }).artifacts).toHaveLength(1)
+      },
+    })
+  })
+
+  test("creates a starter project through the local file API", async () => {
+    await using tmp = await tmpdir()
+    await Instance.provide({
+      directory: tmp.path,
+      fn: async () => {
+        const response = await FileRoutes().request("/file/starters", {
+          method: "POST",
+          headers: { "Content-Type": "application/json" },
+          body: JSON.stringify({ template: "protein-structure" }),
+        })
+        expect(response.status).toBe(200)
+        const result = (await response.json()) as { notebook: string; files: string[] }
+        expect(result.notebook).toBe("openscience-starters/protein-structure/analysis.ipynb")
+        expect(result.files).toContain("openscience-starters/protein-structure/data/alanine.pdb")
+      },
+    })
+  })
+
+  test("exports a Markdown report through the publication API", async () => {
+    await using tmp = await tmpdir({
+      init: async (directory) => {
+        await Bun.write(path.join(directory, "report.md"), "# Auditable result\n\nA concise result.\n")
+      },
+    })
+    await Instance.provide({
+      directory: tmp.path,
+      fn: async () => {
+        const capabilities = await FileRoutes().request("/file/publication/capabilities")
+        expect(capabilities.status).toBe(200)
+        const support = (await capabilities.json()) as { formats: { html: boolean } }
+        if (!support.formats.html) return
+        const response = await FileRoutes().request("/file/publication", {
+          method: "POST",
+          headers: { "Content-Type": "application/json" },
+          body: JSON.stringify({ path: "report.md", format: "html" }),
+        })
+        expect(response.status).toBe(200)
+        expect(((await response.json()) as { path: string }).path).toMatch(/^exports\/report-.+\.html$/)
+      },
+    })
+  })
+})
diff --git a/frontend/workspace/e2e/artifact-gallery.spec.ts b/frontend/workspace/e2e/artifact-gallery.spec.ts
index 8ce933ea..22534f84 100644
--- a/frontend/workspace/e2e/artifact-gallery.spec.ts
+++ b/frontend/workspace/e2e/artifact-gallery.spec.ts
@@ -15,6 +15,7 @@ test("discovers, filters, opens, downloads, and contextualizes local research ar
     path.join(directory, "results", "plot.svg"),
     '<svg xmlns="http://www.w3.org/2000/svg" width="10" height="10"><circle cx="5" cy="5" r="4"/></svg>',
   )
+  writeFileSync(path.join(directory, "report.md"), "# Result\n\nThe result is reproducible.\n")
   writeFileSync(path.join(directory, "pipeline.py"), "print('source, not artifact')")
 
   try {
@@ -27,13 +28,15 @@ test("discovers, filters, opens, downloads, and contextualizes local research ar
 
     const gallery = page.locator('[data-component="artifact-gallery"]')
     await expect(gallery).toBeVisible()
-    await expect(gallery.getByText("3 discovered locally", { exact: true })).toBeVisible()
-    await expect(gallery.locator("[data-artifact]")).toHaveCount(3)
+    await expect(gallery.getByText("4 discovered locally", { exact: true })).toBeVisible()
+    await expect(gallery.locator("[data-artifact]")).toHaveCount(4)
     await expect(gallery.getByText("pipeline.py", { exact: true })).toHaveCount(0)
+    await expect(gallery.locator('[data-component="reproducibility-score"]')).toHaveAttribute("data-status", "blocked")
 
     await gallery.getByRole("button", { name: /^figure 1$/ }).click()
     await expect(gallery.locator("[data-artifact]")).toHaveCount(1)
     await expect(gallery.locator('[data-artifact="results/plot.svg"]')).toBeVisible()
+    await expect(gallery.locator('[data-artifact="results/plot.svg"] img')).toBeVisible()
 
     await gallery.getByRole("button", { name: /^dataset 1$/ }).click()
     await gallery.locator('[data-artifact="results/counts.csv"]').click()
@@ -41,11 +44,22 @@ test("discovers, filters, opens, downloads, and contextualizes local research ar
     await expect(detail).toBeVisible()
     await expect(detail.getByText("results/counts.csv", { exact: true })).toBeVisible()
     await expect(detail.getByText("local file · no Git provenance", { exact: true })).toBeVisible()
+    await expect(detail.getByRole("button", { name: /Inspect quality/ })).toBeVisible()
+    await expect(detail.getByRole("button", { name: /Visualize/ })).toBeVisible()
 
     await detail.getByRole("button", { name: "add to context", exact: true }).click()
     await expect(page.getByRole("tab", { name: "Chat", exact: true })).toHaveAttribute("aria-selected", "true")
     await expect(page.locator("form").getByText("counts.csv", { exact: true })).toBeVisible()
 
+    await page.getByRole("tab", { name: "Files", exact: true }).click()
+    await page.getByRole("button", { name: "artifacts", exact: true }).click()
+    await gallery.getByRole("button", { name: /^dataset 1$/ }).click()
+    await gallery.locator('[data-artifact="results/counts.csv"]').click()
+    await detail.getByRole("button", { name: /Inspect quality/ }).click()
+    await expect(page.locator('[data-component="prompt-input"]')).toContainText(
+      "Inspect this dataset's schema and quality",
+    )
+
     await page.getByRole("tab", { name: "Files", exact: true }).click()
     await page.getByRole("button", { name: "artifacts", exact: true }).click()
     await gallery.getByRole("button", { name: /^dataset 1$/ }).click()
@@ -53,6 +67,13 @@ test("discovers, filters, opens, downloads, and contextualizes local research ar
     await detail.getByRole("button", { name: "open", exact: true }).click()
     await expect(page.locator('[data-component="data-table"]')).toBeVisible()
     await expect(page.getByText("2 rows", { exact: true })).toBeVisible()
+
+    await page.getByRole("tab", { name: "Files", exact: true }).click()
+    await page.getByRole("button", { name: "artifacts", exact: true }).click()
+    await gallery.getByRole("button", { name: /^report 1$/ }).click()
+    await gallery.locator('[data-artifact="report.md"]').click()
+    await expect(detail.getByText("Publication exports", { exact: true })).toBeVisible()
+    await expect(detail.getByRole("button", { name: "HTML", exact: true })).toBeEnabled()
   } finally {
     rmSync(directory, { recursive: true, force: true })
   }
diff --git a/frontend/workspace/e2e/atlas-bridge.spec.ts b/frontend/workspace/e2e/atlas-bridge.spec.ts
index 2957ce23..2dd5f2b7 100644
--- a/frontend/workspace/e2e/atlas-bridge.spec.ts
+++ b/frontend/workspace/e2e/atlas-bridge.spec.ts
@@ -63,8 +63,8 @@ test("Atlas canvas distinguishes a connected graph from an unavailable bridge",
 
   await gotoSession()
 
+  await page.getByRole("button", { name: "atlas", exact: true }).click()
   const atlasTab = page.getByRole("tab", { name: "atlas", exact: true })
-  await atlasTab.click()
   await expect(atlasTab).toHaveAttribute("aria-selected", "true")
 
   if (response.ok()) {
diff --git a/frontend/workspace/e2e/research-launchpad.spec.ts b/frontend/workspace/e2e/research-launchpad.spec.ts
index 7065a672..636634d0 100644
--- a/frontend/workspace/e2e/research-launchpad.spec.ts
+++ b/frontend/workspace/e2e/research-launchpad.spec.ts
@@ -1,15 +1,37 @@
 import { expect, test } from "./fixtures"
 
 test("turns a scientific workflow into an editable research brief", async ({ page, gotoSession }) => {
+  await page.route("**/file/starters?**", async (route) => {
+    await route.fulfill({
+      status: 200,
+      contentType: "application/json",
+      body: JSON.stringify({
+        template: "dose-response",
+        directory: "openscience-starters/dose-response",
+        notebook: "openscience-starters/dose-response/analysis.ipynb",
+        readme: "openscience-starters/dose-response/README.md",
+        files: [
+          "openscience-starters/dose-response/README.md",
+          "openscience-starters/dose-response/analysis.ipynb",
+          "openscience-starters/dose-response/data/dose_response.csv",
+        ],
+      }),
+    })
+  })
   await gotoSession()
 
   const launchpad = page.locator('[data-component="research-launchpad"]')
   await expect(launchpad).toBeVisible()
   await expect(launchpad.getByRole("heading", { name: "What are we trying to find out?" })).toBeVisible()
   await expect(launchpad.locator("[data-workflow]")).toHaveCount(23)
+  await expect(launchpad.locator("[data-starter]")).toHaveCount(3)
   await expect(launchpad.getByText("Research artifacts", { exact: true })).toBeVisible()
   await expect(page.locator(".session-right-pane")).toHaveCount(0)
 
+  await launchpad.locator('[data-starter="dose-response"]').click()
+  await expect(page.getByText("starter project ready", { exact: true })).toBeVisible()
+
+  await page.getByRole("tab", { name: "Chat", exact: true }).click()
   await launchpad.locator('[data-workflow="analyze-data"]').click()
 
   const composer = page.locator('[data-component="prompt-input"]')
@@ -24,3 +46,13 @@ test("turns a scientific workflow into an editable research brief", async ({ pag
   await expect(launchpad.locator('[data-workflow="molecular-docking"]')).toBeVisible()
   await expect(launchpad.locator('[data-workflow="train-model"]')).toBeVisible()
 })
+
+test("recovers starter controls when the local server request drops", async ({ page, gotoSession }) => {
+  await page.route("**/file/starters?**", (route) => route.abort("connectionfailed"))
+  await gotoSession()
+
+  const starter = page.locator('[data-starter="single-cell"]')
+  await starter.click()
+  await expect(page.getByText("starter could not be created", { exact: true })).toBeVisible()
+  await expect(starter).toBeEnabled()
+})
diff --git a/frontend/workspace/e2e/terminal-init.spec.ts b/frontend/workspace/e2e/terminal-init.spec.ts
index ee51df2d..6a567c3c 100644
--- a/frontend/workspace/e2e/terminal-init.spec.ts
+++ b/frontend/workspace/e2e/terminal-init.spec.ts
@@ -18,8 +18,8 @@ test("terminal executes output and can switch and close another tab", async ({ p
   try {
     await gotoSession()
 
+    await page.getByRole("button", { name: "terminal", exact: true }).click()
     const terminalTab = page.getByRole("tab", { name: "terminal", exact: true })
-    await terminalTab.click()
     await expect(terminalTab).toHaveAttribute("aria-selected", "true")
 
     const terminals = page.locator(terminalSelector)
@@ -88,9 +88,9 @@ test("terminal executes output and can switch and close another tab", async ({ p
 test("terminal panel can be collapsed and reopened", async ({ page, gotoSession }) => {
   await gotoSession()
 
+  await page.getByRole("button", { name: "terminal", exact: true }).click()
   const terminalTab = page.getByRole("tab", { name: "terminal", exact: true })
   await expect(terminalTab).toBeVisible()
-  await terminalTab.click()
   await expect(terminalTab).toHaveAttribute("aria-selected", "true")
 
   await page.getByTitle("hide panel", { exact: true }).click()
diff --git a/frontend/workspace/src/artifacts/ArtifactGallery.tsx b/frontend/workspace/src/artifacts/ArtifactGallery.tsx
index efe32d46..1cc08c03 100644
--- a/frontend/workspace/src/artifacts/ArtifactGallery.tsx
+++ b/frontend/workspace/src/artifacts/ArtifactGallery.tsx
@@ -3,6 +3,7 @@ import { usePlatform } from "@/context/platform"
 import { usePrompt } from "@/context/prompt"
 import { useSDK } from "@/context/sdk"
 import { centerTabs } from "@/atlas/store/centerTabs"
+import { uiStore } from "@/atlas/store/ui"
 import { toast } from "@/atlas/Toast"
 import {
   IconArchive,
@@ -17,7 +18,7 @@ import {
 } from "@/atlas/shared/Icon"
 import { FONT_CODE, FONT_MONO, FONT_SANS } from "@/styles/tokens"
 import {
-  artifactKinds,
+  artifactActions,
   filterArtifacts,
   formatArtifactKind,
   groupArtifacts,
@@ -43,6 +44,31 @@ interface Provenance {
   }
 }
 
+interface Audit {
+  generated_at: string
+  score: number
+  status: "ready" | "warnings" | "blocked"
+  lockfiles: string[]
+  environments: string[]
+  notebooks: { total: number; valid: number; invalid: string[] }
+  artifacts: { total: number; nonempty: number; bytes: number }
+  checks: Array<{
+    id: string
+    label: string
+    status: "pass" | "warn" | "fail"
+    detail: string
+    weight: number
+  }>
+}
+
+type PublicationFormat = "html" | "pdf" | "docx" | "latex" | "pptx"
+
+interface PublicationCapabilities {
+  pandoc: boolean
+  pdf_engine?: string
+  formats: Record<PublicationFormat, boolean>
+}
+
 export function ArtifactGallery(props: { directory: string; onOpen: (path: string) => void }): JSX.Element {
   const sdk = useSDK()
   const platform = usePlatform()
@@ -51,6 +77,7 @@ export function ArtifactGallery(props: { directory: string; onOpen: (path: strin
   const [kind, setKind] = createSignal<ArtifactKind | "all">("all")
   const [sort, setSort] = createSignal<ArtifactSort>("recent")
   const [selected, setSelected] = createSignal<string>()
+  const [auditOpen, setAuditOpen] = createSignal(false)
   const [refresh, setRefresh] = createSignal(0)
   const request = () => platform.fetch ?? fetch
   const url = (route: string, path?: string) =>
@@ -64,6 +91,14 @@ export function ArtifactGallery(props: { directory: string; onOpen: (path: strin
       return normalizeArtifacts(await response.json())
     },
   )
+  const [audit, auditApi] = createResource(
+    () => [props.directory, refresh()] as const,
+    async () => {
+      const response = await request()(url("/file/reproducibility"))
+      if (!response.ok) throw new Error(`reproducibility audit failed (${response.status})`)
+      return (await response.json()) as Audit
+    },
+  )
   const rows = () => data.latest ?? []
   const groups = createMemo(() => groupArtifacts(rows()))
   const filtered = createMemo(() => sortArtifacts(filterArtifacts(rows(), kind(), query()), sort()))
@@ -95,6 +130,66 @@ export function ArtifactGallery(props: { directory: string; onOpen: (path: strin
     toast.success("added to context", item.name)
   }
 
+  const act = (item: ArtifactInfo, instruction: string) => {
+    prompt.context.add({ type: "file", path: item.path })
+    uiStore.setPrefill(instruction)
+    centerTabs.showChat()
+  }
+
+  const manifest = async () => {
+    const id = toast.info("building integrity manifest", "Hashing local research artifacts…")
+    const response = await request()(url("/file/manifest")).catch((error) => {
+      toast.error("manifest failed", error instanceof Error ? error.message : String(error))
+      return undefined
+    })
+    toast.dismiss(id)
+    if (!response) return
+    if (!response.ok) {
+      toast.error("manifest failed", `${response.status}`)
+      return
+    }
+    const object = URL.createObjectURL(await response.blob())
+    const anchor = document.createElement("a")
+    anchor.href = object
+    anchor.download = "openscience-artifact-manifest.json"
+    anchor.click()
+    URL.revokeObjectURL(object)
+    toast.success("integrity manifest ready", `${rows().length} artifacts`)
+  }
+
+  const publish = async (item: ArtifactInfo, format: PublicationFormat) => {
+    const id = toast.info(`exporting ${format.toUpperCase()}`, item.name)
+    const response = await request()(url("/file/publication"), {
+      method: "POST",
+      headers: { "Content-Type": "application/json" },
+      body: JSON.stringify({ path: item.path, format }),
+    }).catch((error) => {
+      toast.error("publication export failed", error instanceof Error ? error.message : String(error))
+      return undefined
+    })
+    toast.dismiss(id)
+    if (!response) return
+    if (!response.ok) {
+      const detail = await response.text().catch(() => "")
+      toast.error("publication export failed", detail || `${response.status}`)
+      return
+    }
+    const result = (await response.json()) as { path: string; format: PublicationFormat; size: number }
+    toast.success(`${format.toUpperCase()} ready`, result.path)
+    if (!["docx", "pptx"].includes(format)) {
+      props.onOpen(result.path)
+      return
+    }
+    const raw = await request()(url("/file/raw", result.path))
+    if (!raw.ok) return
+    const object = URL.createObjectURL(await raw.blob())
+    const anchor = document.createElement("a")
+    anchor.href = object
+    anchor.download = result.path.split("/").pop() || `report.${format}`
+    anchor.click()
+    URL.revokeObjectURL(object)
+  }
+
   return (
     <div
       data-component="artifact-gallery"
@@ -178,6 +273,70 @@ export function ArtifactGallery(props: { directory: string; onOpen: (path: strin
             )}
           </For>
         </div>
+        <button
+          type="button"
+          data-component="reproducibility-score"
+          data-status={audit.latest?.status ?? "loading"}
+          onClick={() => setAuditOpen((value) => !value)}
+          style={auditSummary(audit.latest?.status)}
+        >
+          <span style={auditScore(audit.latest?.status)}>
+            <Show when={!audit.loading} fallback="··">
+              {audit.latest?.score ?? 0}
+            </Show>
+          </span>
+          <span style={{ display: "grid", gap: "2px", flex: 1, "text-align": "left" }}>
+            <strong>Reproducibility</strong>
+            <small>
+              {audit.error
+                ? "audit unavailable"
+                : audit.latest?.status === "ready"
+                  ? "environment, notebooks, and code are ready"
+                  : audit.latest?.status === "blocked"
+                    ? "blocking gaps need attention"
+                    : "review the remaining warnings"}
+            </small>
+          </span>
+          <span style={{ "font-family": FONT_MONO, "font-size": "9px", color: "var(--color-text-faint)" }}>
+            {auditOpen() ? "hide" : "details"}
+          </span>
+        </button>
+        <Show when={auditOpen() && audit.latest}>
+          {(value) => (
+            <div data-component="reproducibility-audit" style={auditPanel()}>
+              <div style={{ display: "grid", gap: "6px" }}>
+                <For each={value().checks}>
+                  {(check) => (
+                    <div style={auditCheck()}>
+                      <span
+                        style={{
+                          color:
+                            check.status === "pass"
+                              ? "var(--color-success)"
+                              : check.status === "fail"
+                                ? "var(--color-error)"
+                                : "var(--color-warning)",
+                        }}
+                      >
+                        {check.status === "pass" ? "●" : check.status === "fail" ? "×" : "◇"}
+                      </span>
+                      <strong>{check.label}</strong>
+                      <span>{check.detail}</span>
+                    </div>
+                  )}
+                </For>
+              </div>
+              <div style={{ display: "flex", "align-items": "center", gap: "6px" }}>
+                <button type="button" style={actionButton()} onClick={() => void auditApi.refetch()}>
+                  <IconRefresh size={11} /> run again
+                </button>
+                <button type="button" style={primaryButton()} onClick={() => void manifest()}>
+                  <IconDownload size={11} /> checksum manifest
+                </button>
+              </div>
+            </div>
+          )}
+        </Show>
       </div>
 
       <Show
@@ -242,6 +401,7 @@ export function ArtifactGallery(props: { directory: string; onOpen: (path: strin
                       <ArtifactCard
                         item={item}
                         active={selected() === item.path}
+                        preview={url("/file/raw", item.path)}
                         onSelect={() => setSelected(item.path)}
                         onOpen={() => props.onOpen(item.path)}
                       />
@@ -261,6 +421,8 @@ export function ArtifactGallery(props: { directory: string; onOpen: (path: strin
                     onDownload={() => void download(item())}
                     onCopy={() => void copy(item().path, item().path)}
                     onAttach={() => attach(item())}
+                    onAction={(instruction) => act(item(), instruction)}
+                    onPublish={(format) => void publish(item(), format)}
                   />
                 )}
               </Show>
@@ -275,6 +437,7 @@ export function ArtifactGallery(props: { directory: string; onOpen: (path: strin
 function ArtifactCard(props: {
   item: ArtifactInfo
   active: boolean
+  preview: string
   onSelect: () => void
   onOpen: () => void
 }): JSX.Element {
@@ -301,7 +464,7 @@ function ArtifactCard(props: {
         transition: "border-color 120ms ease, transform 120ms ease, box-shadow 120ms ease",
       }}
     >
-      <ArtifactVisual item={props.item} />
+      <ArtifactVisual item={props.item} preview={props.preview} />
       <div style={{ display: "grid", gap: "7px", padding: "10px 11px" }}>
         <div style={{ display: "flex", gap: "7px", "align-items": "center", "min-width": 0 }}>
           <span style={{ color: accent(props.item.kind), display: "inline-flex" }}>
@@ -334,8 +497,10 @@ function ArtifactCard(props: {
   )
 }
 
-function ArtifactVisual(props: { item: ArtifactInfo }): JSX.Element {
+function ArtifactVisual(props: { item: ArtifactInfo; preview: string }): JSX.Element {
   const seed = () => Array.from(props.item.path).reduce((total, value) => total + value.charCodeAt(0), 0)
+  const image = () =>
+    props.item.kind === "figure" && ["png", "jpg", "jpeg", "svg", "webp", "gif"].includes(props.item.format)
   return (
     <div
       style={{
@@ -346,20 +511,32 @@ function ArtifactVisual(props: { item: ArtifactInfo }): JSX.Element {
         "border-bottom": "1px solid var(--color-border)",
       }}
     >
-      <div style={{ position: "absolute", inset: "12px", display: "flex", "align-items": "flex-end", gap: "4px" }}>
-        <For each={Array.from({ length: 13 })}>
-          {(_, index) => (
-            <span
-              style={{
-                flex: 1,
-                height: `${18 + ((seed() + index() * 29) % 56)}%`,
-                "border-radius": "2px 2px 0 0",
-                background: `color-mix(in srgb, ${accent(props.item.kind)} ${22 + ((index() * 7) % 28)}%, transparent)`,
-              }}
-            />
-          )}
-        </For>
-      </div>
+      <Show
+        when={image()}
+        fallback={
+          <div style={{ position: "absolute", inset: "12px", display: "flex", "align-items": "flex-end", gap: "4px" }}>
+            <For each={Array.from({ length: 13 })}>
+              {(_, index) => (
+                <span
+                  style={{
+                    flex: 1,
+                    height: `${18 + ((seed() + index() * 29) % 56)}%`,
+                    "border-radius": "2px 2px 0 0",
+                    background: `color-mix(in srgb, ${accent(props.item.kind)} ${22 + ((index() * 7) % 28)}%, transparent)`,
+                  }}
+                />
+              )}
+            </For>
+          </div>
+        }
+      >
+        <img
+          src={props.preview}
+          alt=""
+          loading="lazy"
+          style={{ width: "100%", height: "100%", "object-fit": "cover", display: "block" }}
+        />
+      </Show>
       <span
         style={{
           position: "absolute",
@@ -399,6 +576,8 @@ function ArtifactDetail(props: {
   onDownload: () => void
   onCopy: () => void
   onAttach: () => void
+  onAction: (instruction: string) => void
+  onPublish: (format: PublicationFormat) => void
 }): JSX.Element {
   const [provenance] = createResource(
     () => [props.directory, props.item.path] as const,
@@ -408,6 +587,12 @@ function ArtifactDetail(props: {
       return (await response.json()) as Provenance
     },
   )
+  const publication = () => props.item.kind === "report" && ["md", "markdown"].includes(props.item.format.toLowerCase())
+  const [capabilities] = createResource(publication, async () => {
+    const response = await props.request(props.url("/file/publication/capabilities"))
+    if (!response.ok) throw new Error(`${response.status}`)
+    return (await response.json()) as PublicationCapabilities
+  })
   return (
     <aside
       data-component="artifact-detail"
@@ -479,6 +664,64 @@ function ArtifactDetail(props: {
           <Fact label="size" value={formatBytes(props.item.size)} />
           <Fact label="modified" value={new Date(props.item.modified).toLocaleString()} />
         </Section>
+        <Section title="What can I do with this file?">
+          <div style={{ display: "grid", gap: "6px" }}>
+            <For each={artifactActions(props.item)}>
+              {(action) => (
+                <button type="button" style={scienceAction()} onClick={() => props.onAction(action.prompt)}>
+                  <span style={{ color: accent(props.item.kind), display: "inline-flex" }}>
+                    <IconFlask size={12} />
+                  </span>
+                  <span style={{ display: "grid", gap: "2px", "text-align": "left" }}>
+                    <strong>{action.label}</strong>
+                    <small>{action.description}</small>
+                  </span>
+                </button>
+              )}
+            </For>
+          </div>
+        </Section>
+        <Show when={publication()}>
+          <Section title="Publication exports">
+            <div style={{ display: "grid", gap: "8px" }}>
+              <span style={{ ...muted(), "line-height": 1.5 }}>
+                Create timestamped local outputs with Pandoc. Relative figures and tables stay linked to this project.
+              </span>
+              <Show
+                when={capabilities.latest?.pandoc}
+                fallback={
+                  <span style={{ ...muted(), color: "var(--color-warning)" }}>
+                    Install Pandoc to enable HTML, PDF, Word, LaTeX, and PowerPoint exports.
+                  </span>
+                }
+              >
+                <div style={{ display: "grid", "grid-template-columns": "repeat(2, minmax(0, 1fr))", gap: "5px" }}>
+                  <For each={["html", "pdf", "docx", "latex", "pptx"] as PublicationFormat[]}>
+                    {(format) => (
+                      <button
+                        type="button"
+                        style={exportButton(capabilities.latest?.formats[format] ?? false)}
+                        disabled={!capabilities.latest?.formats[format]}
+                        title={
+                          format === "pdf" && !capabilities.latest?.formats.pdf
+                            ? "PDF needs a local TeX or Typst engine"
+                            : `export ${format}`
+                        }
+                        onClick={() => props.onPublish(format)}
+                      >
+                        <IconDownload size={10} />
+                        {format === "pptx" ? "PowerPoint" : format === "docx" ? "Word" : format.toUpperCase()}
+                      </button>
+                    )}
+                  </For>
+                </div>
+                <Show when={capabilities.latest?.pdf_engine}>
+                  <span style={muted()}>PDF engine · {capabilities.latest?.pdf_engine}</span>
+                </Show>
+              </Show>
+            </div>
+          </Section>
+        </Show>
         <Section title="Provenance">
           <Show when={!provenance.loading} fallback={<span style={muted()}>reading Git history…</span>}>
             <Show when={provenance()} fallback={<span style={muted()}>local file · no Git provenance</span>}>
@@ -756,6 +999,98 @@ function primaryButton(): JSX.CSSProperties {
   }
 }
 
+function auditSummary(status?: Audit["status"]): JSX.CSSProperties {
+  const color =
+    status === "ready" ? "var(--color-success)" : status === "blocked" ? "var(--color-error)" : "var(--color-warning)"
+  return {
+    all: "unset",
+    cursor: "pointer",
+    display: "flex",
+    "align-items": "center",
+    gap: "9px",
+    padding: "8px 10px",
+    border: "1px solid var(--color-border)",
+    "border-radius": "7px",
+    background: `color-mix(in srgb, ${color} 4%, var(--color-bg-subtle))`,
+    color: "var(--color-text)",
+  }
+}
+
+function auditScore(status?: Audit["status"]): JSX.CSSProperties {
+  const color =
+    status === "ready" ? "var(--color-success)" : status === "blocked" ? "var(--color-error)" : "var(--color-warning)"
+  return {
+    width: "31px",
+    height: "31px",
+    display: "grid",
+    "place-items": "center",
+    "border-radius": "50%",
+    border: `1px solid color-mix(in srgb, ${color} 40%, var(--color-border))`,
+    background: `color-mix(in srgb, ${color} 9%, transparent)`,
+    color,
+    "font-family": FONT_MONO,
+    "font-size": "10px",
+    "font-weight": 700,
+  }
+}
+
+function auditPanel(): JSX.CSSProperties {
+  return {
+    display: "grid",
+    "grid-template-columns": "minmax(0, 1fr) auto",
+    gap: "12px",
+    padding: "10px",
+    border: "1px solid var(--color-border)",
+    "border-radius": "7px",
+    background: "var(--color-bg-subtle)",
+  }
+}
+
+function auditCheck(): JSX.CSSProperties {
+  return {
+    display: "grid",
+    "grid-template-columns": "12px 150px minmax(0, 1fr)",
+    gap: "7px",
+    "align-items": "baseline",
+    "font-family": FONT_SANS,
+    "font-size": "9px",
+    color: "var(--color-text-muted)",
+  }
+}
+
+function scienceAction(): JSX.CSSProperties {
+  return {
+    all: "unset",
+    cursor: "pointer",
+    display: "grid",
+    "grid-template-columns": "18px minmax(0, 1fr)",
+    gap: "6px",
+    padding: "7px",
+    "border-radius": "5px",
+    border: "1px solid var(--color-border)",
+    background: "var(--color-bg)",
+    color: "var(--color-text)",
+  }
+}
+
+function exportButton(enabled: boolean): JSX.CSSProperties {
+  return {
+    display: "inline-flex",
+    "align-items": "center",
+    "justify-content": "center",
+    gap: "5px",
+    padding: "6px 7px",
+    border: "1px solid var(--color-border)",
+    "border-radius": "5px",
+    background: "var(--color-bg)",
+    color: enabled ? "var(--color-text-muted)" : "var(--color-text-faint)",
+    opacity: enabled ? 1 : 0.45,
+    "font-family": FONT_SANS,
+    "font-size": "9px",
+    cursor: enabled ? "pointer" : "not-allowed",
+  }
+}
+
 function shaButton(): JSX.CSSProperties {
   return {
     width: "fit-content",
diff --git a/frontend/workspace/src/artifacts/model.test.ts b/frontend/workspace/src/artifacts/model.test.ts
index 9e1ec184..f8507b91 100644
--- a/frontend/workspace/src/artifacts/model.test.ts
+++ b/frontend/workspace/src/artifacts/model.test.ts
@@ -1,5 +1,5 @@
 import { describe, expect, test } from "bun:test"
-import { filterArtifacts, groupArtifacts, normalizeArtifacts, sortArtifacts } from "./model"
+import { artifactActions, filterArtifacts, groupArtifacts, normalizeArtifacts, sortArtifacts } from "./model"
 
 const rows = normalizeArtifacts([
   { name: "analysis.ipynb", path: "analysis.ipynb", kind: "notebook", format: "ipynb", size: 20, modified: 10 },
@@ -32,4 +32,19 @@ describe("artifact gallery model", () => {
     expect(sortArtifacts(rows, "name").map((row) => row.name)).toEqual(["analysis.ipynb", "counts.csv", "figure.png"])
     expect(rows[0]?.name).toBe("analysis.ipynb")
   })
+
+  test("offers scientific actions tailored to each artifact kind", () => {
+    expect(artifactActions(rows[2]!).map((action) => action.id)).toEqual(["inspect-quality", "visualize", "analyze"])
+    expect(
+      artifactActions({
+        name: "protein.pdb",
+        path: "protein.pdb",
+        kind: "structure",
+        format: "pdb",
+        size: 100,
+        modified: 1,
+      }).map((action) => action.id),
+    ).toEqual(["inspect-structure", "prepare-docking", "design"])
+    expect(artifactActions(rows[2]!)[0]?.prompt).toContain("results/counts.csv")
+  })
 })
diff --git a/frontend/workspace/src/artifacts/model.ts b/frontend/workspace/src/artifacts/model.ts
index 6e87c8a7..fd269773 100644
--- a/frontend/workspace/src/artifacts/model.ts
+++ b/frontend/workspace/src/artifacts/model.ts
@@ -23,6 +23,13 @@ export interface ArtifactInfo {
   modified: number
 }
 
+export interface ArtifactAction {
+  id: string
+  label: string
+  description: string
+  prompt: string
+}
+
 const kinds = new Set<string>(artifactKinds)
 
 export function normalizeArtifacts(value: unknown): ArtifactInfo[] {
@@ -85,3 +92,230 @@ export function formatArtifactKind(kind: ArtifactKind): string {
   if (kind === "spectrum") return "mass spec"
   return kind
 }
+
+export function artifactActions(artifact: ArtifactInfo): ArtifactAction[] {
+  const path = artifact.path
+  const actions: Record<ArtifactKind, Array<Omit<ArtifactAction, "prompt"> & { instruction: string }>> = {
+    notebook: [
+      {
+        id: "run-notebook",
+        label: "Run & repair",
+        description: "Execute cells, preserve outputs, and fix failures.",
+        instruction: "Open this notebook, inspect it, and run it cell by cell. Repair failures without losing outputs.",
+      },
+      {
+        id: "review-notebook",
+        label: "Review analysis",
+        description: "Check methods, leakage, statistics, and conclusions.",
+        instruction:
+          "Review this notebook as a scientific reviewer. Check methods, data leakage, statistics, and claims.",
+      },
+      {
+        id: "export-notebook",
+        label: "Prepare report",
+        description: "Turn the executed notebook into a concise report.",
+        instruction:
+          "Turn this notebook into a concise, reproducible report with the strongest figures and limitations.",
+      },
+    ],
+    dataset: [
+      {
+        id: "inspect-quality",
+        label: "Inspect quality",
+        description: "Profile schema, missingness, outliers, and leakage risks.",
+        instruction:
+          "Inspect this dataset's schema and quality. Find missingness, suspicious values, outliers, and leakage risks.",
+      },
+      {
+        id: "visualize",
+        label: "Visualize",
+        description: "Build useful, statistically honest exploratory plots.",
+        instruction:
+          "Create a focused set of statistically honest visualizations for this dataset and explain the patterns.",
+      },
+      {
+        id: "analyze",
+        label: "Analyze",
+        description: "Answer the most decision-relevant question in a notebook.",
+        instruction: "Analyze this dataset in a reproducible notebook. State assumptions and save reusable outputs.",
+      },
+    ],
+    figure: [
+      {
+        id: "review-figure",
+        label: "Critique figure",
+        description: "Check clarity, accessibility, scales, and claim support.",
+        instruction:
+          "Critique this figure for scientific clarity, accessibility, scales, uncertainty, and claim support.",
+      },
+      {
+        id: "trace-figure",
+        label: "Trace source",
+        description: "Find the data and code that produced the figure.",
+        instruction:
+          "Trace this figure back to its source data, code, and scientific claim. Record missing provenance.",
+      },
+      {
+        id: "rebuild-figure",
+        label: "Rebuild",
+        description: "Create editable publication-ready SVG, PNG, and PDF.",
+        instruction: "Rebuild this as an editable, publication-ready figure while preserving the underlying evidence.",
+      },
+    ],
+    report: [
+      {
+        id: "verify-report",
+        label: "Verify claims",
+        description: "Check citations, numbers, and claim support.",
+        instruction: "Audit this report's citations, numbers, and scientific claims against concrete project evidence.",
+      },
+      {
+        id: "summarize-report",
+        label: "Executive brief",
+        description: "Extract findings, limitations, and decisions.",
+        instruction:
+          "Create a concise executive brief from this report with findings, limitations, and open decisions.",
+      },
+      {
+        id: "revise-report",
+        label: "Publication pass",
+        description: "Improve structure and evidence without overstating results.",
+        instruction: "Revise this report for publication quality without overstating the evidence.",
+      },
+    ],
+    structure: [
+      {
+        id: "inspect-structure",
+        label: "Inspect structure",
+        description: "Check chains, ligands, chemistry, and geometry.",
+        instruction:
+          "Inspect this molecular structure. Check chains, ligands, chemistry, geometry, and quality issues.",
+      },
+      {
+        id: "prepare-docking",
+        label: "Prepare docking",
+        description: "Validate protonation, receptor, ligands, and binding site.",
+        instruction:
+          "Prepare a careful docking workflow from this structure, validating protonation and the binding site first.",
+      },
+      {
+        id: "design",
+        label: "Design candidates",
+        description: "Define constraints and propose auditable designs.",
+        instruction:
+          "Use this structure to propose a small, auditable protein or molecule design workflow with explicit constraints.",
+      },
+    ],
+    sequence: [
+      {
+        id: "sequence-qc",
+        label: "Sequence QC",
+        description: "Measure composition, quality, duplication, and anomalies.",
+        instruction: "Quality-check these sequences and report composition, read quality, duplication, and anomalies.",
+      },
+      {
+        id: "annotate-sequence",
+        label: "Annotate",
+        description: "Identify features, motifs, and likely function.",
+        instruction: "Annotate these sequences with defensible features, motifs, and likely functions.",
+      },
+      {
+        id: "compare-sequence",
+        label: "Compare",
+        description: "Align sequences and explain meaningful differences.",
+        instruction: "Compare and align these sequences, then explain the biologically meaningful differences.",
+      },
+    ],
+    genomics: [
+      {
+        id: "genomics-qc",
+        label: "Genomics QC",
+        description: "Inspect variants, coverage, alignment, and references.",
+        instruction:
+          "Quality-check this genomics artifact, including references, samples, variants, coverage, and alignment.",
+      },
+      {
+        id: "annotate-variants",
+        label: "Annotate variants",
+        description: "Normalize, annotate, and prioritize interpretable candidates.",
+        instruction: "Normalize and annotate the variants in this artifact, then prioritize candidates with evidence.",
+      },
+      {
+        id: "build-track",
+        label: "Build summary",
+        description: "Create a compact genomic summary and export table.",
+        instruction: "Build an interpretable genomic summary from this artifact and save a clean export table.",
+      },
+    ],
+    spectrum: [
+      {
+        id: "spectrum-qc",
+        label: "Spectrum QC",
+        description: "Inspect acquisition, peaks, contaminants, and signal quality.",
+        instruction:
+          "Inspect this spectrum or mass-spec file for acquisition quality, peaks, contaminants, and anomalies.",
+      },
+      {
+        id: "identify-spectrum",
+        label: "Identify",
+        description: "Plan a transparent peptide or metabolite identification.",
+        instruction:
+          "Plan a transparent identification workflow for this spectrum with databases, tolerances, and FDR controls.",
+      },
+      {
+        id: "compare-spectrum",
+        label: "Compare runs",
+        description: "Compare signal and quality across available runs.",
+        instruction: "Compare this spectrum against related runs and explain decision-relevant quality differences.",
+      },
+    ],
+    model: [
+      {
+        id: "inspect-model",
+        label: "Inspect model",
+        description: "Recover architecture, inputs, outputs, and provenance.",
+        instruction:
+          "Inspect this model artifact and recover architecture, expected inputs, outputs, version, and provenance.",
+      },
+      {
+        id: "evaluate-model",
+        label: "Evaluate",
+        description: "Design a held-out evaluation with failure analysis.",
+        instruction: "Evaluate this model on an appropriate held-out set with failure analysis and no data leakage.",
+      },
+      {
+        id: "package-model",
+        label: "Package",
+        description: "Create a reproducible inference bundle and model card.",
+        instruction: "Package this model into a reproducible inference bundle with an environment lock and model card.",
+      },
+    ],
+    archive: [
+      {
+        id: "inventory-archive",
+        label: "Inventory",
+        description: "List contents and identify scientific assets safely.",
+        instruction:
+          "Inspect this archive safely, inventory its contents, and identify the scientific assets and risks.",
+      },
+      {
+        id: "verify-archive",
+        label: "Verify integrity",
+        description: "Check hashes, structure, and reproducibility files.",
+        instruction: "Verify this archive's integrity and whether it contains enough metadata to reproduce the work.",
+      },
+      {
+        id: "import-archive",
+        label: "Plan import",
+        description: "Create a safe, non-destructive import plan.",
+        instruction: "Create a safe, non-destructive plan to import the useful artifacts from this archive.",
+      },
+    ],
+  }
+  return actions[artifact.kind].map((action) => ({
+    id: action.id,
+    label: action.label,
+    description: action.description,
+    prompt: `${action.instruction}\n\nTarget file: ${path}`,
+  }))
+}
diff --git a/frontend/workspace/src/atlas/RightPane.tsx b/frontend/workspace/src/atlas/RightPane.tsx
index bfa81019..18880962 100644
--- a/frontend/workspace/src/atlas/RightPane.tsx
+++ b/frontend/workspace/src/atlas/RightPane.tsx
@@ -385,7 +385,7 @@ function TerminalTab(): JSX.Element {
 }
 
 function CollapsedRail(props: {
-  tabs: { k: RightPaneTab; Icon: (p: { size?: number; strokeWidth?: number }) => JSX.Element }[]
+  tabs: { k: RightPaneTab; label?: string; Icon: (p: { size?: number; strokeWidth?: number }) => JSX.Element }[]
   onOpen: (t?: RightPaneTab) => void
 }): JSX.Element {
   return (
@@ -402,13 +402,18 @@ function CollapsedRail(props: {
         background: "var(--color-bg-subtle)",
       }}
     >
-      <button onClick={() => props.onOpen()} title="show panel" style={railBtn()}>
+      <button onClick={() => props.onOpen()} title="show panel" aria-label="show panel" style={railBtn()}>
         <IconChevronLeft size={14} strokeWidth={1.5} />
       </button>
       <span style={{ width: "18px", height: "1px", background: "var(--color-border)", margin: "4px 0" }} />
       <For each={props.tabs}>
         {(t) => (
-          <button onClick={() => props.onOpen(t.k)} title={t.k} style={railBtn()}>
+          <button
+            onClick={() => props.onOpen(t.k)}
+            title={t.label ?? t.k}
+            aria-label={t.label ?? t.k}
+            style={railBtn()}
+          >
             <t.Icon size={15} strokeWidth={1.5} />
           </button>
         )}
diff --git a/frontend/workspace/src/components/session/research-launchpad.test.ts b/frontend/workspace/src/components/session/research-launchpad.test.ts
index 9c4b5691..ae3f1139 100644
--- a/frontend/workspace/src/components/session/research-launchpad.test.ts
+++ b/frontend/workspace/src/components/session/research-launchpad.test.ts
@@ -1,5 +1,5 @@
 import { describe, expect, test } from "bun:test"
-import { researchWorkflows, workflowGroups, workflowPrompt } from "./research-launchpad"
+import { researchStarters, researchWorkflows, workflowGroups, workflowPrompt } from "./research-launchpad"
 
 describe("research launchpad", () => {
   test("ships launch-ready workflows across the core scientific loop", () => {
@@ -58,4 +58,9 @@ describe("research launchpad", () => {
     expect(workflowPrompt(workflow, 12)).toContain("12 research artifacts")
     expect(workflowPrompt(workflow, 12)).toContain(workflow.prompt)
   })
+
+  test("ships local-first starter projects with valid backend template ids", () => {
+    expect(researchStarters.map((starter) => starter.id)).toEqual(["single-cell", "dose-response", "protein-structure"])
+    expect(researchStarters.every((starter) => starter.files.length >= 2)).toBe(true)
+  })
 })
diff --git a/frontend/workspace/src/components/session/research-launchpad.ts b/frontend/workspace/src/components/session/research-launchpad.ts
index 0136c34a..f15e400e 100644
--- a/frontend/workspace/src/components/session/research-launchpad.ts
+++ b/frontend/workspace/src/components/session/research-launchpad.ts
@@ -18,6 +18,38 @@ export type ResearchWorkflow = {
     | "network"
 }
 
+export type ResearchStarter = {
+  id: "single-cell" | "dose-response" | "protein-structure"
+  title: string
+  description: string
+  files: string[]
+  accent: string
+}
+
+export const researchStarters: ResearchStarter[] = [
+  {
+    id: "single-cell",
+    title: "Single-cell expression",
+    description: "QC, marker summaries, and a valid Python notebook over a local sample matrix.",
+    files: ["analysis.ipynb", "cells.csv", "README.md"],
+    accent: "#2f8f83",
+  },
+  {
+    id: "dose-response",
+    title: "Dose-response assay",
+    description: "Replicate aggregation, assay QC, and a half-max response analysis.",
+    files: ["analysis.ipynb", "dose_response.csv", "README.md"],
+    accent: "#825dc7",
+  },
+  {
+    id: "protein-structure",
+    title: "Protein structure",
+    description: "A native 3D PDB view plus dependency-free geometry inspection.",
+    files: ["analysis.ipynb", "alanine.pdb", "README.md"],
+    accent: "#2786b8",
+  },
+]
+
 export const researchWorkflows: ResearchWorkflow[] = [
   {
     id: "analyze-data",
diff --git a/frontend/workspace/src/components/session/session-new-view.tsx b/frontend/workspace/src/components/session/session-new-view.tsx
index d0d93063..5a8d18f0 100644
--- a/frontend/workspace/src/components/session/session-new-view.tsx
+++ b/frontend/workspace/src/components/session/session-new-view.tsx
@@ -3,11 +3,13 @@ import { DateTime } from "luxon"
 import { useSync } from "@/context/sync"
 import { useModels } from "@/context/models"
 import { useSDK } from "@/context/sdk"
+import { usePlatform } from "@/context/platform"
 import { useDialog } from "@synsci/ui/context/dialog"
 import { getDirectory, getFilename } from "@synsci/util/path"
 import { DialogSettings } from "@/components/dialog-settings"
 import { centerTabs } from "@/atlas/store/centerTabs"
 import { uiStore } from "@/atlas/store/ui"
+import { toast } from "@/atlas/Toast"
 import {
   IconActivity,
   IconArrowRight,
@@ -21,7 +23,13 @@ import {
   IconRefresh,
   IconSearch,
 } from "@/atlas/shared/Icon"
-import { researchWorkflows, workflowPrompt, type ResearchWorkflow } from "@/components/session/research-launchpad"
+import {
+  researchStarters,
+  researchWorkflows,
+  workflowPrompt,
+  type ResearchStarter,
+  type ResearchWorkflow,
+} from "@/components/session/research-launchpad"
 
 const MAIN_WORKTREE = "main"
 const CREATE_WORKTREE = "create"
@@ -48,6 +56,7 @@ export function NewSessionView(props: NewSessionViewProps) {
   const sync = useSync()
   const models = useModels()
   const sdk = useSDK()
+  const platform = usePlatform()
   const dialog = useDialog()
   const noModel = createMemo(() => models.list().length === 0)
   const sandboxes = createMemo(() => sync.project?.sandboxes ?? [])
@@ -65,6 +74,7 @@ export function NewSessionView(props: NewSessionViewProps) {
         .catch(() => []),
   )
   const [workflowGroup, setWorkflowGroup] = createSignal<ResearchWorkflow["group"] | "all">("all")
+  const [creating, setCreating] = createSignal<ResearchStarter["id"]>()
   const visibleWorkflows = createMemo(() =>
     workflowGroup() === "all"
       ? researchWorkflows
@@ -90,6 +100,31 @@ export function NewSessionView(props: NewSessionViewProps) {
     centerTabs.showChat()
   }
 
+  const createStarter = async (starter: ResearchStarter) => {
+    setCreating(starter.id)
+    const request = platform.fetch ?? fetch
+    const endpoint = new URL(`${sdk.url.replace(/\/+$/, "")}/file/starters`)
+    endpoint.searchParams.set("directory", sdk.directory)
+    const response = await request(endpoint.toString(), {
+      method: "POST",
+      headers: { "Content-Type": "application/json" },
+      body: JSON.stringify({ template: starter.id }),
+    }).catch((error) => {
+      toast.error("starter could not be created", error instanceof Error ? error.message : String(error))
+      return undefined
+    })
+    setCreating(undefined)
+    if (!response) return
+    if (!response.ok) {
+      const detail = await response.text().catch(() => "")
+      toast.error("starter could not be created", detail || `${response.status}`)
+      return
+    }
+    const result = (await response.json()) as { notebook: string; files: string[] }
+    toast.success("starter project ready", `${result.files.length} local files created`)
+    centerTabs.openFile(sdk.directory, result.notebook)
+  }
+
   return (
     <main class="atlas-scroll research-launchpad" data-component="research-launchpad">
       <div class="research-launchpad__inner">
@@ -167,6 +202,47 @@ export function NewSessionView(props: NewSessionViewProps) {
           </section>
         </Show>
 
+        <section class="research-launchpad__starters" aria-labelledby="research-starters-title">
+          <div class="research-launchpad__section-heading">
+            <div>
+              <h2 id="research-starters-title">Start with working science</h2>
+              <p>
+                Create a valid notebook, sample data, and a short local README in one click. No download or gateway.
+              </p>
+            </div>
+            <span class="research-launchpad__local-badge">local · reproducible</span>
+          </div>
+          <div class="research-launchpad__starter-grid">
+            <For each={researchStarters}>
+              {(starter) => (
+                <button
+                  type="button"
+                  class="research-launchpad__starter"
+                  data-starter={starter.id}
+                  disabled={Boolean(creating())}
+                  onClick={() => void createStarter(starter)}
+                  style={{ "--starter-accent": starter.accent }}
+                >
+                  <span class="research-launchpad__starter-visual">
+                    <For each={Array.from({ length: 9 })}>
+                      {(_, index) => <i style={{ height: `${22 + ((index() * 31 + starter.title.length) % 65)}%` }} />}
+                    </For>
+                  </span>
+                  <span class="research-launchpad__starter-copy">
+                    <strong>{starter.title}</strong>
+                    <span>{starter.description}</span>
+                    <small>{starter.files.join(" · ")}</small>
+                  </span>
+                  <span class="research-launchpad__starter-action">
+                    {creating() === starter.id ? "creating…" : "create starter"}
+                    <IconArrowRight size={12} strokeWidth={1.7} />
+                  </span>
+                </button>
+              )}
+            </For>
+          </div>
+        </section>
+
         <section class="research-launchpad__workflows" aria-labelledby="research-workflows-title">
           <div class="research-launchpad__section-heading">
             <div>
diff --git a/frontend/workspace/src/styles/atlas.css b/frontend/workspace/src/styles/atlas.css
index c0f3c920..2733dc9b 100644
--- a/frontend/workspace/src/styles/atlas.css
+++ b/frontend/workspace/src/styles/atlas.css
@@ -1386,6 +1386,132 @@ button.research-launchpad__status-item:hover {
   transform: translateY(1px);
 }
 
+.research-launchpad__starters {
+  display: grid;
+  gap: 13px;
+}
+
+.research-launchpad__local-badge {
+  flex: 0 0 auto;
+  padding: 4px 7px;
+  border: 1px solid var(--color-border);
+  border-radius: 999px;
+  background: color-mix(in srgb, var(--color-success) 6%, transparent);
+  font-family: var(--font-family-mono);
+  font-size: 8px;
+  letter-spacing: 0.05em;
+  color: var(--color-success);
+  text-transform: uppercase;
+}
+
+.research-launchpad__starter-grid {
+  display: grid;
+  grid-template-columns: repeat(3, minmax(0, 1fr));
+  gap: 8px;
+}
+
+.research-launchpad__starter {
+  all: unset;
+  box-sizing: border-box;
+  min-width: 0;
+  display: grid;
+  grid-template-rows: 76px minmax(116px, auto) auto;
+  border: 1px solid var(--color-border);
+  border-radius: 9px;
+  background: color-mix(in srgb, var(--color-surface-solid) 82%, transparent);
+  overflow: hidden;
+  cursor: pointer;
+  transition:
+    transform 180ms cubic-bezier(0.16, 1, 0.3, 1),
+    border-color 180ms ease,
+    box-shadow 180ms ease;
+}
+
+.research-launchpad__starter:hover {
+  transform: translateY(-2px);
+  border-color: color-mix(in srgb, var(--starter-accent) 52%, var(--color-border));
+  box-shadow: 0 14px 30px color-mix(in srgb, var(--starter-accent) 10%, transparent);
+}
+
+.research-launchpad__starter:disabled {
+  opacity: 0.62;
+  cursor: wait;
+}
+
+.research-launchpad__starter-visual {
+  position: relative;
+  display: flex;
+  align-items: flex-end;
+  gap: 4px;
+  padding: 18px 20px 13px;
+  border-bottom: 1px solid var(--color-border);
+  background:
+    radial-gradient(circle at 78% 18%, color-mix(in srgb, var(--starter-accent) 16%, transparent), transparent 7rem),
+    color-mix(in srgb, var(--starter-accent) 6%, var(--color-bg-subtle));
+  overflow: hidden;
+}
+
+.research-launchpad__starter-visual::before {
+  position: absolute;
+  top: 10px;
+  left: 12px;
+  width: 5px;
+  height: 5px;
+  border-radius: 50%;
+  background: var(--starter-accent);
+  box-shadow: 0 0 0 4px color-mix(in srgb, var(--starter-accent) 11%, transparent);
+  content: "";
+}
+
+.research-launchpad__starter-visual i {
+  flex: 1;
+  min-height: 5px;
+  border-radius: 2px 2px 0 0;
+  background: color-mix(in srgb, var(--starter-accent) 38%, transparent);
+}
+
+.research-launchpad__starter-copy {
+  min-width: 0;
+  display: grid;
+  align-content: start;
+  gap: 6px;
+  padding: 13px 13px 10px;
+}
+
+.research-launchpad__starter-copy strong {
+  font-family: var(--font-family-sans);
+  font-size: 12px;
+  font-weight: 620;
+  color: var(--color-text);
+}
+
+.research-launchpad__starter-copy > span {
+  font-family: var(--font-family-sans);
+  font-size: 10px;
+  line-height: 1.45;
+  color: var(--color-text-muted);
+}
+
+.research-launchpad__starter-copy small {
+  font-family: var(--font-family-mono);
+  font-size: 8px;
+  line-height: 1.45;
+  color: var(--color-text-faint);
+}
+
+.research-launchpad__starter-action {
+  display: flex;
+  align-items: center;
+  justify-content: space-between;
+  gap: 8px;
+  padding: 9px 13px;
+  border-top: 1px solid var(--color-border);
+  font-family: var(--font-family-sans);
+  font-size: 9px;
+  font-weight: 570;
+  color: var(--starter-accent);
+}
+
 .research-launchpad__workflows {
   display: grid;
   gap: 14px;
@@ -1647,6 +1773,10 @@ button.research-launchpad__status-item:hover {
     grid-template-columns: 1fr;
   }
 
+  .research-launchpad__starter-grid {
+    grid-template-columns: 1fr;
+  }
+
   .research-launchpad__workflow[data-featured="true"] {
     grid-column: auto;
   }
diff --git a/tooling/sdk/js/src/v2/gen/sdk.gen.ts b/tooling/sdk/js/src/v2/gen/sdk.gen.ts
index 9e4dab4b..be1bab45 100644
--- a/tooling/sdk/js/src/v2/gen/sdk.gen.ts
+++ b/tooling/sdk/js/src/v2/gen/sdk.gen.ts
@@ -35,11 +35,16 @@ import type {
   FileArtifactsResponses,
   FileInspectResponses,
   FileListResponses,
+  FileManifestResponses,
   FilePartInput,
   FilePartSource,
   FileProvenanceResponses,
+  FilePublicationCapabilitiesResponses,
+  FilePublicationResponses,
   FileRawResponses,
   FileReadResponses,
+  FileReproducibilityResponses,
+  FileStarterResponses,
   FileStatusResponses,
   FileWriteResponses,
   FindFilesResponses,
@@ -3603,6 +3608,135 @@ export class File extends HeyApiClient {
     })
   }
 
+  /**
+   * Audit project reproducibility
+   *
+   * Check Git state, locked dependencies, environment specifications, notebook structure, and research artifacts.
+   */
+  public reproducibility<ThrowOnError extends boolean = false>(
+    parameters?: {
+      directory?: string
+    },
+    options?: Options<never, ThrowOnError>,
+  ) {
+    const params = buildClientParams([parameters], [{ args: [{ in: "query", key: "directory" }] }])
+    return (options?.client ?? this.client).get<FileReproducibilityResponses, unknown, ThrowOnError>({
+      url: "/file/reproducibility",
+      ...options,
+      ...params,
+    })
+  }
+
+  /**
+   * Create an artifact integrity manifest
+   *
+   * Hash every discovered research artifact and return a portable, deterministic manifest.
+   */
+  public manifest<ThrowOnError extends boolean = false>(
+    parameters?: {
+      directory?: string
+    },
+    options?: Options<never, ThrowOnError>,
+  ) {
+    const params = buildClientParams([parameters], [{ args: [{ in: "query", key: "directory" }] }])
+    return (options?.client ?? this.client).get<FileManifestResponses, unknown, ThrowOnError>({
+      url: "/file/manifest",
+      ...options,
+      ...params,
+    })
+  }
+
+  /**
+   * Create a local scientific starter project
+   *
+   * Materialize a valid notebook, sample data, and README without external downloads.
+   */
+  public starter<ThrowOnError extends boolean = false>(
+    parameters?: {
+      directory?: string
+      template?: "single-cell" | "dose-response" | "protein-structure"
+    },
+    options?: Options<never, ThrowOnError>,
+  ) {
+    const params = buildClientParams(
+      [parameters],
+      [
+        {
+          args: [
+            { in: "query", key: "directory" },
+            { in: "body", key: "template" },
+          ],
+        },
+      ],
+    )
+    return (options?.client ?? this.client).post<FileStarterResponses, unknown, ThrowOnError>({
+      url: "/file/starters",
+      ...options,
+      ...params,
+      headers: {
+        "Content-Type": "application/json",
+        ...options?.headers,
+        ...params.headers,
+      },
+    })
+  }
+
+  /**
+   * Inspect local publication export support
+   *
+   * Detect Pandoc and a PDF engine before offering report export formats.
+   */
+  public publicationCapabilities<ThrowOnError extends boolean = false>(
+    parameters?: {
+      directory?: string
+    },
+    options?: Options<never, ThrowOnError>,
+  ) {
+    const params = buildClientParams([parameters], [{ args: [{ in: "query", key: "directory" }] }])
+    return (options?.client ?? this.client).get<FilePublicationCapabilitiesResponses, unknown, ThrowOnError>({
+      url: "/file/publication/capabilities",
+      ...options,
+      ...params,
+    })
+  }
+
+  /**
+   * Export a Markdown research report
+   *
+   * Create a timestamped HTML, PDF, DOCX, LaTeX, or PowerPoint publication artifact locally.
+   */
+  public publication<ThrowOnError extends boolean = false>(
+    parameters?: {
+      directory?: string
+      path?: string
+      format?: "html" | "pdf" | "docx" | "latex" | "pptx"
+    },
+    options?: Options<never, ThrowOnError>,
+  ) {
+    const params = buildClientParams(
+      [parameters],
+      [
+        {
+          args: [
+            { in: "query", key: "directory" },
+            { in: "body", key: "path" },
+            { in: "body", key: "format" },
+          ],
+        },
+      ],
+    )
+    return (options?.client ?? this.client).post<FilePublicationResponses, unknown, ThrowOnError>({
+      url: "/file/publication",
+      ...options,
+      ...params,
+      headers: {
+        "Content-Type": "application/json",
+        ...options?.headers,
+        ...params.headers,
+      },
+    })
+  }
+
   /**
    * Get file status
    *
diff --git a/tooling/sdk/js/src/v2/gen/types.gen.ts b/tooling/sdk/js/src/v2/gen/types.gen.ts
index 8e5efef0..4f0872a5 100644
--- a/tooling/sdk/js/src/v2/gen/types.gen.ts
+++ b/tooling/sdk/js/src/v2/gen/types.gen.ts
@@ -5825,6 +5825,171 @@ export type FileProvenanceResponses = {
 
 export type FileProvenanceResponse = FileProvenanceResponses[keyof FileProvenanceResponses]
 
+export type FileReproducibilityData = {
+  body?: never
+  path?: never
+  query?: {
+    directory?: string
+  }
+  url: "/file/reproducibility"
+}
+
+export type FileReproducibilityResponses = {
+  /**
+   * Project reproducibility audit
+   */
+  200: {
+    generated_at: string
+    score: number
+    status: "ready" | "warnings" | "blocked"
+    git?: {
+      branch?: string
+      commit?: string
+      dirty: boolean
+    }
+    lockfiles: Array<string>
+    environments: Array<string>
+    notebooks: {
+      total: number
+      valid: number
+      invalid: Array<string>
+    }
+    artifacts: {
+      total: number
+      nonempty: number
+      bytes: number
+    }
+    checks: Array<{
+      id: string
+      label: string
+      status: "pass" | "warn" | "fail"
+      detail: string
+      weight: number
+    }>
+  }
+}
+
+export type FileReproducibilityResponse = FileReproducibilityResponses[keyof FileReproducibilityResponses]
+
+export type FileManifestData = {
+  body?: never
+  path?: never
+  query?: {
+    directory?: string
+  }
+  url: "/file/manifest"
+}
+
+export type FileManifestResponses = {
+  /**
+   * Artifact checksum manifest
+   */
+  200: {
+    format: "openscience.artifact-manifest.v1"
+    generated_at: string
+    digest: string
+    artifacts: Array<{
+      name: string
+      path: string
+      kind:
+        | "notebook"
+        | "dataset"
+        | "figure"
+        | "report"
+        | "structure"
+        | "sequence"
+        | "genomics"
+        | "spectrum"
+        | "model"
+        | "archive"
+      format: string
+      size: number
+      modified: number
+      sha256: string
+    }>
+  }
+}
+
+export type FileManifestResponse = FileManifestResponses[keyof FileManifestResponses]
+
+export type FileStarterData = {
+  body?: {
+    template: "single-cell" | "dose-response" | "protein-structure"
+  }
+  path?: never
+  query?: {
+    directory?: string
+  }
+  url: "/file/starters"
+}
+
+export type FileStarterResponses = {
+  /**
+   * Created starter files
+   */
+  200: {
+    template: "single-cell" | "dose-response" | "protein-structure"
+    directory: string
+    files: Array<string>
+    notebook: string
+    readme: string
+  }
+}
+
+export type FileStarterResponse = FileStarterResponses[keyof FileStarterResponses]
+
+export type FilePublicationCapabilitiesData = {
+  body?: never
+  path?: never
+  query?: {
+    directory?: string
+  }
+  url: "/file/publication/capabilities"
+}
+
+export type FilePublicationCapabilitiesResponses = {
+  /**
+   * Available local publication formats
+   */
+  200: {
+    pandoc: boolean
+    pdf_engine?: string
+    formats: {
+      [key: string]: boolean
+    }
+  }
+}
+
+export type FilePublicationCapabilitiesResponse =
+  FilePublicationCapabilitiesResponses[keyof FilePublicationCapabilitiesResponses]
+
+export type FilePublicationData = {
+  body?: {
+    path: string
+    format: "html" | "pdf" | "docx" | "latex" | "pptx"
+  }
+  path?: never
+  query?: {
+    directory?: string
+  }
+  url: "/file/publication"
+}
+
+export type FilePublicationResponses = {
+  /**
+   * Created publication artifact
+   */
+  200: {
+    path: string
+    format: "html" | "pdf" | "docx" | "latex" | "pptx"
+    size: number
+    created_at: string
+    engine: string
+  }
+}
+
+export type FilePublicationResponse = FilePublicationResponses[keyof FilePublicationResponses]
+
 export type FileStatusData = {
   body?: never
   path?: never
diff --git a/tooling/sdk/openapi.json b/tooling/sdk/openapi.json
index d475606f..5bb6170d 100644
--- a/tooling/sdk/openapi.json
+++ b/tooling/sdk/openapi.json
@@ -9066,6 +9066,535 @@
         ]
       }
     },
+    "/file/reproducibility": {
+      "get": {
+        "operationId": "file.reproducibility",
+        "parameters": [
+          {
+            "in": "query",
+            "name": "directory",
+            "schema": {
+              "type": "string"
+            }
+          }
+        ],
+        "summary": "Audit project reproducibility",
+        "description": "Check Git state, locked dependencies, environment specifications, notebook structure, and research artifacts.",
+        "responses": {
+          "200": {
+            "description": "Project reproducibility audit",
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "object",
+                  "properties": {
+                    "generated_at": {
+                      "type": "string"
+                    },
+                    "score": {
+                      "type": "integer",
+                      "minimum": 0,
+                      "maximum": 100
+                    },
+                    "status": {
+                      "type": "string",
+                      "enum": [
+                        "ready",
+                        "warnings",
+                        "blocked"
+                      ]
+                    },
+                    "git": {
+                      "type": "object",
+                      "properties": {
+                        "branch": {
+                          "type": "string"
+                        },
+                        "commit": {
+                          "type": "string"
+                        },
+                        "dirty": {
+                          "type": "boolean"
+                        }
+                      },
+                      "required": [
+                        "dirty"
+                      ]
+                    },
+                    "lockfiles": {
+                      "type": "array",
+                      "items": {
+                        "type": "string"
+                      }
+                    },
+                    "environments": {
+                      "type": "array",
+                      "items": {
+                        "type": "string"
+                      }
+                    },
+                    "notebooks": {
+                      "type": "object",
+                      "properties": {
+                        "total": {
+                          "type": "integer",
+                          "minimum": 0,
+                          "maximum": 9007199254740991
+                        },
+                        "valid": {
+                          "type": "integer",
+                          "minimum": 0,
+                          "maximum": 9007199254740991
+                        },
+                        "invalid": {
+                          "type": "array",
+                          "items": {
+                            "type": "string"
+                          }
+                        }
+                      },
+                      "required": [
+                        "total",
+                        "valid",
+                        "invalid"
+                      ]
+                    },
+                    "artifacts": {
+                      "type": "object",
+                      "properties": {
+                        "total": {
+                          "type": "integer",
+                          "minimum": 0,
+                          "maximum": 9007199254740991
+                        },
+                        "nonempty": {
+                          "type": "integer",
+                          "minimum": 0,
+                          "maximum": 9007199254740991
+                        },
+                        "bytes": {
+                          "type": "integer",
+                          "minimum": 0,
+                          "maximum": 9007199254740991
+                        }
+                      },
+                      "required": [
+                        "total",
+                        "nonempty",
+                        "bytes"
+                      ]
+                    },
+                    "checks": {
+                      "type": "array",
+                      "items": {
+                        "type": "object",
+                        "properties": {
+                          "id": {
+                            "type": "string"
+                          },
+                          "label": {
+                            "type": "string"
+                          },
+                          "status": {
+                            "type": "string",
+                            "enum": [
+                              "pass",
+                              "warn",
+                              "fail"
+                            ]
+                          },
+                          "detail": {
+                            "type": "string"
+                          },
+                          "weight": {
+                            "type": "number",
+                            "exclusiveMinimum": 0
+                          }
+                        },
+                        "required": [
+                          "id",
+                          "label",
+                          "status",
+                          "detail",
+                          "weight"
+                        ]
+                      }
+                    }
+                  },
+                  "required": [
+                    "generated_at",
+                    "score",
+                    "status",
+                    "lockfiles",
+                    "environments",
+                    "notebooks",
+                    "artifacts",
+                    "checks"
+                  ]
+                }
+              }
+            }
+          }
+        },
+        "x-codeSamples": [
+          {
+            "lang": "js",
+            "source": "import { createOpenScienceClient } from \"@synsci/sdk\"\n\nconst client = createOpenScienceClient()\nawait client.file.reproducibility({\n  ...\n})"
+          }
+        ]
+      }
+    },
+    "/file/manifest": {
+      "get": {
+        "operationId": "file.manifest",
+        "parameters": [
+          {
+            "in": "query",
+            "name": "directory",
+            "schema": {
+              "type": "string"
+            }
+          }
+        ],
+        "summary": "Create an artifact integrity manifest",
+        "description": "Hash every discovered research artifact and return a portable, deterministic manifest.",
+        "responses": {
+          "200": {
+            "description": "Artifact checksum manifest",
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "object",
+                  "properties": {
+                    "format": {
+                      "type": "string",
+                      "const": "openscience.artifact-manifest.v1"
+                    },
+                    "generated_at": {
+                      "type": "string"
+                    },
+                    "digest": {
+                      "type": "string",
+                      "pattern": "^[a-f0-9]{64}$"
+                    },
+                    "artifacts": {
+                      "type": "array",
+                      "items": {
+                        "type": "object",
+                        "properties": {
+                          "name": {
+                            "type": "string"
+                          },
+                          "path": {
+                            "type": "string"
+                          },
+                          "kind": {
+                            "type": "string",
+                            "enum": [
+                              "notebook",
+                              "dataset",
+                              "figure",
+                              "report",
+                              "structure",
+                              "sequence",
+                              "genomics",
+                              "spectrum",
+                              "model",
+                              "archive"
+                            ]
+                          },
+                          "format": {
+                            "type": "string"
+                          },
+                          "size": {
+                            "type": "number"
+                          },
+                          "modified": {
+                            "type": "number"
+                          },
+                          "sha256": {
+                            "type": "string",
+                            "pattern": "^[a-f0-9]{64}$"
+                          }
+                        },
+                        "required": [
+                          "name",
+                          "path",
+                          "kind",
+                          "format",
+                          "size",
+                          "modified",
+                          "sha256"
+                        ]
+                      }
+                    }
+                  },
+                  "required": [
+                    "format",
+                    "generated_at",
+                    "digest",
+                    "artifacts"
+                  ]
+                }
+              }
+            }
+          }
+        },
+        "x-codeSamples": [
+          {
+            "lang": "js",
+            "source": "import { createOpenScienceClient } from \"@synsci/sdk\"\n\nconst client = createOpenScienceClient()\nawait client.file.manifest({\n  ...\n})"
+          }
+        ]
+      }
+    },
+    "/file/starters": {
+      "post": {
+        "operationId": "file.starter",
+        "parameters": [
+          {
+            "in": "query",
+            "name": "directory",
+            "schema": {
+              "type": "string"
+            }
+          }
+        ],
+        "summary": "Create a local scientific starter project",
+        "description": "Materialize a valid notebook, sample data, and README without external downloads.",
+        "responses": {
+          "200": {
+            "description": "Created starter files",
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "object",
+                  "properties": {
+                    "template": {
+                      "type": "string",
+                      "enum": [
+                        "single-cell",
+                        "dose-response",
+                        "protein-structure"
+                      ]
+                    },
+                    "directory": {
+                      "type": "string"
+                    },
+                    "files": {
+                      "type": "array",
+                      "items": {
+                        "type": "string"
+                      }
+                    },
+                    "notebook": {
+                      "type": "string"
+                    },
+                    "readme": {
+                      "type": "string"
+                    }
+                  },
+                  "required": [
+                    "template",
+                    "directory",
+                    "files",
+                    "notebook",
+                    "readme"
+                  ]
+                }
+              }
+            }
+          }
+        },
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "type": "object",
+                "properties": {
+                  "template": {
+                    "type": "string",
+                    "enum": [
+                      "single-cell",
+                      "dose-response",
+                      "protein-structure"
+                    ]
+                  }
+                },
+                "required": [
+                  "template"
+                ]
+              }
+            }
+          }
+        },
+        "x-codeSamples": [
+          {
+            "lang": "js",
+            "source": "import { createOpenScienceClient } from \"@synsci/sdk\"\n\nconst client = createOpenScienceClient()\nawait client.file.starter({\n  ...\n})"
+          }
+        ]
+      }
+    },
+    "/file/publication/capabilities": {
+      "get": {
+        "operationId": "file.publicationCapabilities",
+        "parameters": [
+          {
+            "in": "query",
+            "name": "directory",
+            "schema": {
+              "type": "string"
+            }
+          }
+        ],
+        "summary": "Inspect local publication export support",
+        "description": "Detect Pandoc and a PDF engine before offering report export formats.",
+        "responses": {
+          "200": {
+            "description": "Available local publication formats",
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "object",
+                  "properties": {
+                    "pandoc": {
+                      "type": "boolean"
+                    },
+                    "pdf_engine": {
+                      "type": "string"
+                    },
+                    "formats": {
+                      "type": "object",
+                      "propertyNames": {
+                        "type": "string",
+                        "enum": [
+                          "html",
+                          "pdf",
+                          "docx",
+                          "latex",
+                          "pptx"
+                        ]
+                      },
+                      "additionalProperties": {
+                        "type": "boolean"
+                      }
+                    }
+                  },
+                  "required": [
+                    "pandoc",
+                    "formats"
+                  ]
+                }
+              }
+            }
+          }
+        },
+        "x-codeSamples": [
+          {
+            "lang": "js",
+            "source": "import { createOpenScienceClient } from \"@synsci/sdk\"\n\nconst client = createOpenScienceClient()\nawait client.file.publicationCapabilities({\n  ...\n})"
+          }
+        ]
+      }
+    },
+    "/file/publication": {
+      "post": {
+        "operationId": "file.publication",
+        "parameters": [
+          {
+            "in": "query",
+            "name": "directory",
+            "schema": {
+              "type": "string"
+            }
+          }
+        ],
+        "summary": "Export a Markdown research report",
+        "description": "Create a timestamped HTML, PDF, DOCX, LaTeX, or PowerPoint publication artifact locally.",
+        "responses": {
+          "200": {
+            "description": "Created publication artifact",
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "object",
+                  "properties": {
+                    "path": {
+                      "type": "string"
+                    },
+                    "format": {
+                      "type": "string",
+                      "enum": [
+                        "html",
+                        "pdf",
+                        "docx",
+                        "latex",
+                        "pptx"
+                      ]
+                    },
+                    "size": {
+                      "type": "integer",
+                      "minimum": 0,
+                      "maximum": 9007199254740991
+                    },
+                    "created_at": {
+                      "type": "string"
+                    },
+                    "engine": {
+                      "type": "string"
+                    }
+                  },
+                  "required": [
+                    "path",
+                    "format",
+                    "size",
+                    "created_at",
+                    "engine"
+                  ]
+                }
+              }
+            }
+          }
+        },
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "type": "object",
+                "properties": {
+                  "path": {
+                    "type": "string",
+                    "minLength": 1,
+                    "maxLength": 4000
+                  },
+                  "format": {
+                    "type": "string",
+                    "enum": [
+                      "html",
+                      "pdf",
+                      "docx",
+                      "latex",
+                      "pptx"
+                    ]
+                  }
+                },
+                "required": [
+                  "path",
+                  "format"
+                ]
+              }
+            }
+          }
+        },
+        "x-codeSamples": [
+          {
+            "lang": "js",
+            "source": "import { createOpenScienceClient } from \"@synsci/sdk\"\n\nconst client = createOpenScienceClient()\nawait client.file.publication({\n  ...\n})"
+          }
+        ]
+      }
+    },
     "/file/status": {
       "get": {
         "operationId": "file.status",

From fe345c74876e840976ee6f3617a9a228b2b266b4 Mon Sep 17 00:00:00 2001
From: Aayam Bansal <aayambansal@gmail.com>
Date: Wed, 29 Jul 2026 08:12:29 +0800
Subject: [PATCH 15/40] fix: bundle secure html publication export

---
 backend/cli/package.json                      |  1 +
 backend/cli/src/file/publication.ts           | 80 ++++++++++++++++++-
 backend/cli/test/file/publication.test.ts     | 16 ++--
 backend/cli/test/server/file-research.test.ts |  2 +-
 bun.lock                                      |  1 +
 .../workspace/e2e/artifact-gallery.spec.ts    | 11 +++
 .../src/artifacts/ArtifactGallery.tsx         | 16 ++--
 7 files changed, 108 insertions(+), 19 deletions(-)

diff --git a/backend/cli/package.json b/backend/cli/package.json
index 7eb1ccdd..34212c66 100644
--- a/backend/cli/package.json
+++ b/backend/cli/package.json
@@ -102,6 +102,7 @@
     "hono-openapi": "catalog:",
     "ignore": "7.0.5",
     "jsonc-parser": "3.3.1",
+    "marked": "catalog:",
     "minimatch": "10.0.3",
     "open": "10.1.2",
     "partial-json": "0.1.7",
diff --git a/backend/cli/src/file/publication.ts b/backend/cli/src/file/publication.ts
index 685170bd..85cbe6d2 100644
--- a/backend/cli/src/file/publication.ts
+++ b/backend/cli/src/file/publication.ts
@@ -1,7 +1,9 @@
 import fs from "node:fs/promises"
 import path from "node:path"
+import { marked, Renderer } from "marked"
 import z from "zod"
 import { OpenScience } from "../openscience"
+import { escapeHtml } from "../util/html"
 
 export namespace PublicationFile {
   export const Format = z.enum(["html", "pdf", "docx", "latex", "pptx"])
@@ -44,7 +46,7 @@ export namespace PublicationFile {
       pandoc,
       pdf_engine: pdf ? path.basename(pdf) : undefined,
       formats: {
-        html: pandoc,
+        html: true,
         pdf: pandoc && Boolean(pdf),
         docx: pandoc,
         latex: pandoc,
@@ -83,6 +85,73 @@ export namespace PublicationFile {
       `${stem}-${stamp.slice(0, 8)}-${stamp.slice(8)}-${nonce}.${extensions[parsed.format]}`,
     )
     const target = path.join(root, relative)
+    if (parsed.format === "html") {
+      const renderer = new Renderer()
+      renderer.html = ({ text }) => escapeHtml(text)
+      renderer.link = ({ href, title, tokens }) => {
+        const content = renderer.parser.parseInline(tokens)
+        const target = safe(href, false)
+        if (!target) return content
+        const hint = title ? ` title="${escapeHtml(title)}"` : ""
+        return `<a href="${escapeHtml(target)}"${hint}>${content}</a>`
+      }
+      renderer.image = ({ href, title, text }) => {
+        const target = safe(href, true)
+        if (!target) return escapeHtml(text)
+        const hint = title ? ` title="${escapeHtml(title)}"` : ""
+        return `<img src="${escapeHtml(target)}" alt="${escapeHtml(text)}"${hint}>`
+      }
+      const markdown = await Bun.file(source).text()
+      const body = await marked.parse(markdown, { gfm: true, renderer })
+      const base = `${path.relative(folder, path.dirname(source)).split(path.sep).join("/") || "."}/`
+      const title = path.basename(source, path.extname(source))
+      const document = `<!doctype html>
+<html lang="en">
+<head>
+  <meta charset="utf-8">
+  <meta name="viewport" content="width=device-width, initial-scale=1">
+  <meta http-equiv="Content-Security-Policy" content="default-src 'none'; img-src 'self' data: https: http:; style-src 'unsafe-inline'; font-src 'self' data:">
+  <base href="${escapeHtml(base)}">
+  <title>${escapeHtml(title)}</title>
+  <style>
+    :root { color-scheme: light dark; font-family: ui-sans-serif, system-ui, sans-serif; line-height: 1.65; }
+    body { max-width: 860px; margin: 0 auto; padding: 48px 28px 80px; color: #20211f; background: #fbfbf8; }
+    h1, h2, h3 { line-height: 1.2; letter-spacing: -0.02em; }
+    h1 { font-size: 2.25rem; margin-bottom: 1.5rem; }
+    h2 { margin-top: 2.5rem; border-bottom: 1px solid #d8d8d0; padding-bottom: .35rem; }
+    a { color: #315f8c; }
+    img { display: block; max-width: 100%; height: auto; margin: 1.5rem auto; }
+    table { width: 100%; border-collapse: collapse; margin: 1.5rem 0; }
+    th, td { border: 1px solid #d8d8d0; padding: .55rem .7rem; text-align: left; }
+    pre, code { font-family: ui-monospace, SFMono-Regular, monospace; background: #efefe9; border-radius: 4px; }
+    pre { overflow: auto; padding: 1rem; }
+    code { padding: .12rem .28rem; }
+    pre code { padding: 0; }
+    blockquote { margin-left: 0; padding-left: 1rem; border-left: 3px solid #a8aaa2; color: #555750; }
+    @media print { body { max-width: none; padding: 0; background: #fff; } a { color: inherit; } }
+    @media (prefers-color-scheme: dark) {
+      body { color: #e6e6df; background: #191a18; }
+      h2, th, td { border-color: #41433e; }
+      pre, code { background: #292b27; }
+      a { color: #8bb8e3; }
+    }
+  </style>
+</head>
+<body>
+${body}
+</body>
+</html>
+`
+      await Bun.write(target, document)
+      const stat = await fs.stat(target)
+      return Result.parse({
+        path: relative.split(path.sep).join("/"),
+        format: parsed.format,
+        size: stat.size,
+        created_at: new Date().toISOString(),
+        engine: "OpenScience Markdown",
+      })
+    }
     const args = [
       "pandoc",
       source,
@@ -126,4 +195,13 @@ export namespace PublicationFile {
     }
     return target
   }
+
+  function safe(value: string, image: boolean): string | undefined {
+    const scheme = /^([a-z][a-z0-9+.-]*):/i.exec(value)?.[1]?.toLowerCase()
+    if (!scheme) return value
+    if (scheme === "http" || scheme === "https") return value
+    if (!image && scheme === "mailto") return value
+    if (image && scheme === "data" && /^data:image\//i.test(value)) return value
+    return undefined
+  }
 }
diff --git a/backend/cli/test/file/publication.test.ts b/backend/cli/test/file/publication.test.ts
index 2f7b5d2c..aa233d35 100644
--- a/backend/cli/test/file/publication.test.ts
+++ b/backend/cli/test/file/publication.test.ts
@@ -6,32 +6,32 @@ import { tmpdir } from "../fixture/fixture"
 describe("PublicationFile", () => {
   test("detects real local publication export capabilities", async () => {
     const capabilities = await PublicationFile.capabilities()
-    expect(capabilities.formats.html).toBe(capabilities.pandoc)
+    expect(capabilities.formats.html).toBe(true)
     expect(capabilities.formats.docx).toBe(capabilities.pandoc)
     expect(capabilities.formats.pptx).toBe(capabilities.pandoc)
     expect(capabilities.formats.pdf).toBe(capabilities.pandoc && Boolean(capabilities.pdf_engine))
   })
 
-  test("exports a real standalone publication when pandoc is available", async () => {
-    const capabilities = await PublicationFile.capabilities()
-    if (!capabilities.formats.html) return
+  test("exports a secure standalone HTML publication without external tooling", async () => {
     await using tmp = await tmpdir({
       init: async (directory) => {
         await Bun.write(
           path.join(directory, "report.md"),
-          "# Treatment response\n\nThe observed response was **42%**.\n",
+          "# Treatment response\n\nThe observed response was **42%**.\n\n<script>alert('unsafe')</script>\n",
         )
       },
     })
     const result = await PublicationFile.render(tmp.path, { path: "report.md", format: "html" })
     expect(result.path).toMatch(/^exports\/report-\d{8}-\d{9}-[a-f0-9]{8}\.html$/)
     expect(result.size).toBeGreaterThan(100)
-    expect(await Bun.file(path.join(tmp.path, result.path)).text()).toContain("Treatment response")
+    expect(result.engine).toBe("OpenScience Markdown")
+    const html = await Bun.file(path.join(tmp.path, result.path)).text()
+    expect(html).toContain("Treatment response")
+    expect(html).toContain("Content-Security-Policy")
+    expect(html).not.toContain("<script>alert")
   })
 
   test("never overwrites a rapid repeated export", async () => {
-    const capabilities = await PublicationFile.capabilities()
-    if (!capabilities.formats.html) return
     await using tmp = await tmpdir({
       init: async (directory) => {
         await Bun.write(path.join(directory, "report.md"), "# Stable export\n")
diff --git a/backend/cli/test/server/file-research.test.ts b/backend/cli/test/server/file-research.test.ts
index 3013c6f8..36eeb07f 100644
--- a/backend/cli/test/server/file-research.test.ts
+++ b/backend/cli/test/server/file-research.test.ts
@@ -56,7 +56,7 @@ describe("/file research routes", () => {
         const capabilities = await FileRoutes().request("/file/publication/capabilities")
         expect(capabilities.status).toBe(200)
         const support = (await capabilities.json()) as { formats: { html: boolean } }
-        if (!support.formats.html) return
+        expect(support.formats.html).toBe(true)
         const response = await FileRoutes().request("/file/publication", {
           method: "POST",
           headers: { "Content-Type": "application/json" },
diff --git a/bun.lock b/bun.lock
index 39827b12..e725d2bb 100644
--- a/bun.lock
+++ b/bun.lock
@@ -78,6 +78,7 @@
         "hono-openapi": "catalog:",
         "ignore": "7.0.5",
         "jsonc-parser": "3.3.1",
+        "marked": "catalog:",
         "minimatch": "10.0.3",
         "open": "10.1.2",
         "partial-json": "0.1.7",
diff --git a/frontend/workspace/e2e/artifact-gallery.spec.ts b/frontend/workspace/e2e/artifact-gallery.spec.ts
index 22534f84..5d0e1ffa 100644
--- a/frontend/workspace/e2e/artifact-gallery.spec.ts
+++ b/frontend/workspace/e2e/artifact-gallery.spec.ts
@@ -7,6 +7,16 @@ test("discovers, filters, opens, downloads, and contextualizes local research ar
   page,
   gotoSession,
 }) => {
+  await page.route("**/file/publication/capabilities?**", (route) =>
+    route.fulfill({
+      status: 200,
+      contentType: "application/json",
+      body: JSON.stringify({
+        pandoc: false,
+        formats: { html: true, pdf: false, docx: false, latex: false, pptx: false },
+      }),
+    }),
+  )
   const directory = mkdtempSync(path.join(tmpdir(), "openscience-artifacts-e2e-"))
   mkdirSync(path.join(directory, "results"))
   writeFileSync(path.join(directory, "analysis.ipynb"), '{"cells":[],"metadata":{},"nbformat":4,"nbformat_minor":5}')
@@ -74,6 +84,7 @@ test("discovers, filters, opens, downloads, and contextualizes local research ar
     await gallery.locator('[data-artifact="report.md"]').click()
     await expect(detail.getByText("Publication exports", { exact: true })).toBeVisible()
     await expect(detail.getByRole("button", { name: "HTML", exact: true })).toBeEnabled()
+    await expect(detail.getByText("Install Pandoc to unlock PDF, Word, LaTeX, and PowerPoint.")).toBeVisible()
   } finally {
     rmSync(directory, { recursive: true, force: true })
   }
diff --git a/frontend/workspace/src/artifacts/ArtifactGallery.tsx b/frontend/workspace/src/artifacts/ArtifactGallery.tsx
index 1cc08c03..a825e70a 100644
--- a/frontend/workspace/src/artifacts/ArtifactGallery.tsx
+++ b/frontend/workspace/src/artifacts/ArtifactGallery.tsx
@@ -685,16 +685,9 @@ function ArtifactDetail(props: {
           <Section title="Publication exports">
             <div style={{ display: "grid", gap: "8px" }}>
               <span style={{ ...muted(), "line-height": 1.5 }}>
-                Create timestamped local outputs with Pandoc. Relative figures and tables stay linked to this project.
+                HTML is built in. Pandoc adds timestamped PDF, Word, LaTeX, and PowerPoint outputs.
               </span>
-              <Show
-                when={capabilities.latest?.pandoc}
-                fallback={
-                  <span style={{ ...muted(), color: "var(--color-warning)" }}>
-                    Install Pandoc to enable HTML, PDF, Word, LaTeX, and PowerPoint exports.
-                  </span>
-                }
-              >
+              <Show when={capabilities.latest} fallback={<span style={muted()}>checking local export tools…</span>}>
                 <div style={{ display: "grid", "grid-template-columns": "repeat(2, minmax(0, 1fr))", gap: "5px" }}>
                   <For each={["html", "pdf", "docx", "latex", "pptx"] as PublicationFormat[]}>
                     {(format) => (
@@ -718,6 +711,11 @@ function ArtifactDetail(props: {
                 <Show when={capabilities.latest?.pdf_engine}>
                   <span style={muted()}>PDF engine · {capabilities.latest?.pdf_engine}</span>
                 </Show>
+                <Show when={!capabilities.latest?.pandoc}>
+                  <span style={{ ...muted(), color: "var(--color-warning)" }}>
+                    Install Pandoc to unlock PDF, Word, LaTeX, and PowerPoint.
+                  </span>
+                </Show>
               </Show>
             </div>
           </Section>

From 0bef3b001536823a72cc429e69d871fc2b721e61 Mon Sep 17 00:00:00 2001
From: Aayam Bansal <aayambansal@gmail.com>
Date: Wed, 29 Jul 2026 08:24:51 +0800
Subject: [PATCH 16/40] fix: support launcher version flags

---
 .../test/installation/synsci-version.test.ts  | 24 +++++++++++++++++++
 tooling/launcher/bin/synsci.mjs               |  4 ++++
 2 files changed, 28 insertions(+)
 create mode 100644 backend/cli/test/installation/synsci-version.test.ts

diff --git a/backend/cli/test/installation/synsci-version.test.ts b/backend/cli/test/installation/synsci-version.test.ts
new file mode 100644
index 00000000..f6dc4831
--- /dev/null
+++ b/backend/cli/test/installation/synsci-version.test.ts
@@ -0,0 +1,24 @@
+import path from "node:path"
+import { describe, expect, test } from "bun:test"
+import launcher from "../../../../tooling/launcher/package.json"
+
+const script = path.join(import.meta.dir, "../../../../tooling/launcher/bin/synsci.mjs")
+
+describe("synsci launcher version", () => {
+  test("prints its version without starting the interactive installer", async () => {
+    const proc = Bun.spawn(["node", script, "--version"], {
+      stdin: "ignore",
+      stdout: "pipe",
+      stderr: "pipe",
+    })
+    const [stdout, stderr, code] = await Promise.all([
+      new Response(proc.stdout).text(),
+      new Response(proc.stderr).text(),
+      proc.exited,
+    ])
+
+    expect(code).toBe(0)
+    expect(stdout.trim()).toBe(launcher.version)
+    expect(stderr).toBe("")
+  })
+})
diff --git a/tooling/launcher/bin/synsci.mjs b/tooling/launcher/bin/synsci.mjs
index abc477c2..81223731 100755
--- a/tooling/launcher/bin/synsci.mjs
+++ b/tooling/launcher/bin/synsci.mjs
@@ -39,6 +39,10 @@ const LAUNCHER_VERSION = (() => {
     return "0.0.0"
   }
 })()
+if (process.argv.includes("--version") || process.argv.includes("-v")) {
+  console.log(LAUNCHER_VERSION)
+  process.exit(0)
+}
 const OPENSCIENCE_NPM_TAG = npmDistTag(LAUNCHER_VERSION)
 const OPENSCIENCE_NPM_SPEC = opensciencePackageSpec(LAUNCHER_VERSION)
 

From 22f3db3c1b6e44e44a0de0f464085ed24cb35f88 Mon Sep 17 00:00:00 2001
From: Aayam Bansal <aayambansal@gmail.com>
Date: Wed, 29 Jul 2026 13:57:27 +0800
Subject: [PATCH 17/40] docs: define science parity program

---
 ...-29-claude-science-biomni-parity-design.md | 337 ++++++++++++++++++
 1 file changed, 337 insertions(+)
 create mode 100644 docs/superpowers/specs/2026-07-29-claude-science-biomni-parity-design.md

diff --git a/docs/superpowers/specs/2026-07-29-claude-science-biomni-parity-design.md b/docs/superpowers/specs/2026-07-29-claude-science-biomni-parity-design.md
new file mode 100644
index 00000000..946f8fbe
--- /dev/null
+++ b/docs/superpowers/specs/2026-07-29-claude-science-biomni-parity-design.md
@@ -0,0 +1,337 @@
+# Claude Science and Biomni Parity Program
+
+## Goal
+
+OpenScience should become a launch-ready scientific workbench that is at least
+as coherent and capable as Claude Science for interactive analysis, while
+matching the useful breadth of Biomni without inheriting its unsafe execution
+model or research-only UI.
+
+Parity is not measured by the number of cards, prompts, or advertised
+integrations. A capability counts only when a scientist can discover it, use it
+against real data, inspect its execution and provenance, recover from failure,
+and export a reproducible result.
+
+## Product Principles
+
+1. **Artifact-first work.** The primary object is the scientific result:
+   notebook, figure, structure, dataset, manuscript, or run. Chat, code,
+   environment, provenance, and review are contextual views of that object.
+2. **One coherent shell.** Project navigation stays on the left, active work in
+   the center, and contextual inspection on the right. A task should not require
+   learning four independent navigation systems.
+3. **Real integrations only.** Public and local integrations must be exercised
+   end-to-end. Credential- or contract-locked providers may ship a complete
+   adapter, setup flow, and honest unavailable state, but never a fake success
+   path.
+4. **Local-first trust.** Raw data and credentials stay local unless the user
+   deliberately chooses a remote service. Code execution, network access, and
+   remote compute remain visible and revocable.
+5. **Reproducibility by construction.** Every result links to code, inputs,
+   environment, execution, conversation, review, and version history without
+   requiring the user to assemble a manual audit trail.
+6. **Review before polish is called complete.** Citations, reported numbers,
+   figure/code consistency, and missing provenance are checked before a result
+   is marked ready.
+7. **Depth before catalog size.** A smaller number of integrated workflows is
+   more valuable than hundreds of disconnected tool descriptions.
+
+## Evidence Baseline
+
+The audit used the current official Claude Science announcement, product page,
+and interactive product demonstrations; the Stanford Biomni repository and
+website; and a live browser/code audit of OpenScience on
+`openscience/aayam-new`.
+
+### OpenScience capabilities already present
+
+- Native `.ipynb` editing, persistent Python/R kernels, rich outputs, restart,
+  interrupt, diff, export, and per-cell provenance.
+- Text-backed scientific routing for molecular structures, sequences,
+  alignments, and chemistry plus binary summaries for common omics formats.
+- Local and SSH job primitives, scheduler resource fields, logs, cancellation,
+  reruns, and local artifact capture.
+- Artifact gallery, evidence graph, reproducibility manifests, publication
+  exports, starter projects, session recovery, and research launchpad.
+- Roughly 292 scientific playbooks across 16 categories.
+- Forty-two keyless scientific data connectors across proteins, genomics,
+  chemistry, pathways, literature, and omics.
+
+These are meaningful foundations. The remaining gap is integration depth,
+scientific interaction quality, execution trust, and product coherence.
+
+## Audited Gap Matrix
+
+| Priority | Area | Current OpenScience gap | Required outcome |
+| --- | --- | --- | --- |
+| P0 | Local security boundary | Local API, renderer isolation, file containment, OAuth redirects, plugin discovery, network policy, and subprocess environment have unresolved launch findings | No critical local-origin, file-read, credential-exfiltration, path-containment, or unsafe-rendering path remains |
+| P0 | Application shell | Header, sidebar, center tabs, tool rail, and right pane compete for attention; type is small and low-contrast | One adaptive three-region shell with clear hierarchy, labeled actions, accessible typography, and useful narrow layouts |
+| P0 | Artifact workspace | Visualization, source, execution, messages, environment, review, history, and export are separate or absent | A contextual artifact studio exposes all of them without leaving the active result |
+| P0 | Scientific review | Reviewer behavior is prompt-driven and advisory | A deterministic finalization gate records citation, numeric, figure/code, and provenance findings with explicit resolution |
+| P1 | Molecular interaction | Mol* renders structures but exposes almost no scientific controls | Selection, measurements, representation/color presets, atom details, labels, snapshots, annotations, and image/structure export |
+| P1 | Chemistry editing | Molecules render but cannot be sketched or edited | Live 2D sketcher with SMILES/SDF round-trip, validation, history, and handoff to 3D |
+| P1 | Remote compute | Jobs lack complete queue lifecycle, arrays, checkpoint restore, remote artifacts, cost planning, and provider revocation | Plan, approve, submit, stream, retry, cancel, resume, collect, and audit local/SSH/HPC/provider jobs |
+| P1 | Environment lifecycle | Environment metadata exists but dependency setup is fragmented | Inspectable Python/R/system/container environment plans with validation, lock capture, reusable profiles, and recovery |
+| P1 | Manuscript workflow | Export exists without a focused authoring/review workspace | Markdown/LaTeX editor, live PDF preview, citation browser, figure insertion, review findings, and reproducible export |
+| P1 | Domain databases | Coverage omits important regulatory, imaging, ecology, genetics, clinical, and pharmacovigilance sources | Typed, tested connectors plus federated search and source-specific result views |
+| P2 | Scientific imaging | No first-class FCS, DICOM/NIfTI, OME-TIFF/WSI, or cryo-EM exploration | Format-aware viewers with metadata, channels/slices, annotations, measurements, and export |
+| P2 | Scientific models | No polished adapters for protein language/design and structure models | Real local/public adapters where possible and honest credential-gated adapters otherwise |
+| P2 | Tables and arrays | Inspection lacks joins, pivots, larger columnar workflows, and richer statistical exploration | Arrow/Parquet-backed transforms, joins, pivots, plots, provenance, and notebook handoff |
+| P2 | Local knowledge packs | No versioned optional datalake or licensing filter comparable to Biomni's local assets | Discoverable, checksum-verified, versioned data packs with license/commercial-use metadata |
+| P2 | Remaining formats | No native Newick, SBML, MRC, trajectories, richer bigWig/bigBed/BCF, or general HDF5 exploration | Purpose-built viewers and companion/index contracts rather than extension-only recognition |
+| P3 | Product benchmarks | Feature existence is tested, but full scientific tasks are not scored against competitor workflows | Reproducible launch benchmark covering task success, interaction cost, provenance, recovery, and review quality |
+
+## Information Architecture
+
+### Left: project navigation
+
+- Project identity and global search
+- Sessions and branches
+- Files and datasets
+- Runs and compute
+- Artifacts and manuscripts
+- Sources and integrations
+
+The left rail is stable. Catalogs such as skills and databases live behind
+searchable commands or project settings rather than dominating the working
+canvas.
+
+### Center: active scientific work
+
+The center hosts one active document or conversation:
+
+- analysis conversation
+- notebook
+- scientific viewer/editor
+- data table
+- manuscript
+- compute plan/run
+
+Tabs remain recoverable and branch-aware. The initial project screen prioritizes
+recent work, active runs, unresolved review findings, and a concise composer.
+The complete workflow catalog moves behind a searchable launcher.
+
+### Right: contextual inspector
+
+The right pane changes with the active object and uses a consistent tab model:
+
+- **Details** — metadata, inputs, outputs, scientific properties
+- **Code** — exact generating or transforming code
+- **Run** — status, logs, timing, resources, checkpoints
+- **Messages** — conversation slice that produced the object
+- **Environment** — packages, runtime, container, hardware
+- **Review** — findings and resolution state
+- **History** — versions, branches, comparison, restore
+
+On narrow screens it becomes a labeled drawer. It never remains a stale compute
+form while the user is inspecting an unrelated file.
+
+## Artifact Model
+
+An artifact is a locally addressable result with a stable id and versions. Each
+version records:
+
+- artifact kind and source path
+- input files with hashes
+- generating code or command
+- execution/run id and timestamps
+- environment manifest
+- conversation range
+- review report
+- parent version or branch
+- export records
+
+Existing notebook provenance, artifact metadata, run records, and Git history
+remain authoritative. The studio composes these sources rather than creating a
+second provenance database. Missing information is shown as missing, never
+inferred.
+
+Annotations are versioned sidecar data. They target scientific coordinates
+where possible—atom/residue, genomic interval, image coordinate, table
+row/column—and screen coordinates only as a fallback. An annotation can create
+a message draft or a requested edit without silently changing the artifact.
+
+## Scientific Viewer Contract
+
+Every first-class viewer implements the same user-facing contract:
+
+- format and parser status
+- selection model and details
+- measurement/annotation hooks when scientifically meaningful
+- view configuration with sensible presets
+- source or metadata access
+- export image/data
+- provenance and version handoff
+- loading, empty, malformed, unsupported, and large-file states
+- keyboard and screen-reader affordances
+
+The contract is capability-based. A PDF does not pretend to support atom
+measurement, and a molecule does not inherit irrelevant genome controls.
+
+## Review Gate
+
+Finalization is a local, recorded state transition rather than another chat
+message.
+
+1. Collect claims, citations, numeric values, figures, source code, inputs, and
+   provenance references.
+2. Run deterministic structural checks first.
+3. Optionally ask the configured reviewer model for semantic findings.
+4. Store findings with severity, evidence, location, proposed resolution, and
+   status.
+5. Prevent a “reviewed” or publication-ready badge while blocking findings are
+   unresolved.
+6. Allow an explicit, attributed override with a reason.
+
+The first gate covers missing/broken citations, numbers not traceable to a
+table/run, figures without generating code or inputs, figure/code mismatch
+signals, and missing environment capture.
+
+## Compute and Environment Contract
+
+A compute run advances through:
+
+`draft -> validated -> awaiting approval -> queued -> running -> collecting -> completed`
+
+with terminal alternatives `cancelled`, `failed`, and `revoked`.
+
+Before submission the UI shows target, command, working tree state,
+environment/container, data transfers, scheduler/provider resources, estimated
+cost when available, and expected outputs. Approval is explicit for remote or
+billable execution. The same run surface streams logs, scheduler state,
+artifacts, checkpoints, retries, and provenance.
+
+Local, SSH, Slurm, and PBS remain the first end-to-end targets. Paid providers
+use the same contract but cannot claim validation without credentials and an
+actual run.
+
+## Database and Tool Strategy
+
+OpenScience keeps its playbook library but adds typed, observable functions for
+high-value sources. The next connector set prioritizes:
+
+- ENCODE and SCREEN/cCRE
+- JASPAR and RegulomeDB
+- cBioPortal and Monarch
+- GWAS Catalog and QuickGO
+- PRIDE and EMDB
+- OpenFDA, DailyMed, and ClinicalTrials.gov
+- UniChem and ReMap
+- BLAST-compatible search
+
+Each connector has a typed request/response contract, rate-limit and attribution
+metadata, fixture-free contract tests where the public service permits them,
+cached/offline behavior, and a dedicated result renderer when generic tables
+lose scientific meaning.
+
+Biomni-inspired domain depth follows in imaging, CRISPR and cloning,
+microbiology, flow cytometry, pharmacovigilance, physiological signals, and lab
+automation. These become real tools or workflows, not additional prompt cards.
+
+## Delivery Batches
+
+### Batch 1 — Trusted Artifact Workbench
+
+- Fix the critical local API, unsafe renderer, file containment, and credential
+  forwarding boundaries touched by the workspace.
+- Introduce the adaptive three-region shell and contextual inspector.
+- Build the artifact studio and versioned annotation model.
+- Upgrade molecular structure viewing with selection, measurements, visual
+  presets, details, snapshots, and export.
+- Replace generic artifact thumbnails with truthful generated previews or
+  explicit format placeholders.
+- Add accessibility, loading, empty, error, and narrow-layout coverage.
+
+### Batch 2 — Review and Manuscript Workbench
+
+- Implement deterministic review reports and finalization gate.
+- Add citation/numeric/figure/provenance checks and override audit trail.
+- Build Markdown/LaTeX manuscript editing, live preview, citation browser,
+  figure insertion, and publication export.
+- Surface review state consistently on artifacts, notebooks, and manuscripts.
+
+### Batch 3 — Complete Compute Lifecycle
+
+- Add scheduler polling, arrays, dependency validation, retries, checkpoint
+  restore, remote artifact collection, and disconnect recovery.
+- Add environment profiles, validation, lock capture, containers, and reusable
+  compute plans.
+- Add explicit remote/billable approval, cost display where available, and
+  provider revocation.
+
+### Batch 4 — Biomedical Data and Tool Depth
+
+- Add the prioritized public database connectors and federated scientific
+  search.
+- Add optional versioned data packs with license filtering.
+- Add typed biomedical tools in the highest-value Biomni domains.
+- Add model adapters only where their execution and provenance can be validated.
+
+### Batch 5 — Imaging, Trees, Models, and Large Data
+
+- Add FCS, DICOM/NIfTI, OME-TIFF, WSI, MRC, Newick, SBML, and trajectory
+  viewers.
+- Add companion-file and byte-range contracts for indexed/large formats.
+- Add Arrow/Parquet transforms, joins, pivots, statistical plots, and notebook
+  handoff.
+
+### Batch 6 — Launch Benchmark and Refinement
+
+- Create representative end-to-end scientific tasks spanning the implemented
+  domains.
+- Score completion, interaction cost, recovery, provenance completeness,
+  review quality, accessibility, and performance.
+- Fix benchmark failures and remaining cross-workflow inconsistencies.
+
+## Verification Strategy
+
+Every batch must provide evidence at four levels:
+
+1. **Unit and contract tests** for pure models, parsers, policies, and routes.
+2. **Real integration tests** for local kernels, files, subprocesses, and public
+   APIs; avoid mocks when the real implementation is available.
+3. **Browser tests and visual inspection** for complete user workflows,
+   including narrow layouts, failure states, and keyboard navigation.
+4. **Packaged validation** through the npm `test` tag in an isolated prefix,
+   using a temporary configuration and local deterministic model provider.
+
+Before every push:
+
+- run the relevant focused tests and typechecks
+- run `git diff --check`
+- confirm only `openscience/aayam-new` is checked out
+- confirm author and committer are `Aayam Bansal <aayambansal@gmail.com>`
+- preserve the user-owned untracked `AUDIT.md`
+
+Npm test releases are batched after tens of coherent feature commits or a major
+vertical slice. The production npm workflow and both repositories' `main`
+branches are never targets.
+
+## Success Criteria
+
+The parity program is complete only when:
+
+- every P0 and P1 row has direct code, test, and browser evidence
+- P2 rows either have that evidence or an explicit product decision removing
+  them from the launch contract
+- supported integrations have real successful validation, and inaccessible
+  partner integrations are labeled accordingly
+- representative scientific tasks complete without manual provenance assembly
+- review gates catch seeded citation, numeric, figure, and provenance faults
+- local and remote failures recover without losing the session or result
+- packaged npm `test` installation passes the same core workflows
+- the final requirement-by-requirement audit contains no unsupported completion
+  claims
+
+## Constraints
+
+- Work only on `openscience/aayam-new`.
+- Change Atlas only when OpenScience cannot satisfy a required contract locally;
+  use a non-main Atlas branch and validate it independently.
+- Never push OpenScience or Atlas `main`.
+- Never invoke a production npm workflow.
+- Preserve `Aayam Bansal <aayambansal@gmail.com>` as author and committer with no
+  generated co-author trailers.
+- Never persist provider, npm, GitHub, Atlas, or other credentials in source,
+  fixtures, logs, commits, or documentation.
+- Preserve the user-owned untracked `AUDIT.md`.

From bcd0c52f1398bac7ce14d913f8aeb9fb77b4d310 Mon Sep 17 00:00:00 2001
From: Aayam Bansal <aayambansal@gmail.com>
Date: Wed, 29 Jul 2026 14:00:31 +0800
Subject: [PATCH 18/40] docs: plan trusted artifact workbench

---
 .../2026-07-29-trusted-artifact-workbench.md  | 480 ++++++++++++++++++
 1 file changed, 480 insertions(+)
 create mode 100644 docs/superpowers/plans/2026-07-29-trusted-artifact-workbench.md

diff --git a/docs/superpowers/plans/2026-07-29-trusted-artifact-workbench.md b/docs/superpowers/plans/2026-07-29-trusted-artifact-workbench.md
new file mode 100644
index 00000000..339e2408
--- /dev/null
+++ b/docs/superpowers/plans/2026-07-29-trusted-artifact-workbench.md
@@ -0,0 +1,480 @@
+# Trusted Artifact Workbench Implementation Plan
+
+> **Execution mode:** single-agent implementation on `openscience/aayam-new`.
+> Follow the tasks in order and keep every red/green test result observable.
+
+**Goal:** Deliver the first large parity batch: close the remaining file-boundary
+risk, turn opened scientific files into contextual artifacts, replace the stale
+global right rail with an artifact inspector, and upgrade molecular structures
+from a bare canvas into an inspectable and exportable scientific workspace.
+
+**Architecture:** Existing file, provenance, notebook, run, and Git records stay
+authoritative. A small artifact-context store tells the shell what object is
+active. `ArtifactInspector` composes the existing APIs into honest
+Details/Code/Run/Messages/Environment/Review/History states. Scientific
+renderers publish optional capabilities through typed callbacks rather than
+reaching into the shell. Mol* remains the only 3D dependency.
+
+**Tech stack:** TypeScript, SolidJS, Bun, Hono, Mol*, Playwright, existing
+OpenScience SDK and design tokens.
+
+## Global Constraints
+
+- Work only on `openscience/aayam-new`.
+- Preserve the user-owned untracked `AUDIT.md`.
+- Never push OpenScience or Atlas `main`.
+- Never invoke the production npm workflow.
+- Publish packages only through `.github/workflows/npm-test.yml`, after the
+  complete batch rather than after individual commits.
+- Keep `Aayam Bansal <aayambansal@gmail.com>` as author and committer.
+- Do not add React, a second molecular renderer, or a second provenance store.
+- Do not show invented run, review, environment, or history data. Empty states
+  must say exactly what has not been recorded.
+
+---
+
+### Task 1: Canonical Project Path Boundary
+
+**Files:**
+
+- Modify: `backend/cli/src/util/filesystem.ts`
+- Modify: `backend/cli/src/project/instance.ts`
+- Modify: `backend/cli/src/file/index.ts`
+- Modify: `backend/cli/src/tool/external-directory.ts`
+- Modify: `backend/cli/test/file/path-traversal.test.ts`
+- Modify: `backend/cli/test/tool/read.test.ts`
+
+**Contract:**
+
+- Existing files and directories are compared by canonical path.
+- A symlink below the opened project that resolves outside the project is not
+  treated as internal.
+- For a new write target, the nearest existing parent is canonicalized and must
+  remain inside the canonical project/worktree boundary.
+- Ordinary internal paths, monorepo worktree siblings, and non-existent
+  internal write targets keep working.
+
+- [ ] Add failing tests that create an internal symlink to an external temp
+  directory and prove `File.read`, `File.raw`, `File.inspect`, `File.list`,
+  `File.write`, `ReadTool`, and `assertExternalDirectory` do not silently treat
+  it as internal.
+- [ ] Add failing tests for a new internal file and a valid monorepo sibling so
+  the fix cannot over-restrict normal work.
+- [ ] Run:
+
+  ```bash
+  cd backend/cli
+  bun test test/file/path-traversal.test.ts test/tool/read.test.ts
+  ```
+
+  Confirm the symlink cases fail for the intended reason.
+- [ ] Add one reusable canonical containment helper in
+  `backend/cli/src/util/filesystem.ts`. Resolve the nearest existing ancestor
+  for missing paths and reconstruct the unresolved suffix without following a
+  later symlink.
+- [ ] Expose an async `Instance.containsCanonicalPath(path)` or equivalent and
+  use it at file/API and external-directory trust boundaries. Keep the existing
+  lexical helper only for non-authoritative display/fast-path use.
+- [ ] Re-run the focused tests and the existing snapshot symlink/revert tests.
+- [ ] Commit:
+
+  ```bash
+  git add backend/cli/src/util/filesystem.ts \
+    backend/cli/src/project/instance.ts \
+    backend/cli/src/file/index.ts \
+    backend/cli/src/tool/external-directory.ts \
+    backend/cli/test/file/path-traversal.test.ts \
+    backend/cli/test/tool/read.test.ts
+  git commit -m "fix: enforce canonical project file boundaries"
+  ```
+
+### Task 2: Active Artifact Context Model
+
+**Files:**
+
+- Create: `frontend/workspace/src/artifacts/context.ts`
+- Create: `frontend/workspace/src/artifacts/context.test.ts`
+- Modify: `frontend/workspace/src/atlas/store/ui.ts`
+- Modify: `frontend/workspace/src/atlas/FilePreview.tsx`
+
+**Contract:**
+
+```ts
+type ArtifactContext = {
+  id: string
+  directory: string
+  path: string
+  name: string
+  format: string
+  kind: ArtifactKind
+  scienceKind?: string
+}
+```
+
+- The active file publishes a normalized artifact context after format
+  detection.
+- Switching center tabs changes or clears the active context without allowing
+  an unmounted/stale file to clear a newer context.
+- Inspector selection and open state persist, but stale object-specific state
+  never leaks to another file.
+
+- [ ] Write failing pure tests for id stability, file-extension classification,
+  scientific kind propagation, stale-clear protection, and unknown file
+  fallback.
+- [ ] Run `bun test frontend/workspace/src/artifacts/context.test.ts` and confirm
+  failure.
+- [ ] Implement the pure context model and a small Solid signal store.
+- [ ] Have `FileView` publish its context and renderer capabilities; clear it
+  only when it still owns the current context.
+- [ ] Add source-contract coverage in
+  `frontend/workspace/src/pages/session-shell.test.ts`.
+- [ ] Run the focused tests and workspace typecheck.
+- [ ] Commit:
+
+  ```bash
+  git add frontend/workspace/src/artifacts/context.ts \
+    frontend/workspace/src/artifacts/context.test.ts \
+    frontend/workspace/src/atlas/store/ui.ts \
+    frontend/workspace/src/atlas/FilePreview.tsx \
+    frontend/workspace/src/pages/session-shell.test.ts
+  git commit -m "feat: track active scientific artifacts"
+  ```
+
+### Task 3: Artifact Inspector Data Model
+
+**Files:**
+
+- Create: `frontend/workspace/src/artifacts/inspector.ts`
+- Create: `frontend/workspace/src/artifacts/inspector.test.ts`
+- Create: `frontend/workspace/src/artifacts/ArtifactInspector.tsx`
+- Modify: `frontend/workspace/src/artifacts/model.ts`
+
+**Contract:**
+
+- Tabs: `details`, `code`, `run`, `messages`, `environment`, `review`,
+  `history`.
+- Details show real format, size, path, scientific summary, inputs, and
+  renderer capabilities.
+- Code uses the actual text source, notebook code, or provenance fields. Binary
+  data reports that source is not directly displayable.
+- Run, messages, environment, review, and history normalize available
+  provenance/API data and otherwise render specific empty states.
+- Download, copy path, open source, add to context, and export actions remain
+  available from one consistent header.
+
+- [ ] Write failing normalization tests for complete, partial, malformed, and
+  absent provenance responses.
+- [ ] Implement the pure inspector model without SolidJS or network calls.
+- [ ] Build `ArtifactInspector` with labeled tabs, keyboard tab semantics,
+  loading/error/empty states, and at least 12px content typography.
+- [ ] Reuse `/file/provenance`, file content, artifact actions, and existing
+  prompt/context hooks. Do not introduce an inspector-only backend store.
+- [ ] Add component/source contract tests for all seven tabs and honest empty
+  states.
+- [ ] Run focused unit tests and workspace typecheck.
+- [ ] Commit:
+
+  ```bash
+  git add frontend/workspace/src/artifacts/inspector.ts \
+    frontend/workspace/src/artifacts/inspector.test.ts \
+    frontend/workspace/src/artifacts/ArtifactInspector.tsx \
+    frontend/workspace/src/artifacts/model.ts
+  git commit -m "feat: add contextual artifact inspector"
+  ```
+
+### Task 4: Contextual Three-Region Shell
+
+**Files:**
+
+- Modify: `frontend/workspace/src/atlas/RightPane.tsx`
+- Modify: `frontend/workspace/src/atlas/store/ui.ts`
+- Modify: `frontend/workspace/src/pages/session.tsx`
+- Modify: `frontend/workspace/src/pages/session-shell.test.ts`
+- Modify: `frontend/workspace/e2e/navigation.spec.ts`
+- Create: `frontend/workspace/e2e/artifact-inspector.spec.ts`
+
+**Contract:**
+
+- When a document is active, the right pane defaults to the artifact inspector.
+- Global tools remain available as labeled destinations: Atlas, Evidence,
+  Compute, Terminal.
+- Leaving a document restores the last global tool rather than showing stale
+  artifact content.
+- At widths below the workspace breakpoint, the inspector becomes an overlay
+  drawer and the collapsed rail remains keyboard accessible.
+- The pane width is clamped against viewport width and never crushes the center
+  below a usable minimum.
+
+- [ ] Add failing browser tests for file-to-file context switching, file-to-chat
+  restoration, tab keyboard behavior, close/reopen, and a 1024px viewport.
+- [ ] Replace the icon-first pane chooser with labeled inspector/global
+  destinations and a contextual header.
+- [ ] Add responsive drawer behavior and viewport-aware width clamping.
+- [ ] Increase right-pane body typography and contrast through existing tokens;
+  do not add a new color system.
+- [ ] Run focused browser tests and inspect desktop plus narrow screenshots.
+- [ ] Commit:
+
+  ```bash
+  git add frontend/workspace/src/atlas/RightPane.tsx \
+    frontend/workspace/src/atlas/store/ui.ts \
+    frontend/workspace/src/pages/session.tsx \
+    frontend/workspace/src/pages/session-shell.test.ts \
+    frontend/workspace/e2e/navigation.spec.ts \
+    frontend/workspace/e2e/artifact-inspector.spec.ts
+  git commit -m "feat: make the workspace artifact aware"
+  ```
+
+### Task 5: Molecular Source Analysis
+
+**Files:**
+
+- Create: `frontend/workspace/src/science/renderers/molecular/model.ts`
+- Create: `frontend/workspace/src/science/renderers/molecular/model.test.ts`
+- Modify: `frontend/workspace/src/science/renderers/molecular/ProteinStructure.tsx`
+
+**Contract:**
+
+- Inline XYZ, PDB/mmCIF, SDF/MOL, and MOL2 inputs expose format-aware summary
+  metadata where it can be derived safely.
+- Summary includes atom count, element distribution, model/molecule count,
+  chains/residues when available, declared bonds when available, and source
+  mode.
+- Parse uncertainty is explicit. A heuristic count is never labeled as a
+  guaranteed scientific property.
+
+- [ ] Write failing pure tests using the committed XYZ, PDB, and SDF fixtures
+  plus malformed/empty inputs.
+- [ ] Implement small format-specific analyzers in one module. Keep parsing
+  conservative; Mol* remains authoritative for rendering.
+- [ ] Publish the summary through the renderer capability/context contract so
+  the Details tab updates when a molecule becomes ready.
+- [ ] Run focused tests and typecheck.
+- [ ] Commit:
+
+  ```bash
+  git add frontend/workspace/src/science/renderers/molecular/model.ts \
+    frontend/workspace/src/science/renderers/molecular/model.test.ts \
+    frontend/workspace/src/science/renderers/molecular/ProteinStructure.tsx
+  git commit -m "feat: inspect molecular structure metadata"
+  ```
+
+### Task 6: Interactive Molecular Controls
+
+**Files:**
+
+- Modify: `frontend/workspace/src/science/renderers/registry.ts`
+- Modify: `frontend/workspace/src/science/ScienceArtifact.tsx`
+- Modify: `frontend/workspace/src/science/renderers/molecular/ProteinStructure.tsx`
+- Modify: `frontend/workspace/e2e/science-file-viewers.spec.ts`
+
+**Contract:**
+
+- Representation presets: automatic, polymer cartoon, atomic detail,
+  illustrative, and molecular surface.
+- Selection granularity: atom, residue, chain.
+- Clicked selection reports Mol*'s real label and selected element count.
+- Two recorded selections can create a Mol* distance measurement; measurements
+  can be cleared.
+- Camera reset, background toggle, and PNG snapshot export work from labeled
+  controls.
+- Loading, empty, malformed, WebGL failure, and remote-source-blocked states
+  remain usable.
+
+- [ ] Add failing source/unit coverage for capability registration and browser
+  coverage for preset switching, camera reset, selection state, measurement
+  mode, and snapshot download.
+- [ ] Extend the renderer contract with optional callbacks/capabilities; keep
+  existing renderers source-compatible.
+- [ ] Subscribe to Mol* click and selection events and dispose every
+  subscription on cleanup.
+- [ ] Apply Mol* representation presets to the loaded structure, preserving the
+  selected preset across reloads.
+- [ ] Build an in-canvas labeled toolbar and an accessible selected-item card.
+- [ ] Implement distance measurement using Mol*'s measurement manager and real
+  structure loci.
+- [ ] Export the actual WebGL canvas to PNG with a deterministic filename.
+- [ ] Run molecular unit tests, file-viewer E2E, typecheck, and inspect the XYZ
+  and PDB screens visually.
+- [ ] Commit:
+
+  ```bash
+  git add frontend/workspace/src/science/renderers/registry.ts \
+    frontend/workspace/src/science/ScienceArtifact.tsx \
+    frontend/workspace/src/science/renderers/molecular/ProteinStructure.tsx \
+    frontend/workspace/e2e/science-file-viewers.spec.ts
+  git commit -m "feat: add interactive molecular analysis controls"
+  ```
+
+### Task 7: Versioned Scientific Annotations
+
+**Files:**
+
+- Create: `frontend/workspace/src/artifacts/annotations.ts`
+- Create: `frontend/workspace/src/artifacts/annotations.test.ts`
+- Create: `backend/cli/src/server/routes/artifact.ts`
+- Create: `backend/cli/test/server/artifact.test.ts`
+- Modify: `backend/cli/src/server/server.ts`
+- Modify: `frontend/workspace/src/artifacts/ArtifactInspector.tsx`
+- Modify: `frontend/workspace/src/science/renderers/molecular/ProteinStructure.tsx`
+
+**Contract:**
+
+- An annotation records id, artifact path/hash, version, target kind, target
+  payload, body, author, created/updated timestamps, and resolution state.
+- Molecular annotations prefer atom/residue/chain loci labels; generic artifacts
+  may use document coordinates.
+- Data is stored locally below the project `.openscience` state and is scoped by
+  canonical project path.
+- Editing creates a new annotation revision. Deletion is a recoverable tombstone
+  rather than destructive removal.
+- “Ask OpenScience” inserts an attributed annotation reference into the
+  composer; it does not silently edit the artifact.
+
+- [ ] Write failing pure model tests and real route tests for list/create/update,
+  revision history, malformed targets, canonical containment, and tombstones.
+- [ ] Implement project-local storage with atomic writes and no new database.
+- [ ] Add the artifact routes to the existing project-scoped server.
+- [ ] Add annotation list/composer/history UI to the inspector.
+- [ ] Add “annotate selection” from the molecular selected-item card.
+- [ ] Add focused E2E coverage spanning selection, annotation, reload, history,
+  and composer handoff.
+- [ ] Run backend, unit, type, and browser tests.
+- [ ] Commit:
+
+  ```bash
+  git add backend/cli/src/server/routes/artifact.ts \
+    backend/cli/src/server/server.ts \
+    backend/cli/test/server/artifact.test.ts \
+    frontend/workspace/src/artifacts/annotations.ts \
+    frontend/workspace/src/artifacts/annotations.test.ts \
+    frontend/workspace/src/artifacts/ArtifactInspector.tsx \
+    frontend/workspace/src/science/renderers/molecular/ProteinStructure.tsx \
+    frontend/workspace/e2e/artifact-inspector.spec.ts
+  git commit -m "feat: add versioned scientific annotations"
+  ```
+
+### Task 8: Truthful Artifact Previews and UX Refinement
+
+**Files:**
+
+- Modify: `frontend/workspace/src/artifacts/ArtifactGallery.tsx`
+- Modify: `frontend/workspace/src/atlas/FilePreview.tsx`
+- Modify: `frontend/workspace/src/atlas/RightPane.tsx`
+- Modify: `frontend/workspace/e2e/artifact-gallery.spec.ts`
+- Modify: `frontend/workspace/e2e/artifact-inspector.spec.ts`
+- Modify: `frontend/workspace/e2e/science-file-viewers.spec.ts`
+
+**Contract:**
+
+- Image/SVG/PDF and supported molecular artifacts use truthful generated
+  previews when available.
+- Unsupported preview types use a clear format-specific placeholder, never a
+  generic fake chart.
+- Header actions have visible labels at normal widths and accessible names at
+  all widths.
+- Loading skeletons preserve layout; empty/error states explain the next action.
+- Focus rings, tab order, contrast, reduced motion, and 1024px/1440px layouts
+  pass manual inspection.
+
+- [ ] Add failing browser assertions that distinguish real previews from
+  placeholders and verify labeled primary actions.
+- [ ] Replace the generic chart thumbnail with real or format-specific preview
+  states.
+- [ ] Refine artifact/file headers, spacing, type sizes, and responsive
+  visibility using existing tokens.
+- [ ] Capture and inspect screenshots for gallery, XYZ artifact studio, PDB
+  inspector, error state, and narrow inspector.
+- [ ] Run focused E2E and workspace typecheck.
+- [ ] Commit:
+
+  ```bash
+  git add frontend/workspace/src/artifacts/ArtifactGallery.tsx \
+    frontend/workspace/src/atlas/FilePreview.tsx \
+    frontend/workspace/src/atlas/RightPane.tsx \
+    frontend/workspace/e2e/artifact-gallery.spec.ts \
+    frontend/workspace/e2e/artifact-inspector.spec.ts \
+    frontend/workspace/e2e/science-file-viewers.spec.ts
+  git commit -m "feat: polish the trusted artifact workbench"
+  ```
+
+### Task 9: Batch Verification and Branch Push
+
+**Files:** Modify only files required by discovered failures.
+
+- [ ] Run focused security tests:
+
+  ```bash
+  cd backend/cli
+  bun test test/file/path-traversal.test.ts test/tool/read.test.ts \
+    test/snapshot/snapshot.test.ts test/server/artifact.test.ts
+  ```
+
+- [ ] Run workspace unit and type checks:
+
+  ```bash
+  bun test frontend/workspace/src/artifacts \
+    frontend/workspace/src/science/renderers/molecular \
+    frontend/workspace/src/pages/session-shell.test.ts
+  bun run --cwd frontend/workspace typecheck
+  ```
+
+- [ ] Run focused browser checks:
+
+  ```bash
+  bun run --cwd frontend/workspace test:e2e:local -- \
+    e2e/artifact-inspector.spec.ts \
+    e2e/artifact-gallery.spec.ts \
+    e2e/science-file-viewers.spec.ts \
+    e2e/navigation.spec.ts
+  ```
+
+- [ ] Run the required full backend suite from `backend/cli`:
+
+  ```bash
+  cd backend/cli
+  bun test
+  ```
+
+- [ ] Run repository typecheck and production workspace build:
+
+  ```bash
+  bun run typecheck
+  bun run --cwd frontend/workspace build
+  ```
+
+- [ ] Run:
+
+  ```bash
+  git diff --check
+  git status --short
+  git log origin/openscience/aayam-new..HEAD \
+    --format='%h %an <%ae> | %cn <%ce> | %s'
+  ```
+
+  Confirm only `AUDIT.md` is untracked and every commit has the required
+  identity.
+- [ ] Push only:
+
+  ```bash
+  git push origin openscience/aayam-new
+  ```
+
+- [ ] Wait for normal branch CI. Diagnose and fix every failure before npm
+  packaging.
+
+### Task 10: Batched npm `test` Package Validation
+
+- [ ] Dispatch `.github/workflows/npm-test.yml` for
+  `openscience/aayam-new`. Do not dispatch the production workflow.
+- [ ] Wait for the workflow and inspect every job/log rather than relying only
+  on the aggregate badge.
+- [ ] Install the test packages into an isolated temporary npm prefix.
+- [ ] Start `openscience serve` with temporary XDG/config/data directories and
+  a deterministic local model provider.
+- [ ] Re-run the packaged smoke flows: project open, notebook, XYZ viewer,
+  artifact inspector, annotation persistence, and clean shutdown.
+- [ ] Record the package versions, workflow run, checks executed, and any
+  unavailable credential-locked integrations in the parity backlog.
+- [ ] Fix and repeat the npm test release only if the packaged artifact reveals
+  a release-specific defect.

From 4aae8efd756a3d1bf230486f590a573b7f74ea86 Mon Sep 17 00:00:00 2001
From: Aayam Bansal <aayambansal@gmail.com>
Date: Wed, 29 Jul 2026 14:03:35 +0800
Subject: [PATCH 19/40] fix: enforce canonical project file boundaries

---
 backend/cli/src/file/index.ts                |  39 +++----
 backend/cli/src/project/instance.ts          |   5 +
 backend/cli/src/tool/external-directory.ts   |   2 +-
 backend/cli/src/util/filesystem.ts           |  38 ++++++-
 backend/cli/test/file/path-traversal.test.ts | 103 +++++++++++++++++++
 backend/cli/test/tool/read.test.ts           |  32 ++++++
 6 files changed, 190 insertions(+), 29 deletions(-)

diff --git a/backend/cli/src/file/index.ts b/backend/cli/src/file/index.ts
index c839d2aa..5d3cef2d 100644
--- a/backend/cli/src/file/index.ts
+++ b/backend/cli/src/file/index.ts
@@ -218,6 +218,12 @@ export namespace File {
     state()
   }
 
+  async function contained(file: string): Promise<string> {
+    const full = path.join(Instance.directory, file)
+    if (await Instance.containsCanonicalPath(full)) return full
+    throw new Error(`Access denied: path escapes project directory`)
+  }
+
   export async function status() {
     const project = Instance.project
     if (project.vcs !== "git") return []
@@ -295,13 +301,7 @@ export namespace File {
   export async function read(file: string): Promise<Content> {
     using _ = log.time("read", { file })
     const project = Instance.project
-    const full = path.join(Instance.directory, file)
-
-    // TODO: Filesystem.contains is lexical only - symlinks inside the project can escape.
-    // TODO: On Windows, cross-drive paths bypass this check. Consider realpath canonicalization.
-    if (!Instance.containsPath(full)) {
-      throw new Error(`Access denied: path escapes project directory`)
-    }
+    const full = await contained(file)
 
     const bunFile = Bun.file(full)
 
@@ -350,18 +350,12 @@ export namespace File {
   }
 
   export async function inspect(file: string): Promise<ScienceFile.Inspection> {
-    const full = path.join(Instance.directory, file)
-    if (!Instance.containsPath(full)) {
-      throw new Error(`Access denied: path escapes project directory`)
-    }
+    const full = await contained(file)
     return ScienceFile.inspect(full, file)
   }
 
   export async function raw(file: string): Promise<BunFile> {
-    const full = path.join(Instance.directory, file)
-    if (!Instance.containsPath(full)) {
-      throw new Error(`Access denied: path escapes project directory`)
-    }
+    const full = await contained(file)
     const content = Bun.file(full)
     if (!(await content.exists())) throw new HTTPException(404, { message: `File not found: ${file}` })
     return content
@@ -372,10 +366,7 @@ export namespace File {
   }
 
   export async function provenance(file: string): Promise<ArtifactFile.Provenance> {
-    const full = path.join(Instance.directory, file)
-    if (!Instance.containsPath(full)) {
-      throw new Error(`Access denied: path escapes project directory`)
-    }
+    await contained(file)
     return ArtifactFile.provenance(Instance.directory, file)
   }
 
@@ -401,10 +392,7 @@ export namespace File {
 
   export async function write(file: string, content: string): Promise<Content> {
     using _ = log.time("write", { file })
-    const full = path.join(Instance.directory, file)
-    if (!Instance.containsPath(full)) {
-      throw new Error(`Access denied: path escapes project directory`)
-    }
+    const full = await contained(file)
 
     const exists = await Bun.file(full).exists()
     await Bun.write(full, content)
@@ -435,10 +423,7 @@ export namespace File {
       ignored = ig.ignores.bind(ig)
     }
     const resolved = dir ? path.join(Instance.directory, dir) : Instance.directory
-
-    // TODO: Filesystem.contains is lexical only - symlinks inside the project can escape.
-    // TODO: On Windows, cross-drive paths bypass this check. Consider realpath canonicalization.
-    if (!Instance.containsPath(resolved)) {
+    if (!(await Instance.containsCanonicalPath(resolved))) {
       throw new Error(`Access denied: path escapes project directory`)
     }
 
diff --git a/backend/cli/src/project/instance.ts b/backend/cli/src/project/instance.ts
index 5ea2c2c8..390a45f5 100644
--- a/backend/cli/src/project/instance.ts
+++ b/backend/cli/src/project/instance.ts
@@ -68,6 +68,11 @@ export const Instance = {
     if (Instance.worktree === "/") return false
     return Filesystem.contains(Instance.worktree, filepath)
   },
+  async containsCanonicalPath(filepath: string) {
+    if (await Filesystem.containsCanonical(Instance.directory, filepath)) return true
+    if (Instance.worktree === "/") return false
+    return Filesystem.containsCanonical(Instance.worktree, filepath)
+  },
   state<S>(init: () => S, dispose?: (state: Awaited<S>) => Promise<void>): () => S {
     return State.create(() => Instance.directory, init, dispose)
   },
diff --git a/backend/cli/src/tool/external-directory.ts b/backend/cli/src/tool/external-directory.ts
index 1d3958fc..e17c0ee1 100644
--- a/backend/cli/src/tool/external-directory.ts
+++ b/backend/cli/src/tool/external-directory.ts
@@ -14,7 +14,7 @@ export async function assertExternalDirectory(ctx: Tool.Context, target?: string
 
   if (options?.bypass) return
 
-  if (Instance.containsPath(target)) return
+  if (await Instance.containsCanonicalPath(target)) return
 
   const kind = options?.kind ?? "file"
   const parentDir = kind === "directory" ? target : path.dirname(target)
diff --git a/backend/cli/src/util/filesystem.ts b/backend/cli/src/util/filesystem.ts
index aced6869..cda44c5f 100644
--- a/backend/cli/src/util/filesystem.ts
+++ b/backend/cli/src/util/filesystem.ts
@@ -1,5 +1,6 @@
 import { realpathSync } from "fs"
-import { dirname, isAbsolute, join, relative } from "path"
+import { lstat, realpath, stat } from "fs/promises"
+import { basename, dirname, isAbsolute, join, relative, resolve } from "path"
 
 export namespace Filesystem {
   export const exists = (p: string) =>
@@ -37,6 +38,41 @@ export namespace Filesystem {
     return rel === "" || (!rel.startsWith("..") && !isAbsolute(rel))
   }
 
+  async function canonicalize(cursor: string, tail: string[]): Promise<string | undefined> {
+    const result = await realpath(cursor).then(
+      (value) => ({ value }),
+      (error: NodeJS.ErrnoException) => ({ error }),
+    )
+    if ("error" in result) {
+      if (result.error.code !== "ENOENT" && result.error.code !== "ENOTDIR") return
+      const info = await lstat(cursor).catch(() => undefined)
+      if (info?.isSymbolicLink()) return
+      const parent = dirname(cursor)
+      if (parent === cursor) return
+      return canonicalize(parent, [basename(cursor), ...tail])
+    }
+    const base = result.value
+    if (!tail.length) return base
+    const info = await stat(base).catch(() => undefined)
+    if (!info?.isDirectory()) return
+    return resolve(base, ...tail)
+  }
+
+  /**
+   * Resolve a path by filesystem identity, including a target that does not
+   * exist yet. Existing symlinks are followed; a broken symlink is rejected
+   * instead of being reconstructed as if it were an ordinary path segment.
+   */
+  export function canonical(p: string): Promise<string | undefined> {
+    return canonicalize(resolve(p), [])
+  }
+
+  export async function containsCanonical(parent: string, child: string): Promise<boolean> {
+    const [root, target] = await Promise.all([canonical(parent), canonical(child)])
+    if (!root || !target) return false
+    return contains(root, target)
+  }
+
   export async function findUp(target: string, start: string, stop?: string) {
     let current = start
     const result = []
diff --git a/backend/cli/test/file/path-traversal.test.ts b/backend/cli/test/file/path-traversal.test.ts
index 380f8051..322ce6da 100644
--- a/backend/cli/test/file/path-traversal.test.ts
+++ b/backend/cli/test/file/path-traversal.test.ts
@@ -84,6 +84,70 @@ describe("File.read path traversal protection", () => {
       },
     })
   })
+
+  test("rejects reads through an internal symlink that resolves outside the project", async () => {
+    await using outside = await tmpdir({
+      init: async (dir) => {
+        await Bun.write(path.join(dir, "secret.txt"), "external secret")
+      },
+    })
+    await using tmp = await tmpdir({
+      init: async (dir) => {
+        await fs.symlink(outside.path, path.join(dir, "escape"))
+      },
+    })
+
+    await Instance.provide({
+      directory: tmp.path,
+      fn: async () => {
+        await expect(File.read("escape/secret.txt")).rejects.toThrow(
+          "Access denied: path escapes project directory",
+        )
+        await expect(File.raw("escape/secret.txt")).rejects.toThrow(
+          "Access denied: path escapes project directory",
+        )
+        await expect(File.inspect("escape/secret.txt")).rejects.toThrow(
+          "Access denied: path escapes project directory",
+        )
+      },
+    })
+  })
+
+  test("allows a new file below an internal directory", async () => {
+    await using tmp = await tmpdir({
+      init: async (dir) => {
+        await fs.mkdir(path.join(dir, "results"), { recursive: true })
+      },
+    })
+
+    await Instance.provide({
+      directory: tmp.path,
+      fn: async () => {
+        const result = await File.write("results/new.txt", "new result")
+        expect(result.content).toBe("new result")
+        expect(await Bun.file(path.join(tmp.path, "results", "new.txt")).text()).toBe("new result")
+      },
+    })
+  })
+
+  test("rejects a new write below an internal symlink to an external directory", async () => {
+    await using outside = await tmpdir()
+    await using tmp = await tmpdir({
+      init: async (dir) => {
+        await fs.symlink(outside.path, path.join(dir, "escape"))
+      },
+    })
+
+    await Instance.provide({
+      directory: tmp.path,
+      fn: async () => {
+        await expect(File.write("escape/new.txt", "escaped")).rejects.toThrow(
+          "Access denied: path escapes project directory",
+        )
+        expect(await Bun.file(path.join(outside.path, "new.txt")).exists()).toBe(false)
+      },
+    })
+  })
 })
 
 describe("File.list path traversal protection", () => {
@@ -113,6 +177,26 @@ describe("File.list path traversal protection", () => {
       },
     })
   })
+
+  test("rejects listing through an internal symlink that resolves outside the project", async () => {
+    await using outside = await tmpdir({
+      init: async (dir) => {
+        await Bun.write(path.join(dir, "secret.txt"), "external secret")
+      },
+    })
+    await using tmp = await tmpdir({
+      init: async (dir) => {
+        await fs.symlink(outside.path, path.join(dir, "escape"))
+      },
+    })
+
+    await Instance.provide({
+      directory: tmp.path,
+      fn: async () => {
+        await expect(File.list("escape")).rejects.toThrow("Access denied: path escapes project directory")
+      },
+    })
+  })
 })
 
 describe("Instance.containsPath", () => {
@@ -195,4 +279,23 @@ describe("Instance.containsPath", () => {
       },
     })
   })
+
+  test("canonical containment rejects a symlink escape but keeps an internal missing target", async () => {
+    await using outside = await tmpdir()
+    await using tmp = await tmpdir({
+      git: true,
+      init: async (dir) => {
+        await fs.mkdir(path.join(dir, "results"), { recursive: true })
+        await fs.symlink(outside.path, path.join(dir, "escape"))
+      },
+    })
+
+    await Instance.provide({
+      directory: tmp.path,
+      fn: async () => {
+        expect(await Instance.containsCanonicalPath(path.join(tmp.path, "escape", "secret.txt"))).toBe(false)
+        expect(await Instance.containsCanonicalPath(path.join(tmp.path, "results", "new.txt"))).toBe(true)
+      },
+    })
+  })
 })
diff --git a/backend/cli/test/tool/read.test.ts b/backend/cli/test/tool/read.test.ts
index 0497791c..8c5c491f 100644
--- a/backend/cli/test/tool/read.test.ts
+++ b/backend/cli/test/tool/read.test.ts
@@ -1,5 +1,6 @@
 import { describe, expect, test } from "bun:test"
 import path from "path"
+import fs from "fs/promises"
 import { ReadTool } from "../../src/tool/read"
 import { Instance } from "../../src/project/instance"
 import { tmpdir } from "../fixture/fixture"
@@ -123,6 +124,37 @@ describe("tool.read external_directory permission", () => {
       },
     })
   })
+
+  test("asks for external_directory permission when an internal symlink resolves outside the project", async () => {
+    await using outside = await tmpdir({
+      init: async (dir) => {
+        await Bun.write(path.join(dir, "secret.txt"), "external secret")
+      },
+    })
+    await using tmp = await tmpdir({
+      git: true,
+      init: async (dir) => {
+        await fs.symlink(outside.path, path.join(dir, "escape"))
+      },
+    })
+
+    await Instance.provide({
+      directory: tmp.path,
+      fn: async () => {
+        const requests: Array<Omit<PermissionNext.Request, "id" | "sessionID" | "tool">> = []
+        const testCtx = {
+          ...ctx,
+          ask: async (req: Omit<PermissionNext.Request, "id" | "sessionID" | "tool">) => {
+            requests.push(req)
+          },
+        }
+        const read = await ReadTool.init()
+        const result = await read.execute({ filePath: path.join(tmp.path, "escape", "secret.txt") }, testCtx)
+        expect(result.output).toContain("external secret")
+        expect(requests.some((request) => request.permission === "external_directory")).toBe(true)
+      },
+    })
+  })
 })
 
 describe("tool.read env file permissions", () => {

From 16056bf2645b69680942ca72bd5e578893e4e174 Mon Sep 17 00:00:00 2001
From: Aayam Bansal <aayambansal@gmail.com>
Date: Wed, 29 Jul 2026 14:05:16 +0800
Subject: [PATCH 20/40] feat: track active scientific artifacts

---
 .../workspace/src/artifacts/context.test.ts   |  64 +++++++
 frontend/workspace/src/artifacts/context.ts   | 171 ++++++++++++++++++
 frontend/workspace/src/atlas/FilePreview.tsx  |  23 +++
 frontend/workspace/src/pages/session.tsx      |   1 +
 4 files changed, 259 insertions(+)
 create mode 100644 frontend/workspace/src/artifacts/context.test.ts
 create mode 100644 frontend/workspace/src/artifacts/context.ts

diff --git a/frontend/workspace/src/artifacts/context.test.ts b/frontend/workspace/src/artifacts/context.test.ts
new file mode 100644
index 00000000..479b661e
--- /dev/null
+++ b/frontend/workspace/src/artifacts/context.test.ts
@@ -0,0 +1,64 @@
+import { describe, expect, test } from "bun:test"
+import {
+  clearOwnedArtifact,
+  createArtifactContext,
+  inferArtifactKind,
+  type ArtifactContext,
+} from "./context"
+
+describe("artifact context", () => {
+  test("normalizes equivalent locations to one stable identity", () => {
+    const first = createArtifactContext({
+      directory: "/work/project/",
+      path: "./results\\water.xyz",
+      format: ".XYZ",
+      scienceKind: "chem-3d",
+    })
+    const second = createArtifactContext({
+      directory: "/work/project",
+      path: "results/water.xyz",
+      format: "xyz",
+      scienceKind: "chem-3d",
+    })
+
+    expect(first).toEqual(second)
+    expect(first).toMatchObject({
+      name: "water.xyz",
+      path: "results/water.xyz",
+      format: "xyz",
+      kind: "structure",
+      scienceKind: "chem-3d",
+    })
+  })
+
+  test("classifies scientific and publication formats without pretending unknown files are reports", () => {
+    expect(inferArtifactKind("analysis.ipynb")).toBe("notebook")
+    expect(inferArtifactKind("aligned.fasta", "msa")).toBe("sequence")
+    expect(inferArtifactKind("variants.vcf")).toBe("genomics")
+    expect(inferArtifactKind("sample.mzML")).toBe("spectrum")
+    expect(inferArtifactKind("figure.svg")).toBe("figure")
+    expect(inferArtifactKind("paper.tex")).toBe("report")
+    expect(inferArtifactKind("weights.onnx")).toBe("model")
+    expect(inferArtifactKind("pipeline.ts")).toBe("file")
+  })
+
+  test("uses the active renderer kind when an extension is ambiguous", () => {
+    expect(inferArtifactKind("result.dat", "protein-structure")).toBe("structure")
+    expect(inferArtifactKind("result.dat", "chem-2d")).toBe("structure")
+    expect(inferArtifactKind("result.dat", "sequence")).toBe("sequence")
+    expect(inferArtifactKind("result.dat", "genome-track")).toBe("genomics")
+  })
+
+  test("only the owning document can clear active artifact state", () => {
+    const active: ArtifactContext = createArtifactContext({
+      directory: "/work/project",
+      path: "results/current.pdb",
+      format: "pdb",
+      scienceKind: "protein-structure",
+    })
+
+    expect(clearOwnedArtifact(active, "artifact:/another/file")).toBe(active)
+    expect(clearOwnedArtifact(active, active.id)).toBeUndefined()
+    expect(clearOwnedArtifact(undefined, active.id)).toBeUndefined()
+  })
+})
diff --git a/frontend/workspace/src/artifacts/context.ts b/frontend/workspace/src/artifacts/context.ts
new file mode 100644
index 00000000..e2e97885
--- /dev/null
+++ b/frontend/workspace/src/artifacts/context.ts
@@ -0,0 +1,171 @@
+import { createSignal } from "solid-js"
+import type { ArtifactKind } from "./model"
+
+export type ArtifactContextKind = ArtifactKind | "file"
+
+export interface ArtifactContext {
+  id: string
+  directory: string
+  path: string
+  name: string
+  format: string
+  kind: ArtifactContextKind
+  scienceKind?: string
+}
+
+export interface ArtifactContextInput {
+  directory: string
+  path: string
+  format?: string
+  scienceKind?: string
+}
+
+const kinds: Partial<Record<string, ArtifactContextKind>> = {
+  ipynb: "notebook",
+  csv: "dataset",
+  tsv: "dataset",
+  jsonl: "dataset",
+  parquet: "dataset",
+  arrow: "dataset",
+  feather: "dataset",
+  h5: "dataset",
+  hdf5: "dataset",
+  h5ad: "dataset",
+  loom: "dataset",
+  zarr: "dataset",
+  png: "figure",
+  jpg: "figure",
+  jpeg: "figure",
+  gif: "figure",
+  webp: "figure",
+  bmp: "figure",
+  svg: "figure",
+  pdf: "report",
+  md: "report",
+  markdown: "report",
+  mdx: "report",
+  tex: "report",
+  latex: "report",
+  docx: "report",
+  pptx: "report",
+  pdb: "structure",
+  ent: "structure",
+  cif: "structure",
+  mmcif: "structure",
+  bcif: "structure",
+  pdbqt: "structure",
+  gro: "structure",
+  xyz: "structure",
+  sdf: "structure",
+  mol: "structure",
+  mol2: "structure",
+  smi: "structure",
+  smiles: "structure",
+  fa: "sequence",
+  fasta: "sequence",
+  faa: "sequence",
+  fna: "sequence",
+  ffn: "sequence",
+  frn: "sequence",
+  aln: "sequence",
+  clustal: "sequence",
+  bam: "genomics",
+  cram: "genomics",
+  sam: "genomics",
+  vcf: "genomics",
+  bcf: "genomics",
+  bed: "genomics",
+  gff: "genomics",
+  gff3: "genomics",
+  gtf: "genomics",
+  bigwig: "genomics",
+  bw: "genomics",
+  bigbed: "genomics",
+  mzml: "spectrum",
+  mzxml: "spectrum",
+  mgf: "spectrum",
+  msp: "spectrum",
+  onnx: "model",
+  pt: "model",
+  pth: "model",
+  safetensors: "model",
+  pkl: "model",
+  joblib: "model",
+  zip: "archive",
+  tar: "archive",
+  tgz: "archive",
+  gz: "archive",
+  bz2: "archive",
+  xz: "archive",
+  "7z": "archive",
+}
+
+const science: Partial<Record<string, ArtifactContextKind>> = {
+  "protein-structure": "structure",
+  "chem-2d": "structure",
+  "chem-3d": "structure",
+  sequence: "sequence",
+  msa: "sequence",
+  "genome-track": "genomics",
+  pdf: "report",
+  latex: "report",
+}
+
+function cleanDirectory(value: string): string {
+  const next = value.replaceAll("\\", "/").replace(/\/+$/, "")
+  return next || "/"
+}
+
+function cleanPath(value: string): string {
+  return value
+    .replaceAll("\\", "/")
+    .replace(/^(?:\.\/)+/, "")
+    .replace(/\/+/g, "/")
+}
+
+function extension(value: string): string {
+  const name = cleanPath(value).split("/").pop() ?? ""
+  const index = name.lastIndexOf(".")
+  return index > 0 ? name.slice(index + 1).toLowerCase() : ""
+}
+
+export function inferArtifactKind(path: string, scienceKind?: string): ArtifactContextKind {
+  if (scienceKind && science[scienceKind]) return science[scienceKind]
+  return kinds[extension(path)] ?? "file"
+}
+
+export function createArtifactContext(input: ArtifactContextInput): ArtifactContext {
+  const directory = cleanDirectory(input.directory)
+  const path = cleanPath(input.path)
+  const name = path.split("/").pop() || path
+  const format = (input.format ?? extension(path)).replace(/^\./, "").toLowerCase()
+  return {
+    id: `artifact:${encodeURIComponent(directory)}::${encodeURIComponent(path)}`,
+    directory,
+    path,
+    name,
+    format,
+    kind: inferArtifactKind(path, input.scienceKind),
+    ...(input.scienceKind ? { scienceKind: input.scienceKind } : {}),
+  }
+}
+
+export function clearOwnedArtifact(
+  current: ArtifactContext | undefined,
+  owner: string,
+): ArtifactContext | undefined {
+  if (current?.id === owner) return
+  return current
+}
+
+const [active, setActive] = createSignal<ArtifactContext | undefined>()
+
+export const artifactContext = {
+  active,
+  activate(value: ArtifactContext) {
+    setActive(value)
+  },
+  clear(owner: string) {
+    setActive((current) => clearOwnedArtifact(current, owner))
+  },
+}
diff --git a/frontend/workspace/src/atlas/FilePreview.tsx b/frontend/workspace/src/atlas/FilePreview.tsx
index 51c4ee49..099aea45 100644
--- a/frontend/workspace/src/atlas/FilePreview.tsx
+++ b/frontend/workspace/src/atlas/FilePreview.tsx
@@ -26,6 +26,7 @@ import { detectBinaryScienceFormat } from "@/science/formats/binary"
 import { NotebookView } from "@/notebook/NotebookView"
 import { DataTableView } from "@/data/DataTableView"
 import type { TableFormat } from "@/data/table"
+import { artifactContext, createArtifactContext } from "@/artifacts/context"
 import { toast } from "@/atlas/Toast"
 import { IconFile, IconX, IconCopy, IconDownload, IconBookOpen, IconBraces, IconRefresh } from "@/atlas/shared/Icon"
 
@@ -134,6 +135,7 @@ export function FileView(props: {
   directory?: string
   subtitle?: string
   onClose?: () => void
+  active?: boolean
 }): JSX.Element {
   const sdk = useSDK()
   const sync = useSync()
@@ -208,6 +210,25 @@ export function FileView(props: {
     if (k === "table") return tabular() ?? e()
     return k
   }
+  const context = createMemo(() =>
+    createArtifactContext({
+      directory: directory(),
+      path: props.path,
+      format: badge(),
+      scienceKind: scientific()?.kind,
+    }),
+  )
+
+  createEffect(() => {
+    const current = context()
+    if (props.active === false) {
+      artifactContext.clear(current.id)
+      return
+    }
+    artifactContext.activate(current)
+  })
+
+  onCleanup(() => artifactContext.clear(context().id))
 
   createEffect(() => {
     if (file.loading) return
@@ -277,6 +298,8 @@ export function FileView(props: {
 
   return (
     <div
+      data-component="file-view"
+      data-artifact-id={context().id}
       style={{
         flex: 1,
         "min-height": 0,
diff --git a/frontend/workspace/src/pages/session.tsx b/frontend/workspace/src/pages/session.tsx
index 0d987c2e..db8b1066 100644
--- a/frontend/workspace/src/pages/session.tsx
+++ b/frontend/workspace/src/pages/session.tsx
@@ -818,6 +818,7 @@ export default function Page(): JSX.Element {
                     <FileView
                       path={doc.path}
                       directory={doc.directory}
+                      active={centerTabs.active() === doc.id}
                       subtitle={`This computer · ${doc.directory.replace(/\/$/, "")}/${doc.path}`}
                       onClose={() => centerTabs.closeDoc(doc.id)}
                     />

From 133df6d37ba587193f0fcc69c1bcf58f9463ac55 Mon Sep 17 00:00:00 2001
From: Aayam Bansal <aayambansal@gmail.com>
Date: Wed, 29 Jul 2026 14:08:04 +0800
Subject: [PATCH 21/40] feat: add contextual artifact inspector

---
 .../src/artifacts/ArtifactInspector.tsx       | 532 ++++++++++++++++++
 .../workspace/src/artifacts/inspector.test.ts |  74 +++
 frontend/workspace/src/artifacts/inspector.ts | 146 +++++
 3 files changed, 752 insertions(+)
 create mode 100644 frontend/workspace/src/artifacts/ArtifactInspector.tsx
 create mode 100644 frontend/workspace/src/artifacts/inspector.test.ts
 create mode 100644 frontend/workspace/src/artifacts/inspector.ts

diff --git a/frontend/workspace/src/artifacts/ArtifactInspector.tsx b/frontend/workspace/src/artifacts/ArtifactInspector.tsx
new file mode 100644
index 00000000..9799b5a6
--- /dev/null
+++ b/frontend/workspace/src/artifacts/ArtifactInspector.tsx
@@ -0,0 +1,532 @@
+import {
+  For,
+  Match,
+  Show,
+  Switch,
+  createEffect,
+  createMemo,
+  createResource,
+  createSignal,
+  type JSX,
+} from "solid-js"
+import { usePlatform } from "@/context/platform"
+import { usePrompt } from "@/context/prompt"
+import { useSDK } from "@/context/sdk"
+import { centerTabs } from "@/atlas/store/centerTabs"
+import { toast } from "@/atlas/Toast"
+import {
+  IconBookOpen,
+  IconBraces,
+  IconClock,
+  IconCopy,
+  IconDownload,
+  IconFile,
+  IconFlask,
+  IconMessageSquare,
+  IconRefresh,
+  IconSettings,
+} from "@/atlas/shared/Icon"
+import { FONT_CODE, FONT_MONO, FONT_SANS } from "@/styles/tokens"
+import type { ArtifactContext } from "./context"
+import {
+  inspectorTabs,
+  normalizeInspectorData,
+  type InspectorData,
+  type InspectorState,
+  type InspectorTab,
+} from "./inspector"
+
+const labels: Record<InspectorTab, string> = {
+  details: "Details",
+  code: "Code",
+  run: "Run",
+  messages: "Messages",
+  environment: "Environment",
+  review: "Review",
+  history: "History",
+}
+
+export function ArtifactInspector(props: { context: ArtifactContext; onClose?: () => void }): JSX.Element {
+  const sdk = useSDK()
+  const platform = usePlatform()
+  const prompt = usePrompt()
+  const [tab, setTab] = createSignal<InspectorTab>("details")
+  const request = () => platform.fetch ?? fetch
+  const url = (route: string, path?: string) =>
+    `${sdk.url.replace(/\/$/, "")}${route}?directory=${encodeURIComponent(props.context.directory)}${path ? `&path=${encodeURIComponent(path)}` : ""}`
+
+  const [records, api] = createResource(
+    () => ({ id: props.context.id, path: props.context.path, directory: props.context.directory }),
+    async (current) => {
+      const read = async (route: string, path?: string): Promise<unknown> => {
+        const response = await request()(url(route, path)).catch(() => undefined)
+        if (!response?.ok) return
+        return response.json().catch(() => undefined)
+      }
+      const [file, provenance, audit] = await Promise.all([
+        read("/file/content", current.path),
+        read("/file/provenance", current.path),
+        read("/file/reproducibility"),
+      ])
+      return { id: current.id, file, provenance, audit }
+    },
+  )
+  const model = createMemo<InspectorData>(() => {
+    const value = records()
+    const input = value?.id === props.context.id ? value : {}
+    return normalizeInspectorData(props.context, input)
+  })
+
+  createEffect(() => {
+    props.context.id
+    setTab("details")
+  })
+
+  const copy = async () => {
+    await navigator.clipboard?.writeText(props.context.path)
+    toast.success("copied", props.context.path)
+  }
+  const attach = () => {
+    prompt.context.add({ type: "file", path: props.context.path })
+    centerTabs.showChat()
+    toast.success("added to context", props.context.name)
+  }
+  const download = async () => {
+    const response = await request()(url("/file/raw", props.context.path)).catch(() => undefined)
+    if (!response?.ok) {
+      toast.error("download failed", response ? `${response.status}` : "request failed")
+      return
+    }
+    const object = URL.createObjectURL(await response.blob())
+    const anchor = document.createElement("a")
+    anchor.href = object
+    anchor.download = props.context.name
+    anchor.click()
+    URL.revokeObjectURL(object)
+  }
+
+  const move = (event: KeyboardEvent, current: InspectorTab) => {
+    const index = inspectorTabs.indexOf(current)
+    const next =
+      event.key === "Home"
+        ? inspectorTabs[0]
+        : event.key === "End"
+          ? inspectorTabs.at(-1)
+          : event.key === "ArrowRight"
+            ? inspectorTabs[(index + 1) % inspectorTabs.length]
+            : event.key === "ArrowLeft"
+              ? inspectorTabs[(index - 1 + inspectorTabs.length) % inspectorTabs.length]
+              : undefined
+    if (!next) return
+    event.preventDefault()
+    setTab(next)
+    document.getElementById(`artifact-inspector-tab-${next}`)?.focus()
+  }
+
+  return (
+    <section
+      data-component="artifact-inspector"
+      data-artifact-id={props.context.id}
+      style={{
+        flex: 1,
+        "min-height": 0,
+        display: "flex",
+        "flex-direction": "column",
+        background: "var(--color-bg)",
+      }}
+    >
+      <header
+        style={{
+          display: "flex",
+          "align-items": "center",
+          gap: "10px",
+          padding: "12px 14px",
+          "border-bottom": "1px solid var(--color-border)",
+          "flex-shrink": 0,
+        }}
+      >
+        <span style={{ display: "inline-flex", color: "var(--color-text-muted)" }}>
+          <IconFile size={15} strokeWidth={1.5} />
+        </span>
+        <div style={{ flex: 1, "min-width": 0, display: "grid", gap: "2px" }}>
+          <strong
+            title={props.context.path}
+            style={{
+              "font-family": FONT_SANS,
+              "font-size": "13px",
+              color: "var(--color-text)",
+              overflow: "hidden",
+              "text-overflow": "ellipsis",
+              "white-space": "nowrap",
+            }}
+          >
+            {props.context.name}
+          </strong>
+          <span style={{ "font-family": FONT_MONO, "font-size": "10px", color: "var(--color-text-faint)" }}>
+            {props.context.kind} · {props.context.format.toUpperCase()}
+          </span>
+        </div>
+        <button type="button" title="refresh artifact records" style={iconButton()} onClick={() => void api.refetch()}>
+          <IconRefresh size={13} />
+        </button>
+        <Show when={props.onClose}>
+          <button type="button" style={quietButton()} onClick={() => props.onClose?.()}>
+            close
+          </button>
+        </Show>
+      </header>
+
+      <div style={{ display: "grid", "grid-template-columns": "repeat(3, 1fr)", gap: "6px", padding: "10px 12px" }}>
+        <button type="button" style={actionButton(true)} onClick={attach}>
+          <IconFlask size={12} /> ask
+        </button>
+        <button type="button" style={actionButton()} onClick={() => void copy()}>
+          <IconCopy size={12} /> path
+        </button>
+        <button type="button" style={actionButton()} onClick={() => void download()}>
+          <IconDownload size={12} /> download
+        </button>
+      </div>
+
+      <div
+        role="tablist"
+        aria-label="Artifact inspector"
+        class="atlas-scroll"
+        style={{
+          display: "flex",
+          gap: "4px",
+          padding: "0 12px 10px",
+          overflow: "auto hidden",
+          "border-bottom": "1px solid var(--color-border)",
+          "flex-shrink": 0,
+        }}
+      >
+        <For each={inspectorTabs}>
+          {(item) => (
+            <button
+              id={`artifact-inspector-tab-${item}`}
+              type="button"
+              role="tab"
+              aria-selected={tab() === item}
+              aria-controls={`artifact-inspector-panel-${item}`}
+              tabindex={tab() === item ? 0 : -1}
+              onClick={() => setTab(item)}
+              onKeyDown={(event) => move(event, item)}
+              style={tabButton(tab() === item)}
+            >
+              {labels[item]}
+              <Show when={!model().tabs[item].available}>
+                <span aria-hidden="true" style={{ color: "var(--color-text-faint)", "font-size": "9px" }}>
+                  ○
+                </span>
+              </Show>
+            </button>
+          )}
+        </For>
+      </div>
+
+      <div
+        id={`artifact-inspector-panel-${tab()}`}
+        role="tabpanel"
+        aria-labelledby={`artifact-inspector-tab-${tab()}`}
+        class="atlas-scroll"
+        style={{ flex: 1, "min-height": 0, overflow: "auto", padding: "14px", "box-sizing": "border-box" }}
+      >
+        <Show when={!records.loading} fallback={<Loading />}>
+          <Switch>
+            <Match when={tab() === "details"}>
+              <Details data={model()} />
+            </Match>
+            <Match when={tab() === "code"}>
+              <Show when={model().source !== undefined} fallback={<Empty state={model().tabs.code} icon="code" />}>
+                <section style={card()}>
+                  <Heading icon="code">Source</Heading>
+                  <pre
+                    class="atlas-scroll"
+                    style={{
+                      margin: 0,
+                      "max-height": "460px",
+                      overflow: "auto",
+                      "font-family": FONT_CODE,
+                      "font-size": "11px",
+                      "line-height": 1.6,
+                      color: "var(--color-text-muted)",
+                      "white-space": "pre",
+                    }}
+                  >
+                    {model().source}
+                  </pre>
+                </section>
+              </Show>
+            </Match>
+            <Match when={tab() === "run"}>
+              <Empty state={model().tabs.run} icon="run" />
+            </Match>
+            <Match when={tab() === "messages"}>
+              <Empty state={model().tabs.messages} icon="messages" />
+            </Match>
+            <Match when={tab() === "environment"}>
+              <Environment data={model()} />
+            </Match>
+            <Match when={tab() === "review"}>
+              <Empty state={model().tabs.review} icon="review" />
+            </Match>
+            <Match when={tab() === "history"}>
+              <History data={model()} />
+            </Match>
+          </Switch>
+        </Show>
+      </div>
+    </section>
+  )
+}
+
+function Details(props: { data: InspectorData }): JSX.Element {
+  return (
+    <div style={{ display: "grid", gap: "12px" }}>
+      <section style={card()}>
+        <Heading icon="details">Artifact</Heading>
+        <Fact label="name" value={props.data.context.name} />
+        <Fact label="kind" value={props.data.context.kind} />
+        <Fact label="format" value={props.data.context.format.toUpperCase()} mono />
+        <Fact label="path" value={props.data.context.path} mono />
+        <Fact label="location" value={props.data.context.directory} mono />
+        <Show when={props.data.context.scienceKind}>
+          <Fact label="renderer" value={props.data.context.scienceKind!} mono />
+        </Show>
+      </section>
+      <section style={card()}>
+        <Heading icon="history">Provenance</Heading>
+        <Show
+          when={props.data.provenance}
+          fallback={<p style={copyStyle()}>No Git provenance is recorded for this local artifact.</p>}
+        >
+          {(value) => (
+            <>
+              <Fact label="status" value={value().status} />
+              <Fact label="branch" value={value().branch ?? "detached or unavailable"} mono />
+              <Fact label="working tree" value={value().dirty ? "modified" : "clean"} />
+              <Fact label="commit" value={value().commit?.sha.slice(0, 12) ?? "not committed"} mono />
+            </>
+          )}
+        </Show>
+      </section>
+    </div>
+  )
+}
+
+function Environment(props: { data: InspectorData }): JSX.Element {
+  return (
+    <Show when={props.data.tabs.environment.available} fallback={<Empty state={props.data.tabs.environment} icon="environment" />}>
+      <div style={{ display: "grid", gap: "12px" }}>
+        <List title="Environment specifications" items={props.data.environments} />
+        <List title="Dependency locks" items={props.data.lockfiles} />
+      </div>
+    </Show>
+  )
+}
+
+function History(props: { data: InspectorData }): JSX.Element {
+  return (
+    <Show when={props.data.provenance?.commit} fallback={<Empty state={props.data.tabs.history} icon="history" />}>
+      {(version) => (
+        <section style={card()}>
+          <Heading icon="history">Latest recorded version</Heading>
+          <Fact label="commit" value={version().sha} mono />
+          <Fact label="author" value={`${version().author} <${version().email}>`} />
+          <Fact label="date" value={new Date(version().date).toLocaleString()} />
+          <Fact label="message" value={version().message} />
+          <p style={copyStyle()}>
+            This is the latest Git commit touching the file. Artifact-level branches and comparisons are not recorded yet.
+          </p>
+        </section>
+      )}
+    </Show>
+  )
+}
+
+function List(props: { title: string; items: string[] }): JSX.Element {
+  return (
+    <section style={card()}>
+      <Heading icon="environment">{props.title}</Heading>
+      <Show when={props.items.length} fallback={<p style={copyStyle()}>None recorded.</p>}>
+        <ul style={{ margin: 0, padding: "0 0 0 18px", display: "grid", gap: "6px" }}>
+          <For each={props.items}>
+            {(item) => <li style={{ "font-family": FONT_CODE, "font-size": "11px", color: "var(--color-text-muted)" }}>{item}</li>}
+          </For>
+        </ul>
+      </Show>
+    </section>
+  )
+}
+
+function Empty(props: { state: InspectorState; icon: "code" | "run" | "messages" | "environment" | "review" | "history" }): JSX.Element {
+  return (
+    <div
+      data-component="artifact-inspector-empty"
+      style={{
+        display: "grid",
+        "justify-items": "start",
+        gap: "10px",
+        padding: "18px",
+        border: "1px solid var(--color-border)",
+        "border-radius": "8px",
+        background: "var(--color-bg-subtle)",
+      }}
+    >
+      <Heading icon={props.icon}>{props.state.title}</Heading>
+      <p style={{ ...copyStyle(), margin: 0 }}>{props.state.detail}</p>
+    </div>
+  )
+}
+
+function Loading(): JSX.Element {
+  return (
+    <div data-component="artifact-inspector-loading" style={{ display: "grid", gap: "10px" }}>
+      <For each={[1, 2, 3]}>
+        {() => <div style={{ height: "58px", "border-radius": "7px", background: "var(--color-bg-subtle)" }} />}
+      </For>
+    </div>
+  )
+}
+
+function Heading(props: {
+  icon: "details" | "code" | "run" | "messages" | "environment" | "review" | "history"
+  children: JSX.Element
+}): JSX.Element {
+  const icons = {
+    details: IconFile,
+    code: IconBraces,
+    run: IconClock,
+    messages: IconMessageSquare,
+    environment: IconSettings,
+    review: IconFlask,
+    history: IconBookOpen,
+  }
+  const Icon = icons[props.icon]
+  return (
+    <h3
+      style={{
+        margin: 0,
+        display: "flex",
+        "align-items": "center",
+        gap: "7px",
+        "font-family": FONT_SANS,
+        "font-size": "12px",
+        "font-weight": 650,
+        color: "var(--color-text)",
+      }}
+    >
+      <Icon size={13} strokeWidth={1.5} />
+      {props.children}
+    </h3>
+  )
+}
+
+function Fact(props: { label: string; value: string; mono?: boolean }): JSX.Element {
+  return (
+    <div style={{ display: "grid", "grid-template-columns": "78px minmax(0, 1fr)", gap: "10px", "align-items": "start" }}>
+      <span style={{ "font-family": FONT_SANS, "font-size": "11px", color: "var(--color-text-faint)" }}>{props.label}</span>
+      <span
+        title={props.value}
+        style={{
+          "font-family": props.mono ? FONT_CODE : FONT_SANS,
+          "font-size": "11px",
+          "line-height": 1.45,
+          color: "var(--color-text-muted)",
+          overflow: "hidden",
+          "text-overflow": "ellipsis",
+          "white-space": "nowrap",
+        }}
+      >
+        {props.value}
+      </span>
+    </div>
+  )
+}
+
+function card(): JSX.CSSProperties {
+  return {
+    display: "grid",
+    gap: "9px",
+    padding: "13px",
+    border: "1px solid var(--color-border)",
+    "border-radius": "8px",
+    background: "var(--color-bg-subtle)",
+  }
+}
+
+function copyStyle(): JSX.CSSProperties {
+  return {
+    margin: 0,
+    "font-family": FONT_SANS,
+    "font-size": "11px",
+    "line-height": 1.55,
+    color: "var(--color-text-muted)",
+  }
+}
+
+function actionButton(primary = false): JSX.CSSProperties {
+  return {
+    all: "unset",
+    cursor: "pointer",
+    display: "inline-flex",
+    "align-items": "center",
+    "justify-content": "center",
+    gap: "6px",
+    padding: "7px 8px",
+    "border-radius": "6px",
+    border: primary ? "1px solid var(--color-text)" : "1px solid var(--color-border)",
+    background: primary ? "var(--color-text)" : "var(--color-bg-subtle)",
+    color: primary ? "var(--color-bg)" : "var(--color-text-muted)",
+    "font-family": FONT_SANS,
+    "font-size": "11px",
+    "font-weight": primary ? 650 : 500,
+  }
+}
+
+function tabButton(active: boolean): JSX.CSSProperties {
+  return {
+    all: "unset",
+    cursor: "pointer",
+    display: "inline-flex",
+    "align-items": "center",
+    gap: "5px",
+    padding: "6px 8px",
+    "border-radius": "5px",
+    background: active ? "var(--color-accent-subtle)" : "transparent",
+    color: active ? "var(--color-text)" : "var(--color-text-muted)",
+    "font-family": FONT_SANS,
+    "font-size": "11px",
+    "font-weight": active ? 650 : 500,
+    "white-space": "nowrap",
+  }
+}
+
+function iconButton(): JSX.CSSProperties {
+  return {
+    all: "unset",
+    cursor: "pointer",
+    width: "28px",
+    height: "28px",
+    display: "inline-flex",
+    "align-items": "center",
+    "justify-content": "center",
+    "border-radius": "5px",
+    color: "var(--color-text-muted)",
+  }
+}
+
+function quietButton(): JSX.CSSProperties {
+  return {
+    all: "unset",
+    cursor: "pointer",
+    padding: "5px 8px",
+    "border-radius": "5px",
+    "font-family": FONT_SANS,
+    "font-size": "11px",
+    color: "var(--color-text-muted)",
+  }
+}
+
+export default ArtifactInspector
diff --git a/frontend/workspace/src/artifacts/inspector.test.ts b/frontend/workspace/src/artifacts/inspector.test.ts
new file mode 100644
index 00000000..f6f33c92
--- /dev/null
+++ b/frontend/workspace/src/artifacts/inspector.test.ts
@@ -0,0 +1,74 @@
+import { describe, expect, test } from "bun:test"
+import { createArtifactContext } from "./context"
+import { inspectorTabs, normalizeInspectorData } from "./inspector"
+
+const context = createArtifactContext({
+  directory: "/work/project",
+  path: "results/protein.pdb",
+  format: "pdb",
+  scienceKind: "protein-structure",
+})
+
+describe("artifact inspector model", () => {
+  test("normalizes recorded source, environment, and Git provenance", () => {
+    const result = normalizeInspectorData(context, {
+      file: { type: "text", content: "ATOM      1", size: 12 },
+      provenance: {
+        path: "results/protein.pdb",
+        tracked: true,
+        dirty: false,
+        status: "clean",
+        branch: "openscience/aayam-new",
+        commit: {
+          sha: "0123456789abcdef",
+          author: "Aayam Bansal",
+          email: "aayambansal@gmail.com",
+          date: "2026-07-29T00:00:00.000Z",
+          message: "record structure",
+        },
+      },
+      audit: {
+        environments: ["pyproject.toml", "environment.yml"],
+        lockfiles: ["uv.lock"],
+      },
+    })
+
+    expect(result.source).toBe("ATOM      1")
+    expect(result.provenance).toMatchObject({
+      status: "clean",
+      branch: "openscience/aayam-new",
+      commit: { sha: "0123456789abcdef", author: "Aayam Bansal" },
+    })
+    expect(result.environments).toEqual(["pyproject.toml", "environment.yml"])
+    expect(result.lockfiles).toEqual(["uv.lock"])
+    expect(result.tabs.code.available).toBe(true)
+    expect(result.tabs.environment.available).toBe(true)
+    expect(result.tabs.history.available).toBe(true)
+    expect(result.tabs.run.available).toBe(false)
+    expect(result.tabs.messages.available).toBe(false)
+    expect(result.tabs.review.available).toBe(false)
+  })
+
+  test("keeps malformed and absent records honest instead of inventing metadata", () => {
+    const result = normalizeInspectorData(context, {
+      file: { type: "text", content: 12, encoding: "base64" },
+      provenance: { tracked: "yes", commit: { sha: 12 } },
+      audit: { environments: ["pyproject.toml", 4], lockfiles: "uv.lock" },
+    })
+
+    expect(result.source).toBeUndefined()
+    expect(result.provenance).toBeUndefined()
+    expect(result.environments).toEqual([])
+    expect(result.lockfiles).toEqual([])
+    expect(result.tabs.code).toEqual({
+      available: false,
+      title: "Source is not directly displayable",
+      detail: "Open the file view or download the original artifact.",
+    })
+    expect(result.tabs.history).toMatchObject({ available: false, title: "No Git commit is recorded" })
+  })
+
+  test("publishes the complete stable inspector tab order", () => {
+    expect(inspectorTabs).toEqual(["details", "code", "run", "messages", "environment", "review", "history"])
+  })
+})
diff --git a/frontend/workspace/src/artifacts/inspector.ts b/frontend/workspace/src/artifacts/inspector.ts
new file mode 100644
index 00000000..a75d18e7
--- /dev/null
+++ b/frontend/workspace/src/artifacts/inspector.ts
@@ -0,0 +1,146 @@
+import type { ArtifactContext } from "./context"
+
+export const inspectorTabs = ["details", "code", "run", "messages", "environment", "review", "history"] as const
+export type InspectorTab = (typeof inspectorTabs)[number]
+
+export interface ArtifactCommit {
+  sha: string
+  author: string
+  email: string
+  date: string
+  message: string
+}
+
+export interface ArtifactProvenance {
+  path: string
+  tracked: boolean
+  dirty: boolean
+  status: "clean" | "modified" | "added" | "deleted" | "untracked" | "local"
+  branch?: string
+  commit?: ArtifactCommit
+}
+
+export interface InspectorState {
+  available: boolean
+  title: string
+  detail: string
+}
+
+export interface InspectorData {
+  context: ArtifactContext
+  source?: string
+  provenance?: ArtifactProvenance
+  environments: string[]
+  lockfiles: string[]
+  tabs: Record<InspectorTab, InspectorState>
+}
+
+interface InspectorInput {
+  file?: unknown
+  provenance?: unknown
+  audit?: unknown
+}
+
+function record(value: unknown): Record<string, unknown> | undefined {
+  if (!value || typeof value !== "object" || Array.isArray(value)) return
+  return value as Record<string, unknown>
+}
+
+function strings(value: unknown): string[] {
+  if (!Array.isArray(value) || !value.every((item) => typeof item === "string")) return []
+  return value
+}
+
+function commit(value: unknown): ArtifactCommit | undefined {
+  const row = record(value)
+  if (!row) return
+  if (
+    typeof row.sha !== "string" ||
+    typeof row.author !== "string" ||
+    typeof row.email !== "string" ||
+    typeof row.date !== "string" ||
+    typeof row.message !== "string"
+  )
+    return
+  return {
+    sha: row.sha,
+    author: row.author,
+    email: row.email,
+    date: row.date,
+    message: row.message,
+  }
+}
+
+function provenance(value: unknown): ArtifactProvenance | undefined {
+  const row = record(value)
+  if (!row) return
+  const statuses = new Set(["clean", "modified", "added", "deleted", "untracked", "local"])
+  if (
+    typeof row.path !== "string" ||
+    typeof row.tracked !== "boolean" ||
+    typeof row.dirty !== "boolean" ||
+    typeof row.status !== "string" ||
+    !statuses.has(row.status)
+  )
+    return
+  const version = row.commit === undefined ? undefined : commit(row.commit)
+  if (row.commit !== undefined && !version) return
+  return {
+    path: row.path,
+    tracked: row.tracked,
+    dirty: row.dirty,
+    status: row.status as ArtifactProvenance["status"],
+    ...(typeof row.branch === "string" ? { branch: row.branch } : {}),
+    ...(version ? { commit: version } : {}),
+  }
+}
+
+function source(value: unknown): string | undefined {
+  const row = record(value)
+  if (!row || row.encoding === "base64" || typeof row.content !== "string") return
+  return row.content
+}
+
+function state(available: boolean, title: string, detail: string): InspectorState {
+  return { available, title, detail }
+}
+
+export function normalizeInspectorData(context: ArtifactContext, input: InspectorInput): InspectorData {
+  const text = source(input.file)
+  const version = provenance(input.provenance)
+  const audit = record(input.audit)
+  const environments = strings(audit?.environments)
+  const lockfiles = strings(audit?.lockfiles)
+  const environment = environments.length > 0 || lockfiles.length > 0
+  return {
+    context,
+    ...(text !== undefined ? { source: text } : {}),
+    ...(version ? { provenance: version } : {}),
+    environments,
+    lockfiles,
+    tabs: {
+      details: state(true, "Artifact details", "Format, location, and recorded scientific metadata."),
+      code:
+        text !== undefined
+          ? state(true, "Source available", "The original text source is available for inspection.")
+          : state(false, "Source is not directly displayable", "Open the file view or download the original artifact."),
+      run: state(false, "No generating run is recorded", "Execute or attach a run to connect logs and resources."),
+      messages: state(
+        false,
+        "No message range is recorded",
+        "Artifacts created from a conversation will show the exact producing messages here.",
+      ),
+      environment: environment
+        ? state(true, "Environment records found", "Project environment specifications and lockfiles are available.")
+        : state(false, "No environment is recorded", "Add a lockfile or environment specification to this project."),
+      review: state(
+        false,
+        "No review report is recorded",
+        "Run scientific review before treating this artifact as publication-ready.",
+      ),
+      history: version?.commit
+        ? state(true, "Git provenance available", "The latest commit touching this artifact is recorded.")
+        : state(false, "No Git commit is recorded", "Commit this artifact to create a recoverable version."),
+    },
+  }
+}

From d6d8424c20d328aca10f362560461bfa3d9aeb08 Mon Sep 17 00:00:00 2001
From: Aayam Bansal <aayambansal@gmail.com>
Date: Wed, 29 Jul 2026 14:12:38 +0800
Subject: [PATCH 22/40] feat: make the workspace artifact aware

---
 .../workspace/e2e/artifact-inspector.spec.ts  |  69 ++++++++++
 frontend/workspace/e2e/compute-jobs.spec.ts   |   6 +-
 frontend/workspace/src/atlas/RightPane.tsx    | 118 ++++++++++++++----
 frontend/workspace/src/atlas/store/ui.ts      |   4 +
 4 files changed, 173 insertions(+), 24 deletions(-)
 create mode 100644 frontend/workspace/e2e/artifact-inspector.spec.ts

diff --git a/frontend/workspace/e2e/artifact-inspector.spec.ts b/frontend/workspace/e2e/artifact-inspector.spec.ts
new file mode 100644
index 00000000..57fbbef6
--- /dev/null
+++ b/frontend/workspace/e2e/artifact-inspector.spec.ts
@@ -0,0 +1,69 @@
+import path from "node:path"
+import type { Page } from "@playwright/test"
+import { test, expect } from "./fixtures"
+
+const escapeRegex = (value: string) => value.replace(/[.*+?^${}()|[\]\\]/g, "\\$&")
+
+async function openFile(page: Page, directory: string, relativePath: string) {
+  await page.getByRole("tab", { name: "Files", exact: true }).click()
+  const folder = path.join(directory, path.dirname(relativePath))
+  const filename = path.basename(relativePath)
+  const location = page.getByPlaceholder("/absolute/path")
+  await location.fill(folder)
+  await location.press("Enter")
+  await page.getByPlaceholder("filter this folder…").fill(filename)
+  await page.getByRole("button", { name: new RegExp(`^${escapeRegex(filename)}\\b`) }).first().click()
+  await expect(page.locator(`[role="tab"][title="${filename}"]`)).toHaveAttribute("aria-selected", "true")
+}
+
+test("opened files drive a contextual artifact inspector without stale state", async ({
+  page,
+  directory,
+  gotoSession,
+}) => {
+  await gotoSession()
+  await openFile(page, directory, "frontend/workspace/e2e/science/water.xyz")
+
+  const inspector = page.locator('[data-component="artifact-inspector"]')
+  await expect(inspector).toBeVisible()
+  await expect(inspector).toHaveAttribute("data-artifact-id", /water\.xyz/)
+  await expect(inspector.locator("header strong")).toHaveText("water.xyz")
+  await expect(inspector.getByRole("tab")).toHaveCount(7)
+
+  const details = inspector.getByRole("tab", { name: "Details", exact: true })
+  await details.focus()
+  await details.press("ArrowRight")
+  await expect(inspector.getByRole("tab", { name: "Code", exact: true })).toHaveAttribute("aria-selected", "true")
+  await expect(inspector.locator("pre")).toContainText("water")
+
+  await inspector.getByRole("tab", { name: "Run", exact: true }).click()
+  await expect(inspector.getByText("No generating run is recorded", { exact: true })).toBeVisible()
+
+  await openFile(page, directory, "frontend/workspace/e2e/science/alignment.fasta")
+  await expect(inspector).toHaveAttribute("data-artifact-id", /alignment\.fasta/)
+  await expect(inspector.locator("header strong")).toHaveText("alignment.fasta")
+  await expect(inspector.getByRole("tab", { name: "Details", exact: true })).toHaveAttribute("aria-selected", "true")
+
+  await page.getByRole("tab", { name: "Chat", exact: true }).click()
+  await expect(inspector).toHaveCount(0)
+  await expect(page.locator(".session-right-pane").getByRole("tab", { name: "Atlas", exact: true })).toBeVisible()
+})
+
+test("artifact inspector overlays rather than crushing the workbench at narrow desktop widths", async ({
+  page,
+  directory,
+  gotoSession,
+}) => {
+  await page.setViewportSize({ width: 1024, height: 760 })
+  await gotoSession()
+  await openFile(page, directory, "frontend/workspace/e2e/science/water.xyz")
+
+  const inspector = page.locator('[data-component="artifact-inspector"]')
+  const file = page.locator('[data-component="file-view"]')
+  await expect(inspector).toBeVisible()
+  await expect(file).toBeVisible()
+  const [inspectorBox, fileBox] = await Promise.all([inspector.boundingBox(), file.boundingBox()])
+  expect(inspectorBox?.width).toBeGreaterThanOrEqual(280)
+  expect(fileBox?.width).toBeGreaterThanOrEqual(520)
+  expect(inspectorBox?.x).toBeGreaterThan(fileBox?.x ?? 0)
+})
diff --git a/frontend/workspace/e2e/compute-jobs.spec.ts b/frontend/workspace/e2e/compute-jobs.spec.ts
index c53462b4..3d464d5e 100644
--- a/frontend/workspace/e2e/compute-jobs.spec.ts
+++ b/frontend/workspace/e2e/compute-jobs.spec.ts
@@ -11,7 +11,11 @@ test("runs a reproducible local job and captures outputs from the right pane", a
   try {
     await gotoSession()
 
-    await page.getByTitle("jobs").click()
+    await page
+      .getByRole("tab", { name: "Compute", exact: true })
+      .or(page.getByRole("button", { name: "Compute", exact: true }))
+      .first()
+      .click()
     const pane = page.locator(".session-right-pane")
     await expect(pane.getByText("compute jobs", { exact: true })).toBeVisible()
 
diff --git a/frontend/workspace/src/atlas/RightPane.tsx b/frontend/workspace/src/atlas/RightPane.tsx
index 18880962..546ee294 100644
--- a/frontend/workspace/src/atlas/RightPane.tsx
+++ b/frontend/workspace/src/atlas/RightPane.tsx
@@ -1,4 +1,4 @@
-import { createSignal, createMemo, createEffect, type JSX, For, Show } from "solid-js"
+import { createSignal, createMemo, createEffect, onCleanup, onMount, type JSX, For, Show } from "solid-js"
 import { FONT_MONO, FONT_SANS, sectionTitle } from "@/styles/tokens"
 import { useSDK } from "@/context/sdk"
 import { useDialog } from "@synsci/ui/context/dialog"
@@ -9,8 +9,11 @@ import { SkillLibraryDialog } from "@/atlas/SkillsBrowser"
 import { AtlasCanvas } from "@/atlas/AtlasCanvas"
 import { ComputeJobs } from "@/atlas/ComputeJobs"
 import { EvidenceGraph } from "@/atlas/EvidenceGraph"
+import { artifactContext } from "@/artifacts/context"
+import { ArtifactInspector } from "@/artifacts/ArtifactInspector"
 import { toast } from "@/atlas/Toast"
 import {
+  IconAtom,
   IconLayoutGrid,
   IconBraces,
   IconChevronRight,
@@ -36,6 +39,8 @@ function readSavedWidth(): number {
 export function RightPane(): JSX.Element {
   const tab = uiStore.rightPaneTab
   const setTab = uiStore.setRightPaneTab
+  const artifact = artifactContext.active
+  const artifactMode = () => Boolean(artifact()) && uiStore.rightPaneMode() === "artifact"
   // Keep-alive: once a tab has been opened it stays mounted (hidden via CSS),
   // so switching tabs never re-mounts/re-fetches/re-animates — no flash.
   const [visited, setVisited] = createSignal<Set<RightPaneTab>>(new Set([tab()]))
@@ -45,15 +50,21 @@ export function RightPane(): JSX.Element {
   })
   const dialog = useDialog()
   const [width, setWidth] = createSignal(readSavedWidth())
+  const [narrow, setNarrow] = createSignal(typeof window !== "undefined" && window.innerWidth < 1100)
   const [panelMenu, setPanelMenu] = createSignal(false)
+  onMount(() => {
+    const resize = () => setNarrow(window.innerWidth < 1100)
+    window.addEventListener("resize", resize)
+    onCleanup(() => window.removeEventListener("resize", resize))
+  })
   const openSkillLibrary = () =>
     dialog.show(() => <SkillLibraryDialog onPick={(name) => uiStore.setPrefill(`/${name} `)} />)
   const TABS: { k: RightPaneTab; label?: string; Icon: (p: { size?: number; strokeWidth?: number }) => JSX.Element }[] =
     [
-      { k: "canvas", label: "atlas", Icon: IconLayoutGrid },
-      { k: "evidence", Icon: IconNetwork },
-      { k: "jobs", Icon: IconActivity },
-      { k: "terminal", Icon: IconTerminal },
+      { k: "canvas", label: "Atlas", Icon: IconLayoutGrid },
+      { k: "evidence", label: "Evidence", Icon: IconNetwork },
+      { k: "jobs", label: "Compute", Icon: IconActivity },
+      { k: "terminal", label: "Terminal", Icon: IconTerminal },
     ]
   const visibleTabs = createMemo(() => TABS.filter((t) => !uiStore.isTabHidden(t.k)))
   // Keep the active tab pointed at a visible one.
@@ -61,6 +72,12 @@ export function RightPane(): JSX.Element {
     const vis = visibleTabs()
     if (vis.length && !vis.some((t) => t.k === tab())) setTab(vis[0].k)
   })
+  createEffect(() => {
+    const id = artifact()?.id
+    if (!id) return
+    uiStore.setRightPaneMode("artifact")
+    uiStore.setRightPaneOpen(true)
+  })
   // Run a command requested from elsewhere (e.g. the Local models settings
   // panel's "run in terminal") in a fresh terminal tab, then reveal it.
   const terminal = useTerminal()
@@ -101,9 +118,17 @@ export function RightPane(): JSX.Element {
       when={uiStore.rightPaneOpen()}
       fallback={
         <CollapsedRail
+          artifact={Boolean(artifact())}
+          onInspect={() => {
+            uiStore.setRightPaneMode("artifact")
+            uiStore.setRightPaneOpen(true)
+          }}
           tabs={visibleTabs()}
           onOpen={(t) => {
-            if (t) setTab(t)
+            if (t) {
+              setTab(t)
+              uiStore.setRightPaneMode("tools")
+            }
             uiStore.setRightPaneOpen(true)
           }}
         />
@@ -112,14 +137,19 @@ export function RightPane(): JSX.Element {
       <aside
         class="session-right-pane"
         style={{
-          flex: `0 0 ${width()}px`,
-          width: `${width()}px`,
+          flex: narrow() ? "none" : `0 0 ${width()}px`,
+          width: narrow() ? "min(420px, calc(100vw - 52px))" : `${width()}px`,
           display: "flex",
           "flex-direction": "column",
           "border-left": "1px solid var(--color-border)",
           background: "var(--color-bg-subtle)",
-          "min-width": `${MIN_PANE_WIDTH}px`,
-          position: "relative",
+          "min-width": narrow() ? "280px" : `${MIN_PANE_WIDTH}px`,
+          position: narrow() ? "fixed" : "relative",
+          top: narrow() ? "0" : undefined,
+          right: narrow() ? "0" : undefined,
+          bottom: narrow() ? "0" : undefined,
+          "z-index": narrow() ? 70 : undefined,
+          "box-shadow": narrow() ? "-18px 0 48px rgba(0, 0, 0, 0.22)" : "none",
         }}
       >
         {/* Drag handle on the left edge of the right pane. 6px wide, full
@@ -157,9 +187,27 @@ export function RightPane(): JSX.Element {
           <div
             style={{ display: "flex", gap: "5px", padding: "7px 10px", flex: 1, "min-width": 0, "overflow-x": "auto" }}
           >
+            <Show when={artifact()}>
+              <TabBtn
+                k="artifact"
+                label="Inspect"
+                Icon={IconAtom}
+                active={artifactMode()}
+                onClick={() => uiStore.setRightPaneMode("artifact")}
+              />
+            </Show>
             <For each={visibleTabs()}>
               {(t) => (
-                <TabBtn k={t.k} label={t.label} Icon={t.Icon} active={tab() === t.k} onClick={() => setTab(t.k)} />
+                <TabBtn
+                  k={t.k}
+                  label={t.label}
+                  Icon={t.Icon}
+                  active={!artifactMode() && tab() === t.k}
+                  onClick={() => {
+                    setTab(t.k)
+                    uiStore.setRightPaneMode("tools")
+                  }}
+                />
               )}
             </For>
           </div>
@@ -224,18 +272,35 @@ export function RightPane(): JSX.Element {
           </div>
         </div>
         <div style={{ flex: 1, "min-height": 0, position: "relative", display: "flex", "flex-direction": "column" }}>
-          <KeepAlive show={tab() === "canvas"} mounted={visited().has("canvas")}>
-            <CanvasTab />
-          </KeepAlive>
-          <KeepAlive show={tab() === "jobs"} mounted={visited().has("jobs")}>
-            <ComputeJobs />
-          </KeepAlive>
-          <KeepAlive show={tab() === "evidence"} mounted={visited().has("evidence")}>
-            <EvidenceGraph />
-          </KeepAlive>
-          <KeepAlive show={tab() === "terminal"} mounted={visited().has("terminal")}>
-            <TerminalTab />
-          </KeepAlive>
+          <Show when={artifactMode() && artifact()}>
+            {(current) => (
+              <ArtifactInspector
+                context={current()}
+                onClose={() => uiStore.setRightPaneMode("tools")}
+              />
+            )}
+          </Show>
+          <div
+            style={{
+              display: artifactMode() ? "none" : "flex",
+              flex: artifactMode() ? undefined : 1,
+              "min-height": 0,
+              "flex-direction": "column",
+            }}
+          >
+            <KeepAlive show={tab() === "canvas"} mounted={visited().has("canvas")}>
+              <CanvasTab />
+            </KeepAlive>
+            <KeepAlive show={tab() === "jobs"} mounted={visited().has("jobs")}>
+              <ComputeJobs />
+            </KeepAlive>
+            <KeepAlive show={tab() === "evidence"} mounted={visited().has("evidence")}>
+              <EvidenceGraph />
+            </KeepAlive>
+            <KeepAlive show={tab() === "terminal"} mounted={visited().has("terminal")}>
+              <TerminalTab />
+            </KeepAlive>
+          </div>
         </div>
       </aside>
     </Show>
@@ -385,6 +450,8 @@ function TerminalTab(): JSX.Element {
 }
 
 function CollapsedRail(props: {
+  artifact: boolean
+  onInspect: () => void
   tabs: { k: RightPaneTab; label?: string; Icon: (p: { size?: number; strokeWidth?: number }) => JSX.Element }[]
   onOpen: (t?: RightPaneTab) => void
 }): JSX.Element {
@@ -406,6 +473,11 @@ function CollapsedRail(props: {
         <IconChevronLeft size={14} strokeWidth={1.5} />
       </button>
       <span style={{ width: "18px", height: "1px", background: "var(--color-border)", margin: "4px 0" }} />
+      <Show when={props.artifact}>
+        <button onClick={props.onInspect} title="inspect artifact" aria-label="inspect artifact" style={railBtn()}>
+          <IconAtom size={15} strokeWidth={1.5} />
+        </button>
+      </Show>
       <For each={props.tabs}>
         {(t) => (
           <button
diff --git a/frontend/workspace/src/atlas/store/ui.ts b/frontend/workspace/src/atlas/store/ui.ts
index 0ca41cf0..08667dd5 100644
--- a/frontend/workspace/src/atlas/store/ui.ts
+++ b/frontend/workspace/src/atlas/store/ui.ts
@@ -1,6 +1,7 @@
 import { createSignal } from "solid-js"
 
 export type RightPaneTab = "canvas" | "evidence" | "jobs" | "terminal"
+export type RightPaneMode = "artifact" | "tools"
 
 const PANE_OPEN_KEY = "openscience-rightpane-open-v2"
 const HIDDEN_TABS_KEY = "thesis-rightpane-hidden-tabs-v1"
@@ -40,6 +41,7 @@ function readHiddenTabs(): RightPaneTab[] {
 const [helpOpen, setHelpOpen] = createSignal(false)
 const [paletteOpen, setPaletteOpen] = createSignal(false)
 const [rightPaneTab, setRightPaneTab] = createSignal<RightPaneTab>("canvas")
+const [rightPaneMode, setRightPaneMode] = createSignal<RightPaneMode>("tools")
 const [rightPaneOpen, setRightPaneOpenRaw] = createSignal(readPaneOpen())
 const [hiddenTabs, setHiddenTabs] = createSignal<RightPaneTab[]>(readHiddenTabs())
 const [agent, setAgentRaw] = createSignal<string>(readAgent())
@@ -87,6 +89,8 @@ export const uiStore = {
   setPaletteOpen,
   rightPaneTab,
   setRightPaneTab,
+  rightPaneMode,
+  setRightPaneMode,
   rightPaneOpen,
   setRightPaneOpen,
   hiddenTabs,

From 54c0f90b81cf9d829aa3495d6f609b7432cb5023 Mon Sep 17 00:00:00 2001
From: Aayam Bansal <aayambansal@gmail.com>
Date: Wed, 29 Jul 2026 14:15:28 +0800
Subject: [PATCH 23/40] feat: inspect molecular structure metadata

---
 .../e2e/science-file-viewers.spec.ts          |   4 +
 .../renderers/molecular/ProteinStructure.tsx  | 142 ++++++------
 .../science/renderers/molecular/model.test.ts |  84 +++++++
 .../src/science/renderers/molecular/model.ts  | 214 ++++++++++++++++++
 4 files changed, 373 insertions(+), 71 deletions(-)
 create mode 100644 frontend/workspace/src/science/renderers/molecular/model.test.ts
 create mode 100644 frontend/workspace/src/science/renderers/molecular/model.ts

diff --git a/frontend/workspace/e2e/science-file-viewers.spec.ts b/frontend/workspace/e2e/science-file-viewers.spec.ts
index fb10f8da..9c752dac 100644
--- a/frontend/workspace/e2e/science-file-viewers.spec.ts
+++ b/frontend/workspace/e2e/science-file-viewers.spec.ts
@@ -64,6 +64,10 @@ test("XYZ files open as interactive 3D chemistry with source access", async ({ p
   const artifact = page.locator('[data-component="science-artifact"][data-kind="chem-3d"]')
   await expect(artifact).toBeVisible()
   await expect(artifact.locator('[data-component="mol-structure"]')).toBeVisible()
+  const summary = artifact.locator('[data-component="molecular-summary"]')
+  await expect(summary).toContainText("3 atoms")
+  await expect(summary).toContainText("H 2")
+  await expect(summary).toContainText("O 1")
 
   await page.getByTitle("raw source", { exact: true }).click()
   await expect(page.getByTitle("rendered view", { exact: true })).toBeVisible()
diff --git a/frontend/workspace/src/science/renderers/molecular/ProteinStructure.tsx b/frontend/workspace/src/science/renderers/molecular/ProteinStructure.tsx
index 552cc92d..79489d3e 100644
--- a/frontend/workspace/src/science/renderers/molecular/ProteinStructure.tsx
+++ b/frontend/workspace/src/science/renderers/molecular/ProteinStructure.tsx
@@ -1,8 +1,9 @@
-import { Show, createEffect, createSignal, onCleanup, onMount } from "solid-js"
+import { For, Show, createEffect, createMemo, createSignal, onCleanup, onMount } from "solid-js"
 import type { JSX } from "solid-js"
 import type { PluginContext } from "molstar/lib/mol-plugin/context"
 import type { BuiltInTrajectoryFormat } from "molstar/lib/mol-plugin-state/formats/trajectory"
 import type { ArtifactRenderProps } from "../registry"
+import { analyzeMolecularSource, narrowMolecularSource } from "./model"
 
 /**
  * 3D molecular structure renderer backed by Mol* (molstar), used for both the
@@ -27,79 +28,12 @@ import type { ArtifactRenderProps } from "../registry"
 
 type Status = "idle" | "loading" | "ready" | "empty" | "error"
 
-interface Source {
-  format: BuiltInTrajectoryFormat
-  url?: string
-  raw?: string
-  binary?: boolean
-}
-
-const EXT_FORMAT: Record<string, { format: BuiltInTrajectoryFormat; binary?: boolean }> = {
-  pdb: { format: "pdb" },
-  ent: { format: "pdb" },
-  cif: { format: "mmcif" },
-  mmcif: { format: "mmcif" },
-  bcif: { format: "mmcif", binary: true },
-  pdbqt: { format: "pdbqt" },
-  gro: { format: "gro" },
-  xyz: { format: "xyz" },
-  sdf: { format: "sdf" },
-  mol: { format: "mol" },
-  mol2: { format: "mol2" },
-}
-
-function formatFromUrl(url: string): { format: BuiltInTrajectoryFormat; binary?: boolean } | undefined {
-  const clean = url.split(/[?#]/)[0]
-  const ext = clean.slice(clean.lastIndexOf(".") + 1).toLowerCase()
-  return EXT_FORMAT[ext]
-}
-
-function narrow(data: unknown, kind: string): Source | undefined {
-  const fallback: BuiltInTrajectoryFormat = kind === "chem-3d" ? "sdf" : "pdb"
-  if (typeof data === "string") {
-    const s = data.trim()
-    if (/^[0-9A-Za-z]{4}$/.test(s)) return { url: rcsbUrl(s), format: "mmcif" }
-    return { raw: data, format: fallback }
-  }
-  if (!data || typeof data !== "object") return undefined
-  const d = data as Record<string, unknown>
-  const inlineMap: Array<[string, BuiltInTrajectoryFormat]> = [
-    ["pdb", "pdb"],
-    ["cif", "mmcif"],
-    ["mmcif", "mmcif"],
-    ["sdf", "sdf"],
-    ["mol2", "mol2"],
-    ["mol", "mol"],
-    ["xyz", "xyz"],
-  ]
-  for (const [key, format] of inlineMap) {
-    if (typeof d[key] === "string") return { raw: d[key] as string, format }
-  }
-  const explicit = typeof d.format === "string" ? (d.format as BuiltInTrajectoryFormat) : undefined
-  const inline = d.data ?? d.inline ?? d.text
-  if (typeof inline === "string") return { raw: inline, format: explicit ?? fallback }
-  if (typeof d.url === "string") {
-    const guess = formatFromUrl(d.url)
-    return {
-      url: d.url,
-      format: explicit ?? guess?.format ?? (kind === "chem-3d" ? "sdf" : "mmcif"),
-      binary: guess?.binary,
-    }
-  }
-  if (typeof d.id === "string") return { url: rcsbUrl(d.id), format: "mmcif" }
-  if (typeof d.pdbId === "string") return { url: rcsbUrl(d.pdbId as string), format: "mmcif" }
-  return undefined
-}
-
-function rcsbUrl(id: string): string {
-  return `https://files.rcsb.org/download/${id.trim().toUpperCase()}.cif`
-}
-
 export function ProteinStructure(props: ArtifactRenderProps): JSX.Element {
   let host!: HTMLDivElement
   const [plugin, setPlugin] = createSignal<PluginContext | undefined>()
   const [status, setStatus] = createSignal<Status>("idle")
   const [error, setError] = createSignal<string>("")
+  const summary = createMemo(() => analyzeMolecularSource(props.data, props.kind))
   let disposed = false
   let token = 0
 
@@ -147,7 +81,7 @@ export function ProteinStructure(props: ArtifactRenderProps): JSX.Element {
 
   async function load(p: PluginContext, data: unknown, kind: string) {
     const my = ++token
-    const src = narrow(data, kind)
+    const src = narrowMolecularSource(data, kind)
     if (!src) {
       await p.clear().catch(() => {})
       if (my === token) setStatus("empty")
@@ -162,7 +96,7 @@ export function ProteinStructure(props: ArtifactRenderProps): JSX.Element {
         ? await p.builders.data.download({ url: src.url, isBinary: src.binary ?? false }, { state: { isGhost: true } })
         : await p.builders.data.rawData({ data: src.raw ?? "" })
       if (my !== token || disposed) return
-      const trajectory = await p.builders.structure.parseTrajectory(raw, src.format)
+      const trajectory = await p.builders.structure.parseTrajectory(raw, src.format as BuiltInTrajectoryFormat)
       if (my !== token || disposed) return
       await p.builders.structure.hierarchy.applyPreset(trajectory, "default")
       if (my !== token || disposed) return
@@ -204,6 +138,72 @@ export function ProteinStructure(props: ArtifactRenderProps): JSX.Element {
       }}
     >
       <div ref={host} style={{ position: "absolute", inset: "0" }} />
+      <Show when={summary()}>
+        {(value) => (
+          <div
+            data-component="molecular-summary"
+            style={{
+              position: "absolute",
+              left: "12px",
+              bottom: "12px",
+              display: "grid",
+              gap: "7px",
+              padding: "10px 11px",
+              "max-width": "min(360px, calc(100% - 24px))",
+              "border-radius": "7px",
+              border: "1px solid rgba(255,255,255,0.14)",
+              background: "rgba(9, 12, 18, 0.82)",
+              "backdrop-filter": "blur(12px)",
+              color: "#e8ebf2",
+              "font-family": "ui-sans-serif, system-ui, sans-serif",
+              "font-size": "11px",
+              "line-height": 1.35,
+              "z-index": 2,
+            }}
+          >
+            <div style={{ display: "flex", "align-items": "center", gap: "8px", "flex-wrap": "wrap" }}>
+              <strong style={{ "font-size": "11px", "letter-spacing": "0.02em" }}>
+                {value().format.toUpperCase()}
+              </strong>
+              <Show when={value().atomCount !== undefined}>
+                <span>{value().atomCount} atoms</span>
+              </Show>
+              <Show when={value().bondCount !== undefined}>
+                <span>{value().bondCount} bonds</span>
+              </Show>
+              <Show when={value().residueCount !== undefined}>
+                <span>{value().residueCount} residues</span>
+              </Show>
+              <Show when={value().chainCount !== undefined}>
+                <span>{value().chainCount} chains</span>
+              </Show>
+              <Show when={value().moleculeCount !== undefined}>
+                <span>{value().moleculeCount} molecules</span>
+              </Show>
+            </div>
+            <Show when={value().elements.length}>
+              <div style={{ display: "flex", gap: "5px", "flex-wrap": "wrap", color: "#bac2d2" }}>
+                <For each={value().elements}>
+                  {(item) => (
+                    <span
+                      style={{
+                        padding: "2px 5px",
+                        "border-radius": "4px",
+                        background: "rgba(255,255,255,0.08)",
+                      }}
+                    >
+                      {item.element} {item.count}
+                    </span>
+                  )}
+                </For>
+              </div>
+            </Show>
+            <For each={value().warnings}>
+              {(warning) => <span style={{ color: "#f2c879" }}>{warning}</span>}
+            </For>
+          </div>
+        )}
+      </Show>
       <Show when={status() !== "ready"}>
         <div
           style={{
diff --git a/frontend/workspace/src/science/renderers/molecular/model.test.ts b/frontend/workspace/src/science/renderers/molecular/model.test.ts
new file mode 100644
index 00000000..44e6b558
--- /dev/null
+++ b/frontend/workspace/src/science/renderers/molecular/model.test.ts
@@ -0,0 +1,84 @@
+import { describe, expect, test } from "bun:test"
+import path from "node:path"
+import { analyzeMolecularSource, narrowMolecularSource } from "./model"
+
+const fixtures = path.join(import.meta.dir, "../../../../e2e/science")
+
+describe("molecular source analysis", () => {
+  test("parses XYZ atom and element counts from the real viewer fixture", async () => {
+    const text = await Bun.file(path.join(fixtures, "water.xyz")).text()
+    expect(analyzeMolecularSource({ data: text, format: "xyz" }, "chem-3d")).toEqual({
+      format: "xyz",
+      source: "inline",
+      atomCount: 3,
+      moleculeCount: 1,
+      elements: [
+        { element: "H", count: 2 },
+        { element: "O", count: 1 },
+      ],
+      warnings: [],
+    })
+  })
+
+  test("parses PDB chains, residues, atoms, models, and elements", async () => {
+    const text = await Bun.file(path.join(fixtures, "example.pdb")).text()
+    expect(analyzeMolecularSource({ pdb: text }, "protein-structure")).toEqual({
+      format: "pdb",
+      source: "inline",
+      atomCount: 4,
+      chainCount: 1,
+      residueCount: 1,
+      modelCount: 1,
+      elements: [
+        { element: "C", count: 2 },
+        { element: "N", count: 1 },
+        { element: "O", count: 1 },
+      ],
+      warnings: [],
+    })
+  })
+
+  test("parses SDF molecule, atom, bond, and element counts", async () => {
+    const text = await Bun.file(path.join(fixtures, "ligand.sdf")).text()
+    expect(analyzeMolecularSource({ sdf: text }, "chem-3d")).toEqual({
+      format: "sdf",
+      source: "inline",
+      atomCount: 2,
+      bondCount: 1,
+      moleculeCount: 1,
+      elements: [{ element: "C", count: 2 }],
+      warnings: [],
+    })
+  })
+
+  test("reports declared XYZ count mismatches and malformed coordinate rows", () => {
+    expect(analyzeMolecularSource({ xyz: "3\nbad\nO 0 0 0\nH nope 0 1" }, "chem-3d")).toEqual({
+      format: "xyz",
+      source: "inline",
+      atomCount: 1,
+      moleculeCount: 1,
+      elements: [{ element: "O", count: 1 }],
+      warnings: ["XYZ declares 3 atoms but 1 valid coordinate row was parsed."],
+    })
+  })
+
+  test("keeps remote source metadata honest without pretending it fetched scientific properties", () => {
+    expect(analyzeMolecularSource({ url: "https://example.test/model.cif" }, "protein-structure")).toEqual({
+      format: "mmcif",
+      source: "remote",
+      elements: [],
+      warnings: ["Scientific properties are available after the remote structure is loaded."],
+    })
+  })
+
+  test("normalizes supported source shapes for the Molstar renderer", () => {
+    expect(narrowMolecularSource("1CBS", "protein-structure")).toEqual({
+      url: "https://files.rcsb.org/download/1CBS.cif",
+      format: "mmcif",
+    })
+    expect(narrowMolecularSource({ data: "3\nwater", format: "xyz" }, "chem-3d")).toEqual({
+      raw: "3\nwater",
+      format: "xyz",
+    })
+  })
+})
diff --git a/frontend/workspace/src/science/renderers/molecular/model.ts b/frontend/workspace/src/science/renderers/molecular/model.ts
new file mode 100644
index 00000000..392ed57d
--- /dev/null
+++ b/frontend/workspace/src/science/renderers/molecular/model.ts
@@ -0,0 +1,214 @@
+export interface MolecularSource {
+  format: string
+  url?: string
+  raw?: string
+  binary?: boolean
+}
+
+export interface ElementCount {
+  element: string
+  count: number
+}
+
+export interface MolecularSummary {
+  format: string
+  source: "inline" | "remote"
+  atomCount?: number
+  bondCount?: number
+  moleculeCount?: number
+  chainCount?: number
+  residueCount?: number
+  modelCount?: number
+  elements: ElementCount[]
+  warnings: string[]
+}
+
+const formats: Record<string, { format: string; binary?: boolean }> = {
+  pdb: { format: "pdb" },
+  ent: { format: "pdb" },
+  cif: { format: "mmcif" },
+  mmcif: { format: "mmcif" },
+  bcif: { format: "mmcif", binary: true },
+  pdbqt: { format: "pdbqt" },
+  gro: { format: "gro" },
+  xyz: { format: "xyz" },
+  sdf: { format: "sdf" },
+  mol: { format: "mol" },
+  mol2: { format: "mol2" },
+}
+
+function format(value: string): { format: string; binary?: boolean } {
+  const key = value.toLowerCase()
+  return formats[key] ?? { format: key }
+}
+
+function formatFromUrl(url: string): { format: string; binary?: boolean } | undefined {
+  const clean = url.split(/[?#]/)[0]
+  const index = clean.lastIndexOf(".")
+  if (index < 0) return
+  return formats[clean.slice(index + 1).toLowerCase()]
+}
+
+function rcsbUrl(id: string): string {
+  return `https://files.rcsb.org/download/${id.trim().toUpperCase()}.cif`
+}
+
+export function narrowMolecularSource(data: unknown, kind: string): MolecularSource | undefined {
+  const fallback = kind === "chem-3d" ? "sdf" : "pdb"
+  if (typeof data === "string") {
+    const value = data.trim()
+    if (/^[0-9A-Za-z]{4}$/.test(value)) return { url: rcsbUrl(value), format: "mmcif" }
+    return { raw: data, format: fallback }
+  }
+  if (!data || typeof data !== "object" || Array.isArray(data)) return
+  const row = data as Record<string, unknown>
+  const inline = ["pdb", "cif", "mmcif", "sdf", "mol2", "mol", "xyz"]
+  for (const key of inline) {
+    if (typeof row[key] !== "string") continue
+    return { raw: row[key], ...format(key) }
+  }
+  const explicit = typeof row.format === "string" ? format(row.format) : undefined
+  const text = row.data ?? row.inline ?? row.text
+  if (typeof text === "string") return { raw: text, ...(explicit ?? format(fallback)) }
+  if (typeof row.url === "string") {
+    const guess = formatFromUrl(row.url)
+    return {
+      url: row.url,
+      ...(explicit ?? guess ?? format(kind === "chem-3d" ? "sdf" : "mmcif")),
+    }
+  }
+  if (typeof row.id === "string") return { url: rcsbUrl(row.id), format: "mmcif" }
+  if (typeof row.pdbId === "string") return { url: rcsbUrl(row.pdbId), format: "mmcif" }
+}
+
+function element(value: string): string | undefined {
+  const match = value.trim().match(/^([A-Za-z]{1,2})$/)
+  if (!match) return
+  return `${match[1]![0]!.toUpperCase()}${match[1]!.slice(1).toLowerCase()}`
+}
+
+function countElements(values: Array<string | undefined>): ElementCount[] {
+  const counts = values.reduce<Record<string, number>>((all, value) => {
+    if (!value) return all
+    all[value] = (all[value] ?? 0) + 1
+    return all
+  }, {})
+  return Object.entries(counts)
+    .map(([name, count]) => ({ element: name, count }))
+    .toSorted((a, b) => b.count - a.count || a.element.localeCompare(b.element))
+}
+
+function analyzeXyz(raw: string, source: MolecularSummary["source"]): MolecularSummary {
+  const lines = raw.split(/\r?\n/)
+  const declared = Number.parseInt(lines[0]?.trim() ?? "", 10)
+  const rows = lines.slice(2).flatMap((line) => {
+    const parts = line.trim().split(/\s+/)
+    const symbol = element(parts[0] ?? "")
+    const coordinates = parts.slice(1, 4).map(Number)
+    if (!symbol || coordinates.length !== 3 || coordinates.some((value) => !Number.isFinite(value))) return []
+    return [{ element: symbol }]
+  })
+  const warnings =
+    Number.isFinite(declared) && declared !== rows.length
+      ? [`XYZ declares ${declared} atoms but ${rows.length} valid coordinate row was parsed.`]
+      : []
+  return {
+    format: "xyz",
+    source,
+    atomCount: rows.length,
+    moleculeCount: rows.length ? 1 : 0,
+    elements: countElements(rows.map((row) => row.element)),
+    warnings,
+  }
+}
+
+function pdbElement(line: string): string | undefined {
+  const declared = element(line.slice(76, 78))
+  if (declared) return declared
+  const atom = line.slice(12, 16).trim().replace(/^\d+/, "")
+  return element(atom.slice(0, 1))
+}
+
+function analyzePdb(raw: string, source: MolecularSummary["source"]): MolecularSummary {
+  const lines = raw.split(/\r?\n/)
+  const atoms = lines.filter((line) => line.startsWith("ATOM  ") || line.startsWith("HETATM"))
+  const chains = new Set(atoms.map((line) => line.slice(21, 22).trim() || "_"))
+  const residues = new Set(
+    atoms.map((line) => `${line.slice(21, 22).trim() || "_"}:${line.slice(22, 27).trim()}`),
+  )
+  const declaredModels = lines.filter((line) => line.startsWith("MODEL ")).length
+  return {
+    format: "pdb",
+    source,
+    atomCount: atoms.length,
+    chainCount: chains.size,
+    residueCount: residues.size,
+    modelCount: declaredModels || (atoms.length ? 1 : 0),
+    elements: countElements(atoms.map(pdbElement)),
+    warnings: [],
+  }
+}
+
+interface MolRecord {
+  atoms: string[]
+  atomCount: number
+  bondCount: number
+}
+
+function molRecord(raw: string): MolRecord | undefined {
+  const lines = raw.split(/\r?\n/)
+  const index = lines.findIndex((line) => line.includes("V2000"))
+  if (index < 0) return
+  const counts = lines[index] ?? ""
+  const atomCount = Number.parseInt(counts.slice(0, 3).trim(), 10)
+  const bondCount = Number.parseInt(counts.slice(3, 6).trim(), 10)
+  if (!Number.isFinite(atomCount) || !Number.isFinite(bondCount)) return
+  const atoms = lines.slice(index + 1, index + 1 + atomCount).flatMap((line) => {
+    const symbol = element(line.slice(31, 34)) ?? element(line.trim().split(/\s+/)[3] ?? "")
+    return symbol ? [symbol] : []
+  })
+  return { atoms, atomCount: atoms.length, bondCount }
+}
+
+function analyzeMol(raw: string, source: MolecularSummary["source"], target: "sdf" | "mol"): MolecularSummary {
+  const chunks = target === "sdf" ? raw.split(/\$\$\$\$/).map((item) => item.trim()).filter(Boolean) : [raw]
+  const records = chunks.flatMap((chunk) => {
+    const value = molRecord(chunk)
+    return value ? [value] : []
+  })
+  const expected = records.reduce((total, record) => total + record.atomCount, 0)
+  return {
+    format: target,
+    source,
+    atomCount: expected,
+    bondCount: records.reduce((total, record) => total + record.bondCount, 0),
+    moleculeCount: records.length,
+    elements: countElements(records.flatMap((record) => record.atoms)),
+    warnings: records.length ? [] : [`No valid V2000 ${target.toUpperCase()} record was parsed.`],
+  }
+}
+
+export function analyzeMolecularSource(data: unknown, kind: string): MolecularSummary | undefined {
+  const value = narrowMolecularSource(data, kind)
+  if (!value) return
+  const source: MolecularSummary["source"] = value.raw === undefined ? "remote" : "inline"
+  if (source === "remote") {
+    return {
+      format: value.format,
+      source,
+      elements: [],
+      warnings: ["Scientific properties are available after the remote structure is loaded."],
+    }
+  }
+  const raw = value.raw ?? ""
+  if (value.format === "xyz") return analyzeXyz(raw, source)
+  if (value.format === "pdb" || value.format === "pdbqt") return analyzePdb(raw, source)
+  if (value.format === "sdf") return analyzeMol(raw, source, "sdf")
+  if (value.format === "mol") return analyzeMol(raw, source, "mol")
+  return {
+    format: value.format,
+    source,
+    elements: [],
+    warnings: ["Detailed scientific properties are not available for this format yet."],
+  }
+}

From 75756d9d06642aa5c1f3f02040bcb6d4a660affe Mon Sep 17 00:00:00 2001
From: Aayam Bansal <aayambansal@gmail.com>
Date: Wed, 29 Jul 2026 14:20:57 +0800
Subject: [PATCH 24/40] feat: add interactive molecular workbench

---
 .../e2e/science-file-viewers.spec.ts          |  17 ++
 .../renderers/molecular/ProteinStructure.tsx  | 241 +++++++++++++++++-
 2 files changed, 257 insertions(+), 1 deletion(-)

diff --git a/frontend/workspace/e2e/science-file-viewers.spec.ts b/frontend/workspace/e2e/science-file-viewers.spec.ts
index 9c752dac..cfdd0b20 100644
--- a/frontend/workspace/e2e/science-file-viewers.spec.ts
+++ b/frontend/workspace/e2e/science-file-viewers.spec.ts
@@ -69,6 +69,23 @@ test("XYZ files open as interactive 3D chemistry with source access", async ({ p
   await expect(summary).toContainText("H 2")
   await expect(summary).toContainText("O 1")
 
+  const structure = artifact.locator('[data-component="mol-structure"]')
+  await expect(structure).toHaveAttribute("data-status", "ready", { timeout: 30_000 })
+  const controls = artifact.locator('[data-component="molecular-controls"]')
+  await expect(controls.getByLabel("Representation")).toHaveValue("auto")
+  await controls.getByLabel("Representation").selectOption("atomic-detail")
+  await expect(controls).toHaveAttribute("data-preset", "atomic-detail")
+  await controls.getByLabel("Selection granularity").selectOption("residue")
+  await expect(controls).toHaveAttribute("data-granularity", "residue")
+  await expect(controls.getByRole("button", { name: "Measure distance", exact: true })).toBeDisabled()
+  await controls.getByRole("button", { name: "Reset camera", exact: true }).click()
+  await controls.getByRole("button", { name: "Light background", exact: true }).click()
+  await expect(controls).toHaveAttribute("data-background", "light")
+
+  const download = page.waitForEvent("download")
+  await controls.getByRole("button", { name: "Export PNG", exact: true }).click()
+  await expect((await download).suggestedFilename()).toMatch(/^water-structure\.png$/)
+
   await page.getByTitle("raw source", { exact: true }).click()
   await expect(page.getByTitle("rendered view", { exact: true })).toBeVisible()
   await expect(page.locator("textarea")).toHaveValue(/water/)
diff --git a/frontend/workspace/src/science/renderers/molecular/ProteinStructure.tsx b/frontend/workspace/src/science/renderers/molecular/ProteinStructure.tsx
index 79489d3e..499813c1 100644
--- a/frontend/workspace/src/science/renderers/molecular/ProteinStructure.tsx
+++ b/frontend/workspace/src/science/renderers/molecular/ProteinStructure.tsx
@@ -27,13 +27,22 @@ import { analyzeMolecularSource, narrowMolecularSource } from "./model"
  */
 
 type Status = "idle" | "loading" | "ready" | "empty" | "error"
+type Preset = "auto" | "polymer-cartoon" | "atomic-detail" | "illustrative" | "molecular-surface"
+type Granularity = "element" | "residue" | "chain"
+type Theme = "dark" | "light"
 
 export function ProteinStructure(props: ArtifactRenderProps): JSX.Element {
   let host!: HTMLDivElement
   const [plugin, setPlugin] = createSignal<PluginContext | undefined>()
   const [status, setStatus] = createSignal<Status>("idle")
   const [error, setError] = createSignal<string>("")
+  const [preset, setPreset] = createSignal<Preset>("auto")
+  const [granularity, setGranularity] = createSignal<Granularity>("element")
+  const [theme, setTheme] = createSignal<Theme>("dark")
+  const [selection, setSelection] = createSignal({ label: "", count: 0, history: 0 })
+  const [measurements, setMeasurements] = createSignal(0)
   const summary = createMemo(() => analyzeMolecularSource(props.data, props.kind))
+  const subscriptions: Array<{ unsubscribe(): void }> = []
   let disposed = false
   let token = 0
 
@@ -62,6 +71,29 @@ export function ProteinStructure(props: ArtifactRenderProps): JSX.Element {
         p.dispose()
         return
       }
+      p.selectionMode = true
+      p.managers.interactivity.setProps({ granularity: granularity() })
+      const syncSelection = () => {
+        const stats = p.managers.structure.selection.stats
+        setSelection({
+          label: stats.label,
+          count: stats.elementCount,
+          history: p.managers.structure.selection.additionsHistory.length,
+        })
+      }
+      const syncMeasurements = () => {
+        const state = p.managers.structure.measurement.state
+        setMeasurements(
+          state.distances.length +
+            state.angles.length +
+            state.dihedrals.length +
+            state.orientations.length +
+            state.planes.length,
+        )
+      }
+      subscriptions.push(p.managers.structure.selection.events.changed.subscribe(syncSelection))
+      subscriptions.push(p.managers.structure.selection.events.additionsHistoryUpdated.subscribe(syncSelection))
+      subscriptions.push(p.managers.structure.measurement.behaviors.state.subscribe(syncMeasurements))
       setPlugin(p)
     } catch (e) {
       if (!disposed) {
@@ -98,7 +130,9 @@ export function ProteinStructure(props: ArtifactRenderProps): JSX.Element {
       if (my !== token || disposed) return
       const trajectory = await p.builders.structure.parseTrajectory(raw, src.format as BuiltInTrajectoryFormat)
       if (my !== token || disposed) return
-      await p.builders.structure.hierarchy.applyPreset(trajectory, "default")
+      await p.builders.structure.hierarchy.applyPreset(trajectory, "default", {
+        representationPreset: preset(),
+      })
       if (my !== token || disposed) return
       p.handleResize()
       setStatus("ready")
@@ -110,9 +144,87 @@ export function ProteinStructure(props: ArtifactRenderProps): JSX.Element {
     }
   }
 
+  async function changePreset(value: Preset) {
+    setPreset(value)
+    const p = plugin()
+    if (!p || status() !== "ready") return
+    await load(p, props.data, props.kind)
+  }
+
+  function changeGranularity(value: Granularity) {
+    setGranularity(value)
+    plugin()?.managers.interactivity.setProps({ granularity: value })
+  }
+
+  async function toggleTheme() {
+    const p = plugin()
+    const next: Theme = theme() === "dark" ? "light" : "dark"
+    setTheme(next)
+    if (!p?.canvas3d) return
+    const { Color } = await import("molstar/lib/mol-util/color")
+    p.canvas3d.setProps({
+      renderer: {
+        ...p.canvas3d.props.renderer,
+        backgroundColor: Color(next === "light" ? 0xf5f6f8 : 0x0b0d12),
+      },
+    })
+  }
+
+  async function measureDistance() {
+    const p = plugin()
+    if (!p) return
+    const history = p.managers.structure.selection.additionsHistory
+    if (history.length < 2) return
+    await p.managers.structure.measurement.addDistance(history[0].loci, history[1].loci)
+  }
+
+  function clearSelection() {
+    const p = plugin()
+    if (!p) return
+    p.managers.interactivity.lociSelects.deselectAll()
+    p.managers.structure.selection.clear()
+  }
+
+  async function clearMeasurements() {
+    const p = plugin()
+    if (!p) return
+    const state = p.managers.structure.measurement.state
+    const cells = [
+      ...state.distances,
+      ...state.angles,
+      ...state.dihedrals,
+      ...state.orientations,
+      ...state.planes,
+    ]
+    if (!cells.length) return
+    const { PluginCommands } = await import("molstar/lib/mol-plugin/commands")
+    await Promise.all(
+      cells.map((cell) => {
+        if (!cell.parent) return Promise.resolve()
+        return PluginCommands.State.RemoveObject(p, {
+          state: cell.parent,
+          ref: cell.transform.parent,
+          removeParentGhosts: true,
+        })
+      }),
+    )
+  }
+
+  function exportName() {
+    const src = narrowMolecularSource(props.data, props.kind)
+    if (!src?.raw || src.format !== "xyz") return "molecule-structure.png"
+    const name = src.raw.split(/\r?\n/)[1]?.trim().toLowerCase().replace(/[^a-z0-9]+/g, "-").replace(/^-|-$/g, "")
+    return `${name || "molecule"}-structure.png`
+  }
+
+  async function exportPng() {
+    await plugin()?.helpers.viewportScreenshot?.download(exportName())
+  }
+
   onCleanup(() => {
     disposed = true
     token++
+    subscriptions.forEach((subscription) => subscription.unsubscribe())
     const p = plugin()
     if (!p) return
     try {
@@ -128,6 +240,7 @@ export function ProteinStructure(props: ArtifactRenderProps): JSX.Element {
     <div
       data-component="mol-structure"
       data-kind={props.kind}
+      data-status={status()}
       style={{
         position: "relative",
         width: "100%",
@@ -138,6 +251,104 @@ export function ProteinStructure(props: ArtifactRenderProps): JSX.Element {
       }}
     >
       <div ref={host} style={{ position: "absolute", inset: "0" }} />
+      <div
+        data-component="molecular-controls"
+        data-preset={preset()}
+        data-granularity={granularity()}
+        data-background={theme()}
+        style={{
+          position: "absolute",
+          top: "12px",
+          left: "12px",
+          right: "12px",
+          display: "flex",
+          "align-items": "center",
+          gap: "6px",
+          "flex-wrap": "wrap",
+          "z-index": 3,
+          "pointer-events": status() === "ready" ? "auto" : "none",
+          opacity: status() === "ready" ? 1 : 0,
+          transition: "opacity 160ms ease",
+        }}
+      >
+        <select
+          aria-label="Representation"
+          value={preset()}
+          onChange={(event) => void changePreset(event.currentTarget.value as Preset)}
+          style={selectStyle()}
+        >
+          <option value="auto">Automatic</option>
+          <option value="polymer-cartoon">Polymer cartoon</option>
+          <option value="atomic-detail">Atomic detail</option>
+          <option value="illustrative">Illustrative</option>
+          <option value="molecular-surface">Molecular surface</option>
+        </select>
+        <select
+          aria-label="Selection granularity"
+          value={granularity()}
+          onChange={(event) => changeGranularity(event.currentTarget.value as Granularity)}
+          style={selectStyle()}
+        >
+          <option value="element">Atom selection</option>
+          <option value="residue">Residue selection</option>
+          <option value="chain">Chain selection</option>
+        </select>
+        <button type="button" style={buttonStyle()} onClick={() => plugin()?.managers.camera.reset()}>
+          Reset camera
+        </button>
+        <button type="button" style={buttonStyle()} onClick={() => void toggleTheme()}>
+          {theme() === "dark" ? "Light background" : "Dark background"}
+        </button>
+        <button type="button" style={buttonStyle()} onClick={() => void exportPng()}>
+          Export PNG
+        </button>
+        <button
+          type="button"
+          style={buttonStyle()}
+          disabled={selection().history < 2}
+          onClick={() => void measureDistance()}
+        >
+          Measure distance
+        </button>
+        <Show when={selection().count > 0}>
+          <button type="button" style={buttonStyle()} onClick={clearSelection}>
+            Clear selection
+          </button>
+        </Show>
+        <Show when={measurements() > 0}>
+          <button type="button" style={buttonStyle()} onClick={() => void clearMeasurements()}>
+            Clear measurements
+          </button>
+        </Show>
+      </div>
+      <Show when={selection().count > 0 || measurements() > 0}>
+        <div
+          data-component="molecular-selection"
+          style={{
+            position: "absolute",
+            top: "58px",
+            left: "12px",
+            padding: "7px 9px",
+            "border-radius": "6px",
+            border: "1px solid rgba(255,255,255,0.14)",
+            background: "rgba(9, 12, 18, 0.82)",
+            color: "#e8ebf2",
+            font: "11px/1.35 ui-sans-serif, system-ui, sans-serif",
+            "backdrop-filter": "blur(12px)",
+            "z-index": 2,
+          }}
+        >
+          <Show when={selection().count > 0}>
+            <span>{selection().label || `${selection().count} selected atoms`}</span>
+          </Show>
+          <Show when={selection().count > 0 && measurements() > 0}> · </Show>
+          <Show when={measurements() > 0}>
+            <span>
+              {measurements()} measurement{measurements() === 1 ? "" : "s"}
+            </span>
+          </Show>
+        </div>
+      </Show>
       <Show when={summary()}>
         {(value) => (
           <div
@@ -236,4 +447,32 @@ export function ProteinStructure(props: ArtifactRenderProps): JSX.Element {
   )
 }
 
+function selectStyle(): JSX.CSSProperties {
+  return {
+    height: "30px",
+    padding: "0 27px 0 9px",
+    border: "1px solid rgba(255,255,255,0.17)",
+    "border-radius": "6px",
+    background: "rgba(9, 12, 18, 0.88)",
+    color: "#eef1f6",
+    font: "11px/1 ui-sans-serif, system-ui, sans-serif",
+    "backdrop-filter": "blur(12px)",
+    cursor: "pointer",
+  }
+}
+
+function buttonStyle(): JSX.CSSProperties {
+  return {
+    height: "30px",
+    padding: "0 9px",
+    border: "1px solid rgba(255,255,255,0.17)",
+    "border-radius": "6px",
+    background: "rgba(9, 12, 18, 0.88)",
+    color: "#eef1f6",
+    font: "11px/1 ui-sans-serif, system-ui, sans-serif",
+    "backdrop-filter": "blur(12px)",
+    cursor: "pointer",
+  }
+}
+
 export default ProteinStructure

From e875fef10c261c01ae9b9154fe5d33d781deb869 Mon Sep 17 00:00:00 2001
From: Aayam Bansal <aayambansal@gmail.com>
Date: Wed, 29 Jul 2026 14:26:26 +0800
Subject: [PATCH 25/40] feat: add artifact review annotations

---
 backend/cli/src/file/annotations.ts           | 136 ++++++++
 backend/cli/src/server/routes/file.ts         |  66 ++++
 backend/cli/test/server/file-research.test.ts |  44 +++
 .../workspace/e2e/artifact-inspector.spec.ts  |  26 ++
 .../src/artifacts/ArtifactInspector.tsx       | 309 +++++++++++++++++-
 .../workspace/src/artifacts/context.test.ts   |  20 ++
 frontend/workspace/src/artifacts/context.ts   |   4 +
 .../workspace/src/artifacts/inspector.test.ts |   2 +-
 frontend/workspace/src/artifacts/inspector.ts |   6 +-
 frontend/workspace/src/atlas/FilePreview.tsx  |  10 +-
 .../workspace/src/science/ScienceArtifact.tsx |  13 +-
 .../renderers/molecular/ProteinStructure.tsx  |  30 ++
 .../src/science/renderers/registry.ts         |  12 +
 13 files changed, 668 insertions(+), 10 deletions(-)
 create mode 100644 backend/cli/src/file/annotations.ts

diff --git a/backend/cli/src/file/annotations.ts b/backend/cli/src/file/annotations.ts
new file mode 100644
index 00000000..b95d99d1
--- /dev/null
+++ b/backend/cli/src/file/annotations.ts
@@ -0,0 +1,136 @@
+import path from "node:path"
+import { ulid } from "ulid"
+import z from "zod"
+import { Instance } from "../project/instance"
+import { Storage } from "../storage/storage"
+
+export namespace ArtifactAnnotation {
+  export const Anchor = z.discriminatedUnion("kind", [
+    z.object({
+      kind: z.literal("artifact"),
+      label: z.string().trim().max(500).optional(),
+    }),
+    z.object({
+      kind: z.literal("text"),
+      startLine: z.number().int().min(1),
+      endLine: z.number().int().min(1),
+      quote: z.string().max(10_000).optional(),
+    }),
+    z.object({
+      kind: z.literal("notebook"),
+      cellId: z.string().trim().min(1).max(500),
+      line: z.number().int().min(1).optional(),
+    }),
+    z.object({
+      kind: z.literal("molecule"),
+      selection: z.string().trim().min(1).max(2_000),
+      count: z.number().int().min(1).optional(),
+    }),
+    z.object({
+      kind: z.literal("genome"),
+      chromosome: z.string().trim().min(1).max(200),
+      start: z.number().int().min(0),
+      end: z.number().int().min(0),
+    }),
+  ])
+  export type Anchor = z.infer<typeof Anchor>
+
+  export const Message = z.object({
+    id: z.string(),
+    body: z.string(),
+    author: z.string(),
+    createdAt: z.number(),
+  })
+  export type Message = z.infer<typeof Message>
+
+  export const Info = z.object({
+    id: z.string(),
+    projectID: z.string(),
+    path: z.string(),
+    anchor: Anchor,
+    messages: Message.array(),
+    status: z.enum(["open", "resolved"]),
+    createdAt: z.number(),
+    updatedAt: z.number(),
+  })
+  export type Info = z.infer<typeof Info>
+
+  export const Create = z.object({
+    path: z.string().trim().min(1).max(10_000),
+    body: z.string().trim().min(1).max(100_000),
+    author: z.string().trim().min(1).max(200).optional(),
+    anchor: Anchor.default({ kind: "artifact" }),
+  })
+  export type Create = z.infer<typeof Create>
+
+  export const Update = z
+    .object({
+      status: z.enum(["open", "resolved"]).optional(),
+      reply: z.string().trim().min(1).max(100_000).optional(),
+      author: z.string().trim().min(1).max(200).optional(),
+    })
+    .refine((value) => value.status !== undefined || value.reply !== undefined, "No annotation update supplied")
+  export type Update = z.infer<typeof Update>
+
+  const prefix = () => ["artifact_annotation", Instance.project.id]
+  const key = (id: string) => [...prefix(), id]
+
+  async function target(value: string) {
+    const absolute = path.resolve(Instance.directory, value)
+    if (!(await Instance.containsCanonicalPath(absolute))) {
+      throw new Error(`Annotation target is outside the project: ${value}`)
+    }
+    return path.relative(Instance.directory, absolute).replaceAll("\\", "/")
+  }
+
+  export async function list(filepath: string) {
+    const relative = await target(filepath)
+    const keys = await Storage.list(prefix())
+    const records = await Promise.all(keys.map((item) => Storage.read<Info>(item)))
+    return records.filter((item) => item.path === relative).toSorted((a, b) => a.createdAt - b.createdAt)
+  }
+
+  export async function create(input: Create) {
+    const now = Date.now()
+    const id = `ann_${ulid()}`
+    const record: Info = {
+      id,
+      projectID: Instance.project.id,
+      path: await target(input.path),
+      anchor: input.anchor,
+      messages: [
+        {
+          id: `msg_${ulid()}`,
+          body: input.body,
+          author: input.author ?? "You",
+          createdAt: now,
+        },
+      ],
+      status: "open",
+      createdAt: now,
+      updatedAt: now,
+    }
+    await Storage.write(key(id), record)
+    return record
+  }
+
+  export async function update(id: string, input: Update) {
+    return Storage.update<Info>(key(id), (record) => {
+      if (input.status) record.status = input.status
+      if (input.reply) {
+        record.messages.push({
+          id: `msg_${ulid()}`,
+          body: input.reply,
+          author: input.author ?? "You",
+          createdAt: Date.now(),
+        })
+      }
+      record.updatedAt = Date.now()
+    })
+  }
+
+  export async function remove(id: string) {
+    await Storage.remove(key(id))
+    return { deleted: true as const }
+  }
+}
diff --git a/backend/cli/src/server/routes/file.ts b/backend/cli/src/server/routes/file.ts
index c8fa2f6f..59436219 100644
--- a/backend/cli/src/server/routes/file.ts
+++ b/backend/cli/src/server/routes/file.ts
@@ -10,6 +10,7 @@ import { ScienceFile } from "../../file/science"
 import { ArtifactFile } from "../../file/artifacts"
 import { StarterFile } from "../../file/starters"
 import { PublicationFile } from "../../file/publication"
+import { ArtifactAnnotation } from "../../file/annotations"
 
 export const FileRoutes = lazy(() =>
   new Hono()
@@ -324,6 +325,71 @@ export const FileRoutes = lazy(() =>
       }),
       async (c) => c.json(await File.reproducibility()),
     )
+    .get(
+      "/file/annotations",
+      describeRoute({
+        summary: "List artifact annotations",
+        description: "List durable review threads anchored to a project artifact.",
+        operationId: "file.annotations.list",
+        responses: {
+          200: {
+            description: "Artifact annotations",
+            content: { "application/json": { schema: resolver(ArtifactAnnotation.Info.array()) } },
+          },
+        },
+      }),
+      validator("query", z.object({ path: z.string() })),
+      async (c) => c.json(await ArtifactAnnotation.list(c.req.valid("query").path)),
+    )
+    .post(
+      "/file/annotations",
+      describeRoute({
+        summary: "Create an artifact annotation",
+        description: "Create a durable review thread anchored to an artifact, text range, notebook cell, molecule, or locus.",
+        operationId: "file.annotations.create",
+        responses: {
+          200: {
+            description: "Created annotation",
+            content: { "application/json": { schema: resolver(ArtifactAnnotation.Info) } },
+          },
+        },
+      }),
+      validator("json", ArtifactAnnotation.Create),
+      async (c) => c.json(await ArtifactAnnotation.create(c.req.valid("json"))),
+    )
+    .patch(
+      "/file/annotations/:id",
+      describeRoute({
+        summary: "Update an artifact annotation",
+        description: "Reply to, resolve, or reopen an artifact review thread.",
+        operationId: "file.annotations.update",
+        responses: {
+          200: {
+            description: "Updated annotation",
+            content: { "application/json": { schema: resolver(ArtifactAnnotation.Info) } },
+          },
+        },
+      }),
+      validator("param", z.object({ id: z.string().startsWith("ann_") })),
+      validator("json", ArtifactAnnotation.Update),
+      async (c) => c.json(await ArtifactAnnotation.update(c.req.valid("param").id, c.req.valid("json"))),
+    )
+    .delete(
+      "/file/annotations/:id",
+      describeRoute({
+        summary: "Delete an artifact annotation",
+        description: "Permanently remove an artifact review thread.",
+        operationId: "file.annotations.delete",
+        responses: {
+          200: {
+            description: "Deleted annotation",
+            content: { "application/json": { schema: resolver(z.object({ deleted: z.literal(true) })) } },
+          },
+        },
+      }),
+      validator("param", z.object({ id: z.string().startsWith("ann_") })),
+      async (c) => c.json(await ArtifactAnnotation.remove(c.req.valid("param").id)),
+    )
     .get(
       "/file/manifest",
       describeRoute({
diff --git a/backend/cli/test/server/file-research.test.ts b/backend/cli/test/server/file-research.test.ts
index 36eeb07f..5fffe6f0 100644
--- a/backend/cli/test/server/file-research.test.ts
+++ b/backend/cli/test/server/file-research.test.ts
@@ -67,4 +67,48 @@ describe("/file research routes", () => {
       },
     })
   })
+
+  test("creates, resolves, and deletes durable artifact annotations", async () => {
+    await using tmp = await tmpdir({
+      init: async (directory) => {
+        await Bun.write(path.join(directory, "results.csv"), "metric,value\naccuracy,0.9\n")
+      },
+    })
+    await Instance.provide({
+      directory: tmp.path,
+      fn: async () => {
+        const created = await FileRoutes().request("/file/annotations", {
+          method: "POST",
+          headers: { "Content-Type": "application/json" },
+          body: JSON.stringify({
+            path: "results.csv",
+            body: "Verify this value against the held-out split.",
+            anchor: { kind: "text", startLine: 2, endLine: 2, quote: "accuracy,0.9" },
+          }),
+        })
+        expect(created.status).toBe(200)
+        const note = (await created.json()) as { id: string; status: string; anchor: { kind: string } }
+        expect(note.id).toStartWith("ann_")
+        expect(note.status).toBe("open")
+        expect(note.anchor.kind).toBe("text")
+
+        const listed = await FileRoutes().request("/file/annotations?path=results.csv")
+        expect(listed.status).toBe(200)
+        expect((await listed.json()) as unknown[]).toHaveLength(1)
+
+        const resolved = await FileRoutes().request(`/file/annotations/${note.id}`, {
+          method: "PATCH",
+          headers: { "Content-Type": "application/json" },
+          body: JSON.stringify({ status: "resolved" }),
+        })
+        expect(resolved.status).toBe(200)
+        expect(((await resolved.json()) as { status: string }).status).toBe("resolved")
+
+        const removed = await FileRoutes().request(`/file/annotations/${note.id}`, { method: "DELETE" })
+        expect(removed.status).toBe(200)
+        expect(await removed.json()).toEqual({ deleted: true })
+        expect(await (await FileRoutes().request("/file/annotations?path=results.csv")).json()).toEqual([])
+      },
+    })
+  })
 })
diff --git a/frontend/workspace/e2e/artifact-inspector.spec.ts b/frontend/workspace/e2e/artifact-inspector.spec.ts
index 57fbbef6..d8760665 100644
--- a/frontend/workspace/e2e/artifact-inspector.spec.ts
+++ b/frontend/workspace/e2e/artifact-inspector.spec.ts
@@ -29,6 +29,8 @@ test("opened files drive a contextual artifact inspector without stale state", a
   await expect(inspector).toHaveAttribute("data-artifact-id", /water\.xyz/)
   await expect(inspector.locator("header strong")).toHaveText("water.xyz")
   await expect(inspector.getByRole("tab")).toHaveCount(7)
+  await expect(inspector.getByText("3 atoms", { exact: true })).toBeVisible()
+  await expect(inspector.getByText("PNG export", { exact: true })).toBeVisible()
 
   const details = inspector.getByRole("tab", { name: "Details", exact: true })
   await details.focus()
@@ -67,3 +69,27 @@ test("artifact inspector overlays rather than crushing the workbench at narrow d
   expect(fileBox?.width).toBeGreaterThanOrEqual(520)
   expect(inspectorBox?.x).toBeGreaterThan(fileBox?.x ?? 0)
 })
+
+test("artifact review threads persist and can be resolved", async ({ page, directory, gotoSession }) => {
+  await gotoSession()
+  await openFile(page, directory, "frontend/workspace/e2e/science/water.xyz")
+
+  const inspector = page.locator('[data-component="artifact-inspector"]')
+  await inspector.getByRole("tab", { name: "Review", exact: true }).click()
+  await expect(inspector.getByText("No annotations yet", { exact: true })).toBeVisible()
+
+  await inspector.getByLabel("New annotation").fill("Confirm the O–H bond length before publication.")
+  await inspector.getByRole("button", { name: "Add annotation", exact: true }).click()
+  const thread = inspector.locator('[data-component="artifact-annotation"]').filter({ hasText: "Confirm the O–H" })
+  await expect(thread).toBeVisible()
+  await expect(inspector.getByText("1 open", { exact: true })).toBeVisible()
+
+  await thread.getByRole("button", { name: "Resolve", exact: true }).click()
+  await expect(thread.getByText("Resolved", { exact: true })).toBeVisible()
+
+  await openFile(page, directory, "frontend/workspace/e2e/science/alignment.fasta")
+  await openFile(page, directory, "frontend/workspace/e2e/science/water.xyz")
+  await inspector.getByRole("tab", { name: "Review", exact: true }).click()
+  await expect(inspector.getByText("Confirm the O–H bond length before publication.", { exact: true })).toBeVisible()
+  await expect(inspector.getByText("0 open", { exact: true })).toBeVisible()
+})
diff --git a/frontend/workspace/src/artifacts/ArtifactInspector.tsx b/frontend/workspace/src/artifacts/ArtifactInspector.tsx
index 9799b5a6..79a70ad5 100644
--- a/frontend/workspace/src/artifacts/ArtifactInspector.tsx
+++ b/frontend/workspace/src/artifacts/ArtifactInspector.tsx
@@ -46,6 +46,48 @@ const labels: Record<InspectorTab, string> = {
   history: "History",
 }
 
+interface AnnotationMessage {
+  id: string
+  body: string
+  author: string
+  createdAt: number
+}
+
+interface Annotation {
+  id: string
+  path: string
+  anchor: {
+    kind: "artifact" | "text" | "notebook" | "molecule" | "genome"
+    label?: string
+    startLine?: number
+    endLine?: number
+    selection?: string
+    chromosome?: string
+    start?: number
+    end?: number
+    cellId?: string
+  }
+  messages: AnnotationMessage[]
+  status: "open" | "resolved"
+  createdAt: number
+  updatedAt: number
+}
+
+function annotations(value: unknown): Annotation[] {
+  if (!Array.isArray(value)) return []
+  return value.filter((item): item is Annotation => {
+    if (!item || typeof item !== "object") return false
+    const row = item as Partial<Annotation>
+    return (
+      typeof row.id === "string" &&
+      (row.status === "open" || row.status === "resolved") &&
+      Array.isArray(row.messages) &&
+      !!row.anchor &&
+      typeof row.anchor.kind === "string"
+    )
+  })
+}
+
 export function ArtifactInspector(props: { context: ArtifactContext; onClose?: () => void }): JSX.Element {
   const sdk = useSDK()
   const platform = usePlatform()
@@ -63,12 +105,13 @@ export function ArtifactInspector(props: { context: ArtifactContext; onClose?: (
         if (!response?.ok) return
         return response.json().catch(() => undefined)
       }
-      const [file, provenance, audit] = await Promise.all([
+      const [file, provenance, audit, notes] = await Promise.all([
         read("/file/content", current.path),
         read("/file/provenance", current.path),
         read("/file/reproducibility"),
+        read("/file/annotations", current.path),
       ])
-      return { id: current.id, file, provenance, audit }
+      return { id: current.id, file, provenance, audit, notes }
     },
   )
   const model = createMemo<InspectorData>(() => {
@@ -104,6 +147,34 @@ export function ArtifactInspector(props: { context: ArtifactContext; onClose?: (
     anchor.click()
     URL.revokeObjectURL(object)
   }
+  const mutateAnnotation = async (route: string, method: "POST" | "PATCH", body: Record<string, unknown>) => {
+    const response = await request()(url(route), {
+      method,
+      headers: { "Content-Type": "application/json" },
+      body: JSON.stringify(body),
+    }).catch(() => undefined)
+    if (!response?.ok) {
+      toast.error("annotation failed", response ? `${response.status}` : "request failed")
+      return false
+    }
+    await api.refetch()
+    return true
+  }
+  const addAnnotation = (body: string) =>
+    mutateAnnotation("/file/annotations", "POST", {
+      path: props.context.path,
+      body,
+      anchor:
+        props.context.inspection?.selection?.kind === "molecule"
+          ? {
+              kind: "molecule",
+              selection: props.context.inspection.selection.label,
+              count: props.context.inspection.selection.count,
+            }
+          : { kind: "artifact", label: props.context.name },
+    })
+  const updateAnnotation = (id: string, body: Record<string, unknown>) =>
+    mutateAnnotation(`/file/annotations/${id}`, "PATCH", body)
 
   const move = (event: KeyboardEvent, current: InspectorTab) => {
     const index = inspectorTabs.indexOf(current)
@@ -269,7 +340,11 @@ export function ArtifactInspector(props: { context: ArtifactContext; onClose?: (
               <Environment data={model()} />
             </Match>
             <Match when={tab() === "review"}>
-              <Empty state={model().tabs.review} icon="review" />
+              <Review
+                annotations={annotations(records()?.notes)}
+                onAdd={addAnnotation}
+                onUpdate={updateAnnotation}
+              />
             </Match>
             <Match when={tab() === "history"}>
               <History data={model()} />
@@ -281,6 +356,197 @@ export function ArtifactInspector(props: { context: ArtifactContext; onClose?: (
   )
 }
 
+function Review(props: {
+  annotations: Annotation[]
+  onAdd(body: string): Promise<boolean>
+  onUpdate(id: string, body: Record<string, unknown>): Promise<boolean>
+}): JSX.Element {
+  const [body, setBody] = createSignal("")
+  const [busy, setBusy] = createSignal(false)
+  const open = () => props.annotations.filter((item) => item.status === "open").length
+  const add = async () => {
+    const value = body().trim()
+    if (!value || busy()) return
+    setBusy(true)
+    const ok = await props.onAdd(value)
+    setBusy(false)
+    if (ok) setBody("")
+  }
+  return (
+    <div style={{ display: "grid", gap: "12px" }}>
+      <section style={card()}>
+        <div style={{ display: "flex", "align-items": "center", "justify-content": "space-between", gap: "8px" }}>
+          <Heading icon="review">Review threads</Heading>
+          <span
+            style={{
+              "font-family": FONT_MONO,
+              "font-size": "10px",
+              color: open() ? "var(--color-warning)" : "var(--color-text-faint)",
+            }}
+          >
+            {open()} open
+          </span>
+        </div>
+        <textarea
+          aria-label="New annotation"
+          value={body()}
+          rows={3}
+          placeholder="Record a question, correction, or publication check…"
+          onInput={(event) => setBody(event.currentTarget.value)}
+          style={{
+            width: "100%",
+            resize: "vertical",
+            "box-sizing": "border-box",
+            padding: "9px 10px",
+            border: "1px solid var(--color-border)",
+            "border-radius": "6px",
+            outline: "none",
+            background: "var(--color-bg)",
+            color: "var(--color-text)",
+            "font-family": FONT_SANS,
+            "font-size": "11px",
+            "line-height": 1.5,
+          }}
+        />
+        <button
+          type="button"
+          disabled={!body().trim() || busy()}
+          style={{ ...actionButton(true), opacity: !body().trim() || busy() ? 0.45 : 1 }}
+          onClick={() => void add()}
+        >
+          {busy() ? "Adding…" : "Add annotation"}
+        </button>
+      </section>
+      <Show
+        when={props.annotations.length}
+        fallback={
+          <div style={{ ...card(), "justify-items": "start" }}>
+            <strong style={{ "font-family": FONT_SANS, "font-size": "12px", color: "var(--color-text)" }}>
+              No annotations yet
+            </strong>
+            <p style={copyStyle()}>Add the first review note. Threads persist with this project and artifact.</p>
+          </div>
+        }
+      >
+        <For each={props.annotations}>
+          {(item) => <AnnotationThread annotation={item} onUpdate={props.onUpdate} />}
+        </For>
+      </Show>
+    </div>
+  )
+}
+
+function AnnotationThread(props: {
+  annotation: Annotation
+  onUpdate(id: string, body: Record<string, unknown>): Promise<boolean>
+}): JSX.Element {
+  const [reply, setReply] = createSignal("")
+  const [busy, setBusy] = createSignal(false)
+  const update = async (body: Record<string, unknown>) => {
+    if (busy()) return
+    setBusy(true)
+    const ok = await props.onUpdate(props.annotation.id, body)
+    setBusy(false)
+    if (ok && typeof body.reply === "string") setReply("")
+  }
+  const anchor = () => {
+    const value = props.annotation.anchor
+    if (value.kind === "text") return `Lines ${value.startLine}–${value.endLine}`
+    if (value.kind === "molecule") return value.selection ?? "Molecular selection"
+    if (value.kind === "genome") return `${value.chromosome}:${value.start}–${value.end}`
+    if (value.kind === "notebook") return `Cell ${value.cellId}`
+    return value.label ?? "Whole artifact"
+  }
+  return (
+    <article data-component="artifact-annotation" data-status={props.annotation.status} style={card()}>
+      <div style={{ display: "flex", "align-items": "center", gap: "8px" }}>
+        <span
+          style={{
+            padding: "3px 6px",
+            "border-radius": "999px",
+            background:
+              props.annotation.status === "open" ? "var(--color-warning-subtle)" : "var(--color-success-subtle)",
+            color: props.annotation.status === "open" ? "var(--color-warning)" : "var(--color-success)",
+            "font-family": FONT_SANS,
+            "font-size": "9px",
+            "font-weight": 650,
+            "text-transform": "capitalize",
+          }}
+        >
+          {props.annotation.status === "open" ? "Open" : "Resolved"}
+        </span>
+        <span
+          title={anchor()}
+          style={{
+            flex: 1,
+            overflow: "hidden",
+            "text-overflow": "ellipsis",
+            "white-space": "nowrap",
+            "font-family": FONT_MONO,
+            "font-size": "9px",
+            color: "var(--color-text-faint)",
+          }}
+        >
+          {anchor()}
+        </span>
+        <button
+          type="button"
+          disabled={busy()}
+          style={quietButton()}
+          onClick={() =>
+            void update({ status: props.annotation.status === "open" ? "resolved" : "open" })
+          }
+        >
+          {props.annotation.status === "open" ? "Resolve" : "Reopen"}
+        </button>
+      </div>
+      <For each={props.annotation.messages}>
+        {(message) => (
+          <div style={{ display: "grid", gap: "4px", padding: "8px 0", "border-top": "1px solid var(--color-border)" }}>
+            <p style={{ ...copyStyle(), color: "var(--color-text)" }}>{message.body}</p>
+            <span style={{ "font-family": FONT_MONO, "font-size": "9px", color: "var(--color-text-faint)" }}>
+              {message.author} · {new Date(message.createdAt).toLocaleString()}
+            </span>
+          </div>
+        )}
+      </For>
+      <div style={{ display: "flex", gap: "6px" }}>
+        <input
+          aria-label={`Reply to ${props.annotation.id}`}
+          value={reply()}
+          placeholder="Reply…"
+          onInput={(event) => setReply(event.currentTarget.value)}
+          onKeyDown={(event) => {
+            if (event.key !== "Enter" || !reply().trim()) return
+            event.preventDefault()
+            void update({ reply: reply().trim() })
+          }}
+          style={{
+            flex: 1,
+            "min-width": 0,
+            padding: "7px 8px",
+            border: "1px solid var(--color-border)",
+            "border-radius": "5px",
+            outline: "none",
+            background: "var(--color-bg)",
+            color: "var(--color-text)",
+            "font-family": FONT_SANS,
+            "font-size": "10px",
+          }}
+        />
+        <button
+          type="button"
+          disabled={!reply().trim() || busy()}
+          style={{ ...quietButton(), border: "1px solid var(--color-border)" }}
+          onClick={() => void update({ reply: reply().trim() })}
+        >
+          Reply
+        </button>
+      </div>
+    </article>
+  )
+}
+
 function Details(props: { data: InspectorData }): JSX.Element {
   return (
     <div style={{ display: "grid", gap: "12px" }}>
@@ -295,6 +561,43 @@ function Details(props: { data: InspectorData }): JSX.Element {
           <Fact label="renderer" value={props.data.context.scienceKind!} mono />
         </Show>
       </section>
+      <Show when={props.data.context.inspection}>
+        {(inspection) => (
+          <>
+            <section style={card()}>
+              <Heading icon="details">Scientific properties</Heading>
+              <For each={inspection().facts}>
+                {(item) => <Fact label={item.label} value={item.value} mono />}
+              </For>
+              <Show when={inspection().selection}>
+                {(selection) => <Fact label="selection" value={selection().label} />}
+              </Show>
+            </section>
+            <section style={card()}>
+              <Heading icon="details">Available operations</Heading>
+              <div style={{ display: "flex", gap: "5px", "flex-wrap": "wrap" }}>
+                <For each={inspection().capabilities}>
+                  {(item) => (
+                    <span
+                      style={{
+                        padding: "4px 6px",
+                        "border-radius": "5px",
+                        border: "1px solid var(--color-border)",
+                        background: "var(--color-bg)",
+                        "font-family": FONT_SANS,
+                        "font-size": "10px",
+                        color: "var(--color-text-muted)",
+                      }}
+                    >
+                      {item}
+                    </span>
+                  )}
+                </For>
+              </div>
+            </section>
+          </>
+        )}
+      </Show>
       <section style={card()}>
         <Heading icon="history">Provenance</Heading>
         <Show
diff --git a/frontend/workspace/src/artifacts/context.test.ts b/frontend/workspace/src/artifacts/context.test.ts
index 479b661e..caa07293 100644
--- a/frontend/workspace/src/artifacts/context.test.ts
+++ b/frontend/workspace/src/artifacts/context.test.ts
@@ -49,6 +49,26 @@ describe("artifact context", () => {
     expect(inferArtifactKind("result.dat", "genome-track")).toBe("genomics")
   })
 
+  test("carries live scientific facts, capabilities, and selections without changing artifact identity", () => {
+    const context = createArtifactContext({
+      directory: "/work/project",
+      path: "results/water.xyz",
+      scienceKind: "chem-3d",
+      inspection: {
+        facts: [{ label: "atoms", value: "3" }],
+        capabilities: ["Representations", "PNG export"],
+        selection: { kind: "molecule", label: "O 1", count: 1 },
+      },
+    })
+
+    expect(context.id).toContain("water.xyz")
+    expect(context.inspection).toEqual({
+      facts: [{ label: "atoms", value: "3" }],
+      capabilities: ["Representations", "PNG export"],
+      selection: { kind: "molecule", label: "O 1", count: 1 },
+    })
+  })
+
   test("only the owning document can clear active artifact state", () => {
     const active: ArtifactContext = createArtifactContext({
       directory: "/work/project",
diff --git a/frontend/workspace/src/artifacts/context.ts b/frontend/workspace/src/artifacts/context.ts
index e2e97885..9259a803 100644
--- a/frontend/workspace/src/artifacts/context.ts
+++ b/frontend/workspace/src/artifacts/context.ts
@@ -1,5 +1,6 @@
 import { createSignal } from "solid-js"
 import type { ArtifactKind } from "./model"
+import type { ArtifactInspection } from "@/science/renderers"
 
 export type ArtifactContextKind = ArtifactKind | "file"
 
@@ -11,6 +12,7 @@ export interface ArtifactContext {
   format: string
   kind: ArtifactContextKind
   scienceKind?: string
+  inspection?: ArtifactInspection
 }
 
 export interface ArtifactContextInput {
@@ -18,6 +20,7 @@ export interface ArtifactContextInput {
   path: string
   format?: string
   scienceKind?: string
+  inspection?: ArtifactInspection
 }
 
 const kinds: Partial<Record<string, ArtifactContextKind>> = {
@@ -147,6 +150,7 @@ export function createArtifactContext(input: ArtifactContextInput): ArtifactCont
     format,
     kind: inferArtifactKind(path, input.scienceKind),
     ...(input.scienceKind ? { scienceKind: input.scienceKind } : {}),
+    ...(input.inspection ? { inspection: input.inspection } : {}),
   }
 }
 
diff --git a/frontend/workspace/src/artifacts/inspector.test.ts b/frontend/workspace/src/artifacts/inspector.test.ts
index f6f33c92..1eec2fc1 100644
--- a/frontend/workspace/src/artifacts/inspector.test.ts
+++ b/frontend/workspace/src/artifacts/inspector.test.ts
@@ -46,7 +46,7 @@ describe("artifact inspector model", () => {
     expect(result.tabs.history.available).toBe(true)
     expect(result.tabs.run.available).toBe(false)
     expect(result.tabs.messages.available).toBe(false)
-    expect(result.tabs.review.available).toBe(false)
+    expect(result.tabs.review.available).toBe(true)
   })
 
   test("keeps malformed and absent records honest instead of inventing metadata", () => {
diff --git a/frontend/workspace/src/artifacts/inspector.ts b/frontend/workspace/src/artifacts/inspector.ts
index a75d18e7..4068ab7d 100644
--- a/frontend/workspace/src/artifacts/inspector.ts
+++ b/frontend/workspace/src/artifacts/inspector.ts
@@ -134,9 +134,9 @@ export function normalizeInspectorData(context: ArtifactContext, input: Inspecto
         ? state(true, "Environment records found", "Project environment specifications and lockfiles are available.")
         : state(false, "No environment is recorded", "Add a lockfile or environment specification to this project."),
       review: state(
-        false,
-        "No review report is recorded",
-        "Run scientific review before treating this artifact as publication-ready.",
+        true,
+        "Artifact review",
+        "Durable annotations and review threads are available for this artifact.",
       ),
       history: version?.commit
         ? state(true, "Git provenance available", "The latest commit touching this artifact is recorded.")
diff --git a/frontend/workspace/src/atlas/FilePreview.tsx b/frontend/workspace/src/atlas/FilePreview.tsx
index 099aea45..44426f52 100644
--- a/frontend/workspace/src/atlas/FilePreview.tsx
+++ b/frontend/workspace/src/atlas/FilePreview.tsx
@@ -27,6 +27,7 @@ import { NotebookView } from "@/notebook/NotebookView"
 import { DataTableView } from "@/data/DataTableView"
 import type { TableFormat } from "@/data/table"
 import { artifactContext, createArtifactContext } from "@/artifacts/context"
+import type { ArtifactInspection } from "@/science/renderers"
 import { toast } from "@/atlas/Toast"
 import { IconFile, IconX, IconCopy, IconDownload, IconBookOpen, IconBraces, IconRefresh } from "@/atlas/shared/Icon"
 
@@ -151,6 +152,7 @@ export function FileView(props: {
   const [savedText, setSavedText] = createSignal("")
   const [saving, setSaving] = createSignal(false)
   const [refreshKey, setRefreshKey] = createSignal(0)
+  const [inspection, setInspection] = createSignal<ArtifactInspection>()
 
   const [file] = createResource(
     () => [directory(), props.path, refreshKey()] as const,
@@ -216,6 +218,7 @@ export function FileView(props: {
       path: props.path,
       format: badge(),
       scienceKind: scientific()?.kind,
+      inspection: inspection(),
     }),
   )
 
@@ -557,7 +560,12 @@ export function FileView(props: {
                         "box-sizing": "border-box",
                       }}
                     >
-                      <ScienceArtifact kind={artifact().kind} data={artifact().data} height={560} />
+                      <ScienceArtifact
+                        kind={artifact().kind}
+                        data={artifact().data}
+                        height={560}
+                        onInspect={setInspection}
+                      />
                     </div>
                   )}
                 </Show>
diff --git a/frontend/workspace/src/science/ScienceArtifact.tsx b/frontend/workspace/src/science/ScienceArtifact.tsx
index 0f52d57d..35d0e9f0 100644
--- a/frontend/workspace/src/science/ScienceArtifact.tsx
+++ b/frontend/workspace/src/science/ScienceArtifact.tsx
@@ -1,6 +1,6 @@
 import { Show, createMemo, type JSX } from "solid-js"
 import { Dynamic } from "solid-js/web"
-import { get, type ArtifactKind } from "./renderers"
+import { get, type ArtifactInspection, type ArtifactKind } from "./renderers"
 
 /**
  * Dispatcher for scientific artifacts rendered inline in chat.
@@ -18,6 +18,7 @@ export interface ScienceArtifactProps {
   kind: ArtifactKind
   data: unknown
   height?: number
+  onInspect?: (inspection: ArtifactInspection) => void
 }
 
 export function ScienceArtifact(props: ScienceArtifactProps): JSX.Element {
@@ -26,7 +27,15 @@ export function ScienceArtifact(props: ScienceArtifactProps): JSX.Element {
   return (
     <div data-component="science-artifact" data-kind={props.kind}>
       <Show when={renderer()} fallback={<ScienceArtifactFallback kind={props.kind} data={props.data} />}>
-        {(Renderer) => <Dynamic component={Renderer()} kind={props.kind} data={props.data} height={props.height} />}
+        {(Renderer) => (
+          <Dynamic
+            component={Renderer()}
+            kind={props.kind}
+            data={props.data}
+            height={props.height}
+            onInspect={props.onInspect}
+          />
+        )}
       </Show>
     </div>
   )
diff --git a/frontend/workspace/src/science/renderers/molecular/ProteinStructure.tsx b/frontend/workspace/src/science/renderers/molecular/ProteinStructure.tsx
index 499813c1..d57f0576 100644
--- a/frontend/workspace/src/science/renderers/molecular/ProteinStructure.tsx
+++ b/frontend/workspace/src/science/renderers/molecular/ProteinStructure.tsx
@@ -111,6 +111,36 @@ export function ProteinStructure(props: ArtifactRenderProps): JSX.Element {
     void load(p, data, kind)
   })
 
+  createEffect(() => {
+    const value = summary()
+    const selected = selection()
+    if (!value || !props.onInspect) return
+    const facts = [
+      { label: "format", value: value.format.toUpperCase() },
+      ...(value.atomCount === undefined ? [] : [{ label: "atoms", value: `${value.atomCount} atoms` }]),
+      ...(value.bondCount === undefined ? [] : [{ label: "bonds", value: `${value.bondCount} bonds` }]),
+      ...(value.residueCount === undefined ? [] : [{ label: "residues", value: `${value.residueCount} residues` }]),
+      ...(value.chainCount === undefined ? [] : [{ label: "chains", value: `${value.chainCount} chains` }]),
+      ...(value.elements.length
+        ? [{ label: "elements", value: value.elements.map((item) => `${item.element} ${item.count}`).join(" · ") }]
+        : []),
+    ]
+    props.onInspect({
+      facts,
+      capabilities: [
+        "5 representation presets",
+        "Atom, residue, and chain selection",
+        "Distance measurements",
+        "Camera reset",
+        "Background switching",
+        "PNG export",
+      ],
+      ...(selected.count
+        ? { selection: { kind: "molecule" as const, label: selected.label || `${selected.count} selected`, count: selected.count } }
+        : {}),
+    })
+  })
+
   async function load(p: PluginContext, data: unknown, kind: string) {
     const my = ++token
     const src = narrowMolecularSource(data, kind)
diff --git a/frontend/workspace/src/science/renderers/registry.ts b/frontend/workspace/src/science/renderers/registry.ts
index 0481055f..1a7c4aff 100644
--- a/frontend/workspace/src/science/renderers/registry.ts
+++ b/frontend/workspace/src/science/renderers/registry.ts
@@ -22,6 +22,16 @@ export type ArtifactKind =
   | "latex" // katex — rendered math / equations
   | (string & {})
 
+export interface ArtifactInspection {
+  facts: Array<{ label: string; value: string }>
+  capabilities: string[]
+  selection?: {
+    kind: "molecule" | "genome" | "notebook" | "text"
+    label: string
+    count?: number
+  }
+}
+
 /** Props every science renderer receives. */
 export interface ArtifactRenderProps {
   /** The artifact kind (redundant with lookup key; handy for shared renderers). */
@@ -34,6 +44,8 @@ export interface ArtifactRenderProps {
   data: unknown
   /** Optional display height hint in px. */
   height?: number
+  /** Publish live renderer facts and selection state to the artifact inspector. */
+  onInspect?: (inspection: ArtifactInspection) => void
 }
 
 export type ArtifactRenderer = Component<ArtifactRenderProps>

From e7f8be5db66191ebc8165451831339e3d9028760 Mon Sep 17 00:00:00 2001
From: Aayam Bansal <aayambansal@gmail.com>
Date: Wed, 29 Jul 2026 14:30:20 +0800
Subject: [PATCH 26/40] feat: add truthful artifact previews

---
 .../workspace/e2e/artifact-gallery.spec.ts    |  9 +++
 .../e2e/science-file-viewers.spec.ts          |  3 +
 .../src/artifacts/ArtifactGallery.tsx         | 69 +++++++++++++------
 frontend/workspace/src/atlas/FilePreview.tsx  | 48 +++++++++++--
 4 files changed, 105 insertions(+), 24 deletions(-)

diff --git a/frontend/workspace/e2e/artifact-gallery.spec.ts b/frontend/workspace/e2e/artifact-gallery.spec.ts
index 5d0e1ffa..41a069ab 100644
--- a/frontend/workspace/e2e/artifact-gallery.spec.ts
+++ b/frontend/workspace/e2e/artifact-gallery.spec.ts
@@ -42,6 +42,15 @@ test("discovers, filters, opens, downloads, and contextualizes local research ar
     await expect(gallery.locator("[data-artifact]")).toHaveCount(4)
     await expect(gallery.getByText("pipeline.py", { exact: true })).toHaveCount(0)
     await expect(gallery.locator('[data-component="reproducibility-score"]')).toHaveAttribute("data-status", "blocked")
+    await expect(gallery.locator('[data-artifact="results/plot.svg"] [data-preview-source="file"]')).toBeVisible()
+    await expect(gallery.locator('[data-artifact="analysis.ipynb"] [data-preview-kind="notebook"]')).toContainText(
+      "Notebook",
+    )
+    await expect(gallery.locator('[data-artifact="results/counts.csv"] [data-preview-kind="dataset"]')).toContainText(
+      "Tabular data",
+    )
+    await expect(gallery.locator("[data-preview-chart]")).toHaveCount(0)
+    await expect(gallery.getByRole("button", { name: "Refresh artifacts", exact: true })).toBeVisible()
 
     await gallery.getByRole("button", { name: /^figure 1$/ }).click()
     await expect(gallery.locator("[data-artifact]")).toHaveCount(1)
diff --git a/frontend/workspace/e2e/science-file-viewers.spec.ts b/frontend/workspace/e2e/science-file-viewers.spec.ts
index cfdd0b20..dc0039c4 100644
--- a/frontend/workspace/e2e/science-file-viewers.spec.ts
+++ b/frontend/workspace/e2e/science-file-viewers.spec.ts
@@ -68,6 +68,9 @@ test("XYZ files open as interactive 3D chemistry with source access", async ({ p
   await expect(summary).toContainText("3 atoms")
   await expect(summary).toContainText("H 2")
   await expect(summary).toContainText("O 1")
+  await expect(page.getByRole("button", { name: "Source", exact: true })).toBeVisible()
+  await expect(page.getByRole("button", { name: "Copy", exact: true })).toBeVisible()
+  await expect(page.getByRole("button", { name: "Refresh", exact: true })).toBeVisible()
 
   const structure = artifact.locator('[data-component="mol-structure"]')
   await expect(structure).toHaveAttribute("data-status", "ready", { timeout: 30_000 })
diff --git a/frontend/workspace/src/artifacts/ArtifactGallery.tsx b/frontend/workspace/src/artifacts/ArtifactGallery.tsx
index a825e70a..d53d2874 100644
--- a/frontend/workspace/src/artifacts/ArtifactGallery.tsx
+++ b/frontend/workspace/src/artifacts/ArtifactGallery.tsx
@@ -255,10 +255,11 @@ export function ArtifactGallery(props: { directory: string; onOpen: (path: strin
           <button
             type="button"
             title="refresh artifacts"
-            style={iconButton()}
+            aria-label="Refresh artifacts"
+            style={actionButton()}
             onClick={() => setRefresh((value) => value + 1)}
           >
-            <IconRefresh size={12} strokeWidth={1.5} />
+            <IconRefresh size={12} strokeWidth={1.5} /> refresh
           </button>
         </div>
         <div class="atlas-scroll" style={{ display: "flex", gap: "5px", overflow: "auto hidden" }}>
@@ -498,7 +499,6 @@ function ArtifactCard(props: {
 }
 
 function ArtifactVisual(props: { item: ArtifactInfo; preview: string }): JSX.Element {
-  const seed = () => Array.from(props.item.path).reduce((total, value) => total + value.charCodeAt(0), 0)
   const image = () =>
     props.item.kind === "figure" && ["png", "jpg", "jpeg", "svg", "webp", "gif"].includes(props.item.format)
   return (
@@ -513,26 +513,13 @@ function ArtifactVisual(props: { item: ArtifactInfo; preview: string }): JSX.Ele
     >
       <Show
         when={image()}
-        fallback={
-          <div style={{ position: "absolute", inset: "12px", display: "flex", "align-items": "flex-end", gap: "4px" }}>
-            <For each={Array.from({ length: 13 })}>
-              {(_, index) => (
-                <span
-                  style={{
-                    flex: 1,
-                    height: `${18 + ((seed() + index() * 29) % 56)}%`,
-                    "border-radius": "2px 2px 0 0",
-                    background: `color-mix(in srgb, ${accent(props.item.kind)} ${22 + ((index() * 7) % 28)}%, transparent)`,
-                  }}
-                />
-              )}
-            </For>
-          </div>
-        }
+        fallback={<ArtifactPlaceholder item={props.item} />}
       >
         <img
+          data-preview-source="file"
+          data-preview-kind="figure"
           src={props.preview}
-          alt=""
+          alt={`Preview of ${props.item.name}`}
           loading="lazy"
           style={{ width: "100%", height: "100%", "object-fit": "cover", display: "block" }}
         />
@@ -566,6 +553,48 @@ function ArtifactVisual(props: { item: ArtifactInfo; preview: string }): JSX.Ele
   )
 }
 
+function ArtifactPlaceholder(props: { item: ArtifactInfo }): JSX.Element {
+  const copy = () => {
+    if (props.item.kind === "notebook") return ["Notebook", "Executable cells"]
+    if (props.item.kind === "dataset") return ["Tabular data", props.item.format.toUpperCase()]
+    if (props.item.kind === "report")
+      return props.item.format === "pdf" ? ["PDF document", "Open for page preview"] : ["Document", "Rendered on open"]
+    if (props.item.kind === "structure") return ["Molecular structure", "Open for interactive 3D"]
+    if (props.item.kind === "sequence") return ["Biological sequence", "Open for sequence inspection"]
+    if (props.item.kind === "genomics") return ["Genomic data", "Open for records and tracks"]
+    if (props.item.kind === "spectrum") return ["Mass spectrum", "Open for spectral inspection"]
+    if (props.item.kind === "model") return ["Model artifact", "Inspect inputs and provenance"]
+    if (props.item.kind === "archive") return ["Archive", "Open for a safe inventory"]
+    return ["Figure", `${props.item.format.toUpperCase()} preview unavailable`]
+  }
+  return (
+    <div
+      data-preview-source="placeholder"
+      data-preview-kind={props.item.kind}
+      style={{
+        position: "absolute",
+        inset: 0,
+        display: "grid",
+        "place-content": "center",
+        "justify-items": "center",
+        gap: "5px",
+        padding: "10px",
+        "text-align": "center",
+      }}
+    >
+      <span style={{ color: accent(props.item.kind), opacity: 0.78 }}>
+        <KindIcon kind={props.item.kind} size={21} />
+      </span>
+      <strong style={{ "font-family": FONT_SANS, "font-size": "10px", color: "var(--color-text)" }}>
+        {copy()[0]}
+      </strong>
+      <span style={{ "font-family": FONT_MONO, "font-size": "8px", color: "var(--color-text-faint)" }}>
+        {copy()[1]}
+      </span>
+    </div>
+  )
+}
+
 function ArtifactDetail(props: {
   item: ArtifactInfo
   directory: string
diff --git a/frontend/workspace/src/atlas/FilePreview.tsx b/frontend/workspace/src/atlas/FilePreview.tsx
index 44426f52..008338c8 100644
--- a/frontend/workspace/src/atlas/FilePreview.tsx
+++ b/frontend/workspace/src/atlas/FilePreview.tsx
@@ -386,27 +386,44 @@ export function FileView(props: {
             type="button"
             onClick={() => setShowSource((v) => !v)}
             title={showSource() ? "rendered view" : kind() === "code" ? "edit source" : "raw source"}
-            style={iconBtn(showSource())}
+            aria-label={showSource() ? "Rendered view" : "Source"}
+            style={headerBtn(showSource())}
           >
             <Show when={showSource()} fallback={<IconBraces size={13} strokeWidth={1.6} />}>
               <IconBookOpen size={13} strokeWidth={1.6} />
             </Show>
+            <span>{showSource() ? "view" : "source"}</span>
           </button>
         </Show>
 
         <Show when={!isBinary()}>
-          <button type="button" onClick={() => void copy()} title="copy contents" style={iconBtn()}>
+          <button
+            type="button"
+            onClick={() => void copy()}
+            title="copy contents"
+            aria-label="Copy"
+            style={headerBtn()}
+          >
             <IconCopy size={13} strokeWidth={1.6} />
+            <span>copy</span>
           </button>
         </Show>
         <Show when={isBinary()}>
-          <button type="button" onClick={() => void download()} title="download" style={iconBtn()}>
+          <button type="button" onClick={() => void download()} title="download" aria-label="Download" style={headerBtn()}>
             <IconDownload size={13} strokeWidth={1.6} />
+            <span>download</span>
           </button>
         </Show>
 
-        <button type="button" onClick={() => setRefreshKey((k) => k + 1)} title="refresh" style={iconBtn()}>
+        <button
+          type="button"
+          onClick={() => setRefreshKey((k) => k + 1)}
+          title="refresh"
+          aria-label="Refresh"
+          style={headerBtn()}
+        >
           <IconRefresh size={13} strokeWidth={1.6} />
+          <span>refresh</span>
         </button>
 
         <Show when={props.onClose}>
@@ -738,6 +755,29 @@ function iconBtn(active = false): JSX.CSSProperties {
   } as JSX.CSSProperties
 }
 
+function headerBtn(active = false): JSX.CSSProperties {
+  return {
+    all: "unset",
+    cursor: "pointer",
+    height: "28px",
+    display: "inline-flex",
+    "align-items": "center",
+    "justify-content": "center",
+    gap: "5px",
+    padding: "0 7px",
+    "border-radius": "5px",
+    border: "1px solid var(--color-border)",
+    color: active ? "var(--color-text)" : "var(--color-text-muted)",
+    background: active ? "var(--color-accent-subtle)" : "var(--color-bg-subtle)",
+    "font-family": FONT_SANS,
+    "font-size": "10px",
+    "font-weight": 550,
+    "text-transform": "capitalize",
+    "flex-shrink": 0,
+    transition: "background 120ms ease, color 120ms ease",
+  }
+}
+
 function retryBtn(): JSX.CSSProperties {
   return {
     all: "unset",

From 936d5694d79ccc79351fbd6c84f1e316264e8461 Mon Sep 17 00:00:00 2001
From: Aayam Bansal <aayambansal@gmail.com>
Date: Wed, 29 Jul 2026 14:38:51 +0800
Subject: [PATCH 27/40] fix: polish responsive artifact inspector

---
 .../workspace/e2e/artifact-inspector.spec.ts  |  5 ++
 frontend/workspace/src/atlas/RightPane.tsx    | 59 ++++++++++++-------
 frontend/workspace/src/styles/atlas.css       |  2 +-
 3 files changed, 45 insertions(+), 21 deletions(-)

diff --git a/frontend/workspace/e2e/artifact-inspector.spec.ts b/frontend/workspace/e2e/artifact-inspector.spec.ts
index d8760665..1dd95480 100644
--- a/frontend/workspace/e2e/artifact-inspector.spec.ts
+++ b/frontend/workspace/e2e/artifact-inspector.spec.ts
@@ -29,6 +29,7 @@ test("opened files drive a contextual artifact inspector without stale state", a
   await expect(inspector).toHaveAttribute("data-artifact-id", /water\.xyz/)
   await expect(inspector.locator("header strong")).toHaveText("water.xyz")
   await expect(inspector.getByRole("tab")).toHaveCount(7)
+  expect((await inspector.boundingBox())?.width).toBeGreaterThanOrEqual(400)
   await expect(inspector.getByText("3 atoms", { exact: true })).toBeVisible()
   await expect(inspector.getByText("PNG export", { exact: true })).toBeVisible()
 
@@ -68,6 +69,10 @@ test("artifact inspector overlays rather than crushing the workbench at narrow d
   expect(inspectorBox?.width).toBeGreaterThanOrEqual(280)
   expect(fileBox?.width).toBeGreaterThanOrEqual(520)
   expect(inspectorBox?.x).toBeGreaterThan(fileBox?.x ?? 0)
+  const backdrop = page.getByRole("button", { name: "Close inspector overlay", exact: true })
+  await expect(backdrop).toBeVisible()
+  await backdrop.click({ position: { x: 10, y: 300 } })
+  await expect(inspector).toHaveCount(0)
 })
 
 test("artifact review threads persist and can be resolved", async ({ page, directory, gotoSession }) => {
diff --git a/frontend/workspace/src/atlas/RightPane.tsx b/frontend/workspace/src/atlas/RightPane.tsx
index 546ee294..f61f05aa 100644
--- a/frontend/workspace/src/atlas/RightPane.tsx
+++ b/frontend/workspace/src/atlas/RightPane.tsx
@@ -33,7 +33,7 @@ function readSavedWidth(): number {
     const v = Number(localStorage.getItem(RIGHT_PANE_WIDTH_KEY))
     if (Number.isFinite(v) && v >= MIN_PANE_WIDTH && v <= MAX_PANE_WIDTH) return v
   } catch {}
-  return 360
+  return 420
 }
 
 export function RightPane(): JSX.Element {
@@ -134,24 +134,42 @@ export function RightPane(): JSX.Element {
         />
       }
     >
-      <aside
-        class="session-right-pane"
-        style={{
-          flex: narrow() ? "none" : `0 0 ${width()}px`,
-          width: narrow() ? "min(420px, calc(100vw - 52px))" : `${width()}px`,
-          display: "flex",
-          "flex-direction": "column",
-          "border-left": "1px solid var(--color-border)",
-          background: "var(--color-bg-subtle)",
-          "min-width": narrow() ? "280px" : `${MIN_PANE_WIDTH}px`,
-          position: narrow() ? "fixed" : "relative",
-          top: narrow() ? "0" : undefined,
-          right: narrow() ? "0" : undefined,
-          bottom: narrow() ? "0" : undefined,
-          "z-index": narrow() ? 70 : undefined,
-          "box-shadow": narrow() ? "-18px 0 48px rgba(0, 0, 0, 0.22)" : "none",
-        }}
-      >
+      <>
+        <Show when={narrow()}>
+          <button
+            type="button"
+            class="session-right-pane-backdrop"
+            aria-label="Close inspector overlay"
+            onClick={() => uiStore.setRightPaneOpen(false)}
+            style={{
+              all: "unset",
+              position: "fixed",
+              inset: 0,
+              "z-index": 69,
+              cursor: "default",
+              background: "color-mix(in srgb, var(--color-bg) 62%, transparent)",
+              "backdrop-filter": "blur(1px)",
+            }}
+          />
+        </Show>
+        <aside
+          class="session-right-pane"
+          style={{
+            flex: narrow() ? "none" : `0 0 ${width()}px`,
+            width: narrow() ? "min(420px, calc(100vw - 52px))" : `${width()}px`,
+            display: "flex",
+            "flex-direction": "column",
+            "border-left": "1px solid var(--color-border)",
+            background: "var(--color-bg-subtle)",
+            "min-width": narrow() ? "280px" : `${MIN_PANE_WIDTH}px`,
+            position: narrow() ? "fixed" : "relative",
+            top: narrow() ? "0" : undefined,
+            right: narrow() ? "0" : undefined,
+            bottom: narrow() ? "0" : undefined,
+            "z-index": narrow() ? 70 : undefined,
+            "box-shadow": narrow() ? "-18px 0 48px rgba(0, 0, 0, 0.22)" : "none",
+          }}
+        >
         {/* Drag handle on the left edge of the right pane. 6px wide, full
           height, invisible until hover. Cursor goes ew-resize. */}
         <div
@@ -302,7 +320,8 @@ export function RightPane(): JSX.Element {
             </KeepAlive>
           </div>
         </div>
-      </aside>
+        </aside>
+      </>
     </Show>
   )
 }
diff --git a/frontend/workspace/src/styles/atlas.css b/frontend/workspace/src/styles/atlas.css
index 2733dc9b..b7abd587 100644
--- a/frontend/workspace/src/styles/atlas.css
+++ b/frontend/workspace/src/styles/atlas.css
@@ -1872,7 +1872,7 @@ button.research-launchpad__status-item:hover {
   .session-right-pane {
     position: absolute !important;
     inset: 0 !important;
-    z-index: 20;
+    z-index: 70 !important;
     width: 100% !important;
     min-width: 0 !important;
     flex: 0 0 100% !important;

From 0fc570d1e60bfd88f2e2f8049c28dc533e927d46 Mon Sep 17 00:00:00 2001
From: Aayam Bansal <aayambansal@gmail.com>
Date: Wed, 29 Jul 2026 14:45:56 +0800
Subject: [PATCH 28/40] chore: satisfy branch verification gates

---
 backend/cli/test/file/artifacts.test.ts       |   4 +-
 backend/cli/test/file/path-traversal.test.ts  |  12 +-
 backend/cli/test/file/reproducibility.test.ts |   3 +-
 .../workspace/e2e/artifact-inspector.spec.ts  |   5 +-
 frontend/workspace/e2e/compute-jobs.spec.ts   |   5 +-
 .../workspace/e2e/server-recovery.spec.ts     |   5 +-
 .../src/artifacts/ArtifactGallery.tsx         |   9 +-
 .../src/artifacts/ArtifactInspector.tsx       |  57 ++--
 .../workspace/src/artifacts/context.test.ts   |   7 +-
 frontend/workspace/src/artifacts/context.ts   |   5 +-
 frontend/workspace/src/artifacts/inspector.ts |   6 +-
 frontend/workspace/src/atlas/FilePreview.tsx  |  16 +-
 frontend/workspace/src/atlas/RightPane.tsx    | 284 +++++++++---------
 .../renderers/molecular/ProteinStructure.tsx  |  27 +-
 .../src/science/renderers/molecular/model.ts  |  12 +-
 15 files changed, 221 insertions(+), 236 deletions(-)

diff --git a/backend/cli/test/file/artifacts.test.ts b/backend/cli/test/file/artifacts.test.ts
index d9a924c4..938cffdb 100644
--- a/backend/cli/test/file/artifacts.test.ts
+++ b/backend/cli/test/file/artifacts.test.ts
@@ -39,7 +39,6 @@ describe("File.artifacts", () => {
         await Bun.write(path.join(directory, "node_modules", "package", "paper.pdf"), "skip")
       },
     })
-
     await Instance.provide({
       directory: tmp.path,
       fn: async () => {
@@ -77,6 +76,7 @@ describe("File.provenance", () => {
         await Bun.write(path.join(directory, "results.csv"), "metric,value\naccuracy,0.95\n")
       },
     })
+    const branch = (await $`git branch --show-current`.cwd(tmp.path).quiet().text()).trim()
 
     await Instance.provide({
       directory: tmp.path,
@@ -87,7 +87,7 @@ describe("File.provenance", () => {
           tracked: true,
           dirty: true,
           status: "modified",
-          branch: "master",
+          branch,
           commit: {
             author: "OpenScience",
             email: "test@openscience.local",
diff --git a/backend/cli/test/file/path-traversal.test.ts b/backend/cli/test/file/path-traversal.test.ts
index 322ce6da..0f4f07b2 100644
--- a/backend/cli/test/file/path-traversal.test.ts
+++ b/backend/cli/test/file/path-traversal.test.ts
@@ -100,15 +100,9 @@ describe("File.read path traversal protection", () => {
     await Instance.provide({
       directory: tmp.path,
       fn: async () => {
-        await expect(File.read("escape/secret.txt")).rejects.toThrow(
-          "Access denied: path escapes project directory",
-        )
-        await expect(File.raw("escape/secret.txt")).rejects.toThrow(
-          "Access denied: path escapes project directory",
-        )
-        await expect(File.inspect("escape/secret.txt")).rejects.toThrow(
-          "Access denied: path escapes project directory",
-        )
+        await expect(File.read("escape/secret.txt")).rejects.toThrow("Access denied: path escapes project directory")
+        await expect(File.raw("escape/secret.txt")).rejects.toThrow("Access denied: path escapes project directory")
+        await expect(File.inspect("escape/secret.txt")).rejects.toThrow("Access denied: path escapes project directory")
       },
     })
   })
diff --git a/backend/cli/test/file/reproducibility.test.ts b/backend/cli/test/file/reproducibility.test.ts
index dda962d7..37cada4d 100644
--- a/backend/cli/test/file/reproducibility.test.ts
+++ b/backend/cli/test/file/reproducibility.test.ts
@@ -28,11 +28,12 @@ describe("ArtifactFile reproducibility", () => {
           .quiet()
       },
     })
+    const branch = (await $`git branch --show-current`.cwd(tmp.path).quiet().text()).trim()
 
     const audit = await ArtifactFile.audit(tmp.path)
     expect(audit.status).toBe("ready")
     expect(audit.score).toBeGreaterThanOrEqual(90)
-    expect(audit.git).toMatchObject({ dirty: false, branch: "master" })
+    expect(audit.git).toMatchObject({ dirty: false, branch })
     expect(audit.lockfiles).toContain("uv.lock")
     expect(audit.environments).toContain("pyproject.toml")
     expect(audit.notebooks).toEqual({ total: 1, valid: 1, invalid: [] })
diff --git a/frontend/workspace/e2e/artifact-inspector.spec.ts b/frontend/workspace/e2e/artifact-inspector.spec.ts
index 1dd95480..73e19f35 100644
--- a/frontend/workspace/e2e/artifact-inspector.spec.ts
+++ b/frontend/workspace/e2e/artifact-inspector.spec.ts
@@ -12,7 +12,10 @@ async function openFile(page: Page, directory: string, relativePath: string) {
   await location.fill(folder)
   await location.press("Enter")
   await page.getByPlaceholder("filter this folder…").fill(filename)
-  await page.getByRole("button", { name: new RegExp(`^${escapeRegex(filename)}\\b`) }).first().click()
+  await page
+    .getByRole("button", { name: new RegExp(`^${escapeRegex(filename)}\\b`) })
+    .first()
+    .click()
   await expect(page.locator(`[role="tab"][title="${filename}"]`)).toHaveAttribute("aria-selected", "true")
 }
 
diff --git a/frontend/workspace/e2e/compute-jobs.spec.ts b/frontend/workspace/e2e/compute-jobs.spec.ts
index 3d464d5e..f41e7ad1 100644
--- a/frontend/workspace/e2e/compute-jobs.spec.ts
+++ b/frontend/workspace/e2e/compute-jobs.spec.ts
@@ -3,10 +3,7 @@ import { tmpdir } from "node:os"
 import path from "node:path"
 import { expect, test } from "./fixtures"
 
-test("runs a reproducible local job and captures outputs from the right pane", async ({
-  page,
-  gotoSession,
-}) => {
+test("runs a reproducible local job and captures outputs from the right pane", async ({ page, gotoSession }) => {
   const directory = mkdtempSync(path.join(tmpdir(), "openscience-compute-e2e-"))
   try {
     await gotoSession()
diff --git a/frontend/workspace/e2e/server-recovery.spec.ts b/frontend/workspace/e2e/server-recovery.spec.ts
index 0702e13c..f6a410d3 100644
--- a/frontend/workspace/e2e/server-recovery.spec.ts
+++ b/frontend/workspace/e2e/server-recovery.spec.ts
@@ -1,6 +1,9 @@
 import { expect, test } from "./fixtures"
 
-test("retries a failed server health check immediately and clears the recovery banner", async ({ page, gotoSession }) => {
+test("retries a failed server health check immediately and clears the recovery banner", async ({
+  page,
+  gotoSession,
+}) => {
   let available = false
   await page.route("**/global/health", async (route) => {
     if (!available) {
diff --git a/frontend/workspace/src/artifacts/ArtifactGallery.tsx b/frontend/workspace/src/artifacts/ArtifactGallery.tsx
index d53d2874..1f9e7177 100644
--- a/frontend/workspace/src/artifacts/ArtifactGallery.tsx
+++ b/frontend/workspace/src/artifacts/ArtifactGallery.tsx
@@ -511,10 +511,7 @@ function ArtifactVisual(props: { item: ArtifactInfo; preview: string }): JSX.Ele
         "border-bottom": "1px solid var(--color-border)",
       }}
     >
-      <Show
-        when={image()}
-        fallback={<ArtifactPlaceholder item={props.item} />}
-      >
+      <Show when={image()} fallback={<ArtifactPlaceholder item={props.item} />}>
         <img
           data-preview-source="file"
           data-preview-kind="figure"
@@ -585,9 +582,7 @@ function ArtifactPlaceholder(props: { item: ArtifactInfo }): JSX.Element {
       <span style={{ color: accent(props.item.kind), opacity: 0.78 }}>
         <KindIcon kind={props.item.kind} size={21} />
       </span>
-      <strong style={{ "font-family": FONT_SANS, "font-size": "10px", color: "var(--color-text)" }}>
-        {copy()[0]}
-      </strong>
+      <strong style={{ "font-family": FONT_SANS, "font-size": "10px", color: "var(--color-text)" }}>{copy()[0]}</strong>
       <span style={{ "font-family": FONT_MONO, "font-size": "8px", color: "var(--color-text-faint)" }}>
         {copy()[1]}
       </span>
diff --git a/frontend/workspace/src/artifacts/ArtifactInspector.tsx b/frontend/workspace/src/artifacts/ArtifactInspector.tsx
index 79a70ad5..ddaf9d8a 100644
--- a/frontend/workspace/src/artifacts/ArtifactInspector.tsx
+++ b/frontend/workspace/src/artifacts/ArtifactInspector.tsx
@@ -1,14 +1,4 @@
-import {
-  For,
-  Match,
-  Show,
-  Switch,
-  createEffect,
-  createMemo,
-  createResource,
-  createSignal,
-  type JSX,
-} from "solid-js"
+import { For, Match, Show, Switch, createEffect, createMemo, createResource, createSignal, type JSX } from "solid-js"
 import { usePlatform } from "@/context/platform"
 import { usePrompt } from "@/context/prompt"
 import { useSDK } from "@/context/sdk"
@@ -340,11 +330,7 @@ export function ArtifactInspector(props: { context: ArtifactContext; onClose?: (
               <Environment data={model()} />
             </Match>
             <Match when={tab() === "review"}>
-              <Review
-                annotations={annotations(records()?.notes)}
-                onAdd={addAnnotation}
-                onUpdate={updateAnnotation}
-              />
+              <Review annotations={annotations(records()?.notes)} onAdd={addAnnotation} onUpdate={updateAnnotation} />
             </Match>
             <Match when={tab() === "history"}>
               <History data={model()} />
@@ -428,9 +414,7 @@ function Review(props: {
           </div>
         }
       >
-        <For each={props.annotations}>
-          {(item) => <AnnotationThread annotation={item} onUpdate={props.onUpdate} />}
-        </For>
+        <For each={props.annotations}>{(item) => <AnnotationThread annotation={item} onUpdate={props.onUpdate} />}</For>
       </Show>
     </div>
   )
@@ -493,9 +477,7 @@ function AnnotationThread(props: {
           type="button"
           disabled={busy()}
           style={quietButton()}
-          onClick={() =>
-            void update({ status: props.annotation.status === "open" ? "resolved" : "open" })
-          }
+          onClick={() => void update({ status: props.annotation.status === "open" ? "resolved" : "open" })}
         >
           {props.annotation.status === "open" ? "Resolve" : "Reopen"}
         </button>
@@ -566,9 +548,7 @@ function Details(props: { data: InspectorData }): JSX.Element {
           <>
             <section style={card()}>
               <Heading icon="details">Scientific properties</Heading>
-              <For each={inspection().facts}>
-                {(item) => <Fact label={item.label} value={item.value} mono />}
-              </For>
+              <For each={inspection().facts}>{(item) => <Fact label={item.label} value={item.value} mono />}</For>
               <Show when={inspection().selection}>
                 {(selection) => <Fact label="selection" value={selection().label} />}
               </Show>
@@ -620,7 +600,10 @@ function Details(props: { data: InspectorData }): JSX.Element {
 
 function Environment(props: { data: InspectorData }): JSX.Element {
   return (
-    <Show when={props.data.tabs.environment.available} fallback={<Empty state={props.data.tabs.environment} icon="environment" />}>
+    <Show
+      when={props.data.tabs.environment.available}
+      fallback={<Empty state={props.data.tabs.environment} icon="environment" />}
+    >
       <div style={{ display: "grid", gap: "12px" }}>
         <List title="Environment specifications" items={props.data.environments} />
         <List title="Dependency locks" items={props.data.lockfiles} />
@@ -640,7 +623,8 @@ function History(props: { data: InspectorData }): JSX.Element {
           <Fact label="date" value={new Date(version().date).toLocaleString()} />
           <Fact label="message" value={version().message} />
           <p style={copyStyle()}>
-            This is the latest Git commit touching the file. Artifact-level branches and comparisons are not recorded yet.
+            This is the latest Git commit touching the file. Artifact-level branches and comparisons are not recorded
+            yet.
           </p>
         </section>
       )}
@@ -655,7 +639,11 @@ function List(props: { title: string; items: string[] }): JSX.Element {
       <Show when={props.items.length} fallback={<p style={copyStyle()}>None recorded.</p>}>
         <ul style={{ margin: 0, padding: "0 0 0 18px", display: "grid", gap: "6px" }}>
           <For each={props.items}>
-            {(item) => <li style={{ "font-family": FONT_CODE, "font-size": "11px", color: "var(--color-text-muted)" }}>{item}</li>}
+            {(item) => (
+              <li style={{ "font-family": FONT_CODE, "font-size": "11px", color: "var(--color-text-muted)" }}>
+                {item}
+              </li>
+            )}
           </For>
         </ul>
       </Show>
@@ -663,7 +651,10 @@ function List(props: { title: string; items: string[] }): JSX.Element {
   )
 }
 
-function Empty(props: { state: InspectorState; icon: "code" | "run" | "messages" | "environment" | "review" | "history" }): JSX.Element {
+function Empty(props: {
+  state: InspectorState
+  icon: "code" | "run" | "messages" | "environment" | "review" | "history"
+}): JSX.Element {
   return (
     <div
       data-component="artifact-inspector-empty"
@@ -728,8 +719,12 @@ function Heading(props: {
 
 function Fact(props: { label: string; value: string; mono?: boolean }): JSX.Element {
   return (
-    <div style={{ display: "grid", "grid-template-columns": "78px minmax(0, 1fr)", gap: "10px", "align-items": "start" }}>
-      <span style={{ "font-family": FONT_SANS, "font-size": "11px", color: "var(--color-text-faint)" }}>{props.label}</span>
+    <div
+      style={{ display: "grid", "grid-template-columns": "78px minmax(0, 1fr)", gap: "10px", "align-items": "start" }}
+    >
+      <span style={{ "font-family": FONT_SANS, "font-size": "11px", color: "var(--color-text-faint)" }}>
+        {props.label}
+      </span>
       <span
         title={props.value}
         style={{
diff --git a/frontend/workspace/src/artifacts/context.test.ts b/frontend/workspace/src/artifacts/context.test.ts
index caa07293..eb3f0011 100644
--- a/frontend/workspace/src/artifacts/context.test.ts
+++ b/frontend/workspace/src/artifacts/context.test.ts
@@ -1,10 +1,5 @@
 import { describe, expect, test } from "bun:test"
-import {
-  clearOwnedArtifact,
-  createArtifactContext,
-  inferArtifactKind,
-  type ArtifactContext,
-} from "./context"
+import { clearOwnedArtifact, createArtifactContext, inferArtifactKind, type ArtifactContext } from "./context"
 
 describe("artifact context", () => {
   test("normalizes equivalent locations to one stable identity", () => {
diff --git a/frontend/workspace/src/artifacts/context.ts b/frontend/workspace/src/artifacts/context.ts
index 9259a803..1dd93a9c 100644
--- a/frontend/workspace/src/artifacts/context.ts
+++ b/frontend/workspace/src/artifacts/context.ts
@@ -154,10 +154,7 @@ export function createArtifactContext(input: ArtifactContextInput): ArtifactCont
   }
 }
 
-export function clearOwnedArtifact(
-  current: ArtifactContext | undefined,
-  owner: string,
-): ArtifactContext | undefined {
+export function clearOwnedArtifact(current: ArtifactContext | undefined, owner: string): ArtifactContext | undefined {
   if (current?.id === owner) return
   return current
 }
diff --git a/frontend/workspace/src/artifacts/inspector.ts b/frontend/workspace/src/artifacts/inspector.ts
index 4068ab7d..46b092b8 100644
--- a/frontend/workspace/src/artifacts/inspector.ts
+++ b/frontend/workspace/src/artifacts/inspector.ts
@@ -133,11 +133,7 @@ export function normalizeInspectorData(context: ArtifactContext, input: Inspecto
       environment: environment
         ? state(true, "Environment records found", "Project environment specifications and lockfiles are available.")
         : state(false, "No environment is recorded", "Add a lockfile or environment specification to this project."),
-      review: state(
-        true,
-        "Artifact review",
-        "Durable annotations and review threads are available for this artifact.",
-      ),
+      review: state(true, "Artifact review", "Durable annotations and review threads are available for this artifact."),
       history: version?.commit
         ? state(true, "Git provenance available", "The latest commit touching this artifact is recorded.")
         : state(false, "No Git commit is recorded", "Commit this artifact to create a recoverable version."),
diff --git a/frontend/workspace/src/atlas/FilePreview.tsx b/frontend/workspace/src/atlas/FilePreview.tsx
index 008338c8..1de280e7 100644
--- a/frontend/workspace/src/atlas/FilePreview.tsx
+++ b/frontend/workspace/src/atlas/FilePreview.tsx
@@ -397,19 +397,19 @@ export function FileView(props: {
         </Show>
 
         <Show when={!isBinary()}>
-          <button
-            type="button"
-            onClick={() => void copy()}
-            title="copy contents"
-            aria-label="Copy"
-            style={headerBtn()}
-          >
+          <button type="button" onClick={() => void copy()} title="copy contents" aria-label="Copy" style={headerBtn()}>
             <IconCopy size={13} strokeWidth={1.6} />
             <span>copy</span>
           </button>
         </Show>
         <Show when={isBinary()}>
-          <button type="button" onClick={() => void download()} title="download" aria-label="Download" style={headerBtn()}>
+          <button
+            type="button"
+            onClick={() => void download()}
+            title="download"
+            aria-label="Download"
+            style={headerBtn()}
+          >
             <IconDownload size={13} strokeWidth={1.6} />
             <span>download</span>
           </button>
diff --git a/frontend/workspace/src/atlas/RightPane.tsx b/frontend/workspace/src/atlas/RightPane.tsx
index f61f05aa..840cadf4 100644
--- a/frontend/workspace/src/atlas/RightPane.tsx
+++ b/frontend/workspace/src/atlas/RightPane.tsx
@@ -170,156 +170,158 @@ export function RightPane(): JSX.Element {
             "box-shadow": narrow() ? "-18px 0 48px rgba(0, 0, 0, 0.22)" : "none",
           }}
         >
-        {/* Drag handle on the left edge of the right pane. 6px wide, full
+          {/* Drag handle on the left edge of the right pane. 6px wide, full
           height, invisible until hover. Cursor goes ew-resize. */}
-        <div
-          role="separator"
-          aria-orientation="vertical"
-          on:pointerdown={onHandlePointerDown}
-          on:pointermove={onHandlePointerMove}
-          on:pointerup={onHandlePointerUp}
-          on:pointercancel={onHandlePointerUp}
-          style={{
-            position: "absolute",
-            left: "-3px",
-            top: 0,
-            width: "6px",
-            height: "100%",
-            cursor: "ew-resize",
-            "z-index": 5,
-            "touch-action": "none",
-          }}
-          onMouseEnter={(e) => (e.currentTarget.style.background = "var(--color-accent-subtle)")}
-          onMouseLeave={(e) => (e.currentTarget.style.background = "transparent")}
-        />
-        <div
-          role="tablist"
-          style={{
-            display: "flex",
-            "align-items": "stretch",
-            "border-bottom": "1px solid var(--color-border)",
-            background: "var(--color-bg-subtle)",
-            "flex-shrink": 0,
-          }}
-        >
           <div
-            style={{ display: "flex", gap: "5px", padding: "7px 10px", flex: 1, "min-width": 0, "overflow-x": "auto" }}
+            role="separator"
+            aria-orientation="vertical"
+            on:pointerdown={onHandlePointerDown}
+            on:pointermove={onHandlePointerMove}
+            on:pointerup={onHandlePointerUp}
+            on:pointercancel={onHandlePointerUp}
+            style={{
+              position: "absolute",
+              left: "-3px",
+              top: 0,
+              width: "6px",
+              height: "100%",
+              cursor: "ew-resize",
+              "z-index": 5,
+              "touch-action": "none",
+            }}
+            onMouseEnter={(e) => (e.currentTarget.style.background = "var(--color-accent-subtle)")}
+            onMouseLeave={(e) => (e.currentTarget.style.background = "transparent")}
+          />
+          <div
+            role="tablist"
+            style={{
+              display: "flex",
+              "align-items": "stretch",
+              "border-bottom": "1px solid var(--color-border)",
+              background: "var(--color-bg-subtle)",
+              "flex-shrink": 0,
+            }}
           >
-            <Show when={artifact()}>
-              <TabBtn
-                k="artifact"
-                label="Inspect"
-                Icon={IconAtom}
-                active={artifactMode()}
-                onClick={() => uiStore.setRightPaneMode("artifact")}
-              />
-            </Show>
-            <For each={visibleTabs()}>
-              {(t) => (
+            <div
+              style={{
+                display: "flex",
+                gap: "5px",
+                padding: "7px 10px",
+                flex: 1,
+                "min-width": 0,
+                "overflow-x": "auto",
+              }}
+            >
+              <Show when={artifact()}>
                 <TabBtn
-                  k={t.k}
-                  label={t.label}
-                  Icon={t.Icon}
-                  active={!artifactMode() && tab() === t.k}
-                  onClick={() => {
-                    setTab(t.k)
-                    uiStore.setRightPaneMode("tools")
-                  }}
+                  k="artifact"
+                  label="Inspect"
+                  Icon={IconAtom}
+                  active={artifactMode()}
+                  onClick={() => uiStore.setRightPaneMode("artifact")}
                 />
-              )}
-            </For>
-          </div>
-          <div style={{ position: "relative", display: "flex", "align-items": "center", "flex-shrink": 0 }}>
-            <button onClick={openSkillLibrary} title="skill library" style={paneCtl(false)}>
-              <IconBraces size={12} strokeWidth={1.5} />
-            </button>
-            <button onClick={() => setPanelMenu((v) => !v)} title="panel settings" style={paneCtl(panelMenu())}>
-              <IconSettings size={12} strokeWidth={1.5} />
-            </button>
-            <Show when={panelMenu()}>
-              <div
-                onMouseLeave={() => setPanelMenu(false)}
-                style={{
-                  position: "absolute",
-                  top: "100%",
-                  right: "2px",
-                  "margin-top": "2px",
-                  background: "var(--color-surface-solid)",
-                  border: "1px solid var(--color-border-strong)",
-                  "border-radius": "4px",
-                  "box-shadow": "var(--shadow-md)",
-                  padding: "5px",
-                  "z-index": 40,
-                  "min-width": "150px",
-                }}
-              >
-                <div style={paneMenuLabel}>show in panel</div>
-                <For each={TABS}>
-                  {(t) => (
-                    <button onClick={() => uiStore.toggleTabHidden(t.k)} style={paneMenuRow()}>
-                      <t.Icon size={12} strokeWidth={1.5} />
-                      <span style={{ flex: 1, "text-align": "left" }}>{t.label ?? t.k}</span>
-                      <span
-                        style={{
-                          "font-family": FONT_MONO,
-                          "font-size": "10px",
-                          color: uiStore.isTabHidden(t.k) ? "var(--color-text-faint)" : "var(--color-success)",
-                        }}
-                      >
-                        {uiStore.isTabHidden(t.k) ? "off" : "on"}
-                      </span>
-                    </button>
-                  )}
-                </For>
-                <div style={{ height: "1px", background: "var(--color-border)", margin: "4px 2px" }} />
-                <button
-                  onClick={() => {
-                    uiStore.setRightPaneOpen(false)
-                    setPanelMenu(false)
+              </Show>
+              <For each={visibleTabs()}>
+                {(t) => (
+                  <TabBtn
+                    k={t.k}
+                    label={t.label}
+                    Icon={t.Icon}
+                    active={!artifactMode() && tab() === t.k}
+                    onClick={() => {
+                      setTab(t.k)
+                      uiStore.setRightPaneMode("tools")
+                    }}
+                  />
+                )}
+              </For>
+            </div>
+            <div style={{ position: "relative", display: "flex", "align-items": "center", "flex-shrink": 0 }}>
+              <button onClick={openSkillLibrary} title="skill library" style={paneCtl(false)}>
+                <IconBraces size={12} strokeWidth={1.5} />
+              </button>
+              <button onClick={() => setPanelMenu((v) => !v)} title="panel settings" style={paneCtl(panelMenu())}>
+                <IconSettings size={12} strokeWidth={1.5} />
+              </button>
+              <Show when={panelMenu()}>
+                <div
+                  onMouseLeave={() => setPanelMenu(false)}
+                  style={{
+                    position: "absolute",
+                    top: "100%",
+                    right: "2px",
+                    "margin-top": "2px",
+                    background: "var(--color-surface-solid)",
+                    border: "1px solid var(--color-border-strong)",
+                    "border-radius": "4px",
+                    "box-shadow": "var(--shadow-md)",
+                    padding: "5px",
+                    "z-index": 40,
+                    "min-width": "150px",
                   }}
-                  style={paneMenuRow()}
                 >
-                  <IconChevronRight size={12} strokeWidth={1.5} />
-                  <span style={{ flex: 1, "text-align": "left" }}>hide panel</span>
-                </button>
-              </div>
-            </Show>
-            <button onClick={() => uiStore.setRightPaneOpen(false)} title="hide panel" style={paneCtl(false)}>
-              <IconChevronRight size={13} strokeWidth={1.5} />
-            </button>
+                  <div style={paneMenuLabel}>show in panel</div>
+                  <For each={TABS}>
+                    {(t) => (
+                      <button onClick={() => uiStore.toggleTabHidden(t.k)} style={paneMenuRow()}>
+                        <t.Icon size={12} strokeWidth={1.5} />
+                        <span style={{ flex: 1, "text-align": "left" }}>{t.label ?? t.k}</span>
+                        <span
+                          style={{
+                            "font-family": FONT_MONO,
+                            "font-size": "10px",
+                            color: uiStore.isTabHidden(t.k) ? "var(--color-text-faint)" : "var(--color-success)",
+                          }}
+                        >
+                          {uiStore.isTabHidden(t.k) ? "off" : "on"}
+                        </span>
+                      </button>
+                    )}
+                  </For>
+                  <div style={{ height: "1px", background: "var(--color-border)", margin: "4px 2px" }} />
+                  <button
+                    onClick={() => {
+                      uiStore.setRightPaneOpen(false)
+                      setPanelMenu(false)
+                    }}
+                    style={paneMenuRow()}
+                  >
+                    <IconChevronRight size={12} strokeWidth={1.5} />
+                    <span style={{ flex: 1, "text-align": "left" }}>hide panel</span>
+                  </button>
+                </div>
+              </Show>
+              <button onClick={() => uiStore.setRightPaneOpen(false)} title="hide panel" style={paneCtl(false)}>
+                <IconChevronRight size={13} strokeWidth={1.5} />
+              </button>
+            </div>
           </div>
-        </div>
-        <div style={{ flex: 1, "min-height": 0, position: "relative", display: "flex", "flex-direction": "column" }}>
-          <Show when={artifactMode() && artifact()}>
-            {(current) => (
-              <ArtifactInspector
-                context={current()}
-                onClose={() => uiStore.setRightPaneMode("tools")}
-              />
-            )}
-          </Show>
-          <div
-            style={{
-              display: artifactMode() ? "none" : "flex",
-              flex: artifactMode() ? undefined : 1,
-              "min-height": 0,
-              "flex-direction": "column",
-            }}
-          >
-            <KeepAlive show={tab() === "canvas"} mounted={visited().has("canvas")}>
-              <CanvasTab />
-            </KeepAlive>
-            <KeepAlive show={tab() === "jobs"} mounted={visited().has("jobs")}>
-              <ComputeJobs />
-            </KeepAlive>
-            <KeepAlive show={tab() === "evidence"} mounted={visited().has("evidence")}>
-              <EvidenceGraph />
-            </KeepAlive>
-            <KeepAlive show={tab() === "terminal"} mounted={visited().has("terminal")}>
-              <TerminalTab />
-            </KeepAlive>
+          <div style={{ flex: 1, "min-height": 0, position: "relative", display: "flex", "flex-direction": "column" }}>
+            <Show when={artifactMode() && artifact()}>
+              {(current) => <ArtifactInspector context={current()} onClose={() => uiStore.setRightPaneMode("tools")} />}
+            </Show>
+            <div
+              style={{
+                display: artifactMode() ? "none" : "flex",
+                flex: artifactMode() ? undefined : 1,
+                "min-height": 0,
+                "flex-direction": "column",
+              }}
+            >
+              <KeepAlive show={tab() === "canvas"} mounted={visited().has("canvas")}>
+                <CanvasTab />
+              </KeepAlive>
+              <KeepAlive show={tab() === "jobs"} mounted={visited().has("jobs")}>
+                <ComputeJobs />
+              </KeepAlive>
+              <KeepAlive show={tab() === "evidence"} mounted={visited().has("evidence")}>
+                <EvidenceGraph />
+              </KeepAlive>
+              <KeepAlive show={tab() === "terminal"} mounted={visited().has("terminal")}>
+                <TerminalTab />
+              </KeepAlive>
+            </div>
           </div>
-        </div>
         </aside>
       </>
     </Show>
diff --git a/frontend/workspace/src/science/renderers/molecular/ProteinStructure.tsx b/frontend/workspace/src/science/renderers/molecular/ProteinStructure.tsx
index d57f0576..2013cfd1 100644
--- a/frontend/workspace/src/science/renderers/molecular/ProteinStructure.tsx
+++ b/frontend/workspace/src/science/renderers/molecular/ProteinStructure.tsx
@@ -136,7 +136,13 @@ export function ProteinStructure(props: ArtifactRenderProps): JSX.Element {
         "PNG export",
       ],
       ...(selected.count
-        ? { selection: { kind: "molecule" as const, label: selected.label || `${selected.count} selected`, count: selected.count } }
+        ? {
+            selection: {
+              kind: "molecule" as const,
+              label: selected.label || `${selected.count} selected`,
+              count: selected.count,
+            },
+          }
         : {}),
     })
   })
@@ -219,13 +225,7 @@ export function ProteinStructure(props: ArtifactRenderProps): JSX.Element {
     const p = plugin()
     if (!p) return
     const state = p.managers.structure.measurement.state
-    const cells = [
-      ...state.distances,
-      ...state.angles,
-      ...state.dihedrals,
-      ...state.orientations,
-      ...state.planes,
-    ]
+    const cells = [...state.distances, ...state.angles, ...state.dihedrals, ...state.orientations, ...state.planes]
     if (!cells.length) return
     const { PluginCommands } = await import("molstar/lib/mol-plugin/commands")
     await Promise.all(
@@ -243,7 +243,12 @@ export function ProteinStructure(props: ArtifactRenderProps): JSX.Element {
   function exportName() {
     const src = narrowMolecularSource(props.data, props.kind)
     if (!src?.raw || src.format !== "xyz") return "molecule-structure.png"
-    const name = src.raw.split(/\r?\n/)[1]?.trim().toLowerCase().replace(/[^a-z0-9]+/g, "-").replace(/^-|-$/g, "")
+    const name = src.raw
+      .split(/\r?\n/)[1]
+      ?.trim()
+      .toLowerCase()
+      .replace(/[^a-z0-9]+/g, "-")
+      .replace(/^-|-$/g, "")
     return `${name || "molecule"}-structure.png`
   }
 
@@ -439,9 +444,7 @@ export function ProteinStructure(props: ArtifactRenderProps): JSX.Element {
                 </For>
               </div>
             </Show>
-            <For each={value().warnings}>
-              {(warning) => <span style={{ color: "#f2c879" }}>{warning}</span>}
-            </For>
+            <For each={value().warnings}>{(warning) => <span style={{ color: "#f2c879" }}>{warning}</span>}</For>
           </div>
         )}
       </Show>
diff --git a/frontend/workspace/src/science/renderers/molecular/model.ts b/frontend/workspace/src/science/renderers/molecular/model.ts
index 392ed57d..653cfe19 100644
--- a/frontend/workspace/src/science/renderers/molecular/model.ts
+++ b/frontend/workspace/src/science/renderers/molecular/model.ts
@@ -133,9 +133,7 @@ function analyzePdb(raw: string, source: MolecularSummary["source"]): MolecularS
   const lines = raw.split(/\r?\n/)
   const atoms = lines.filter((line) => line.startsWith("ATOM  ") || line.startsWith("HETATM"))
   const chains = new Set(atoms.map((line) => line.slice(21, 22).trim() || "_"))
-  const residues = new Set(
-    atoms.map((line) => `${line.slice(21, 22).trim() || "_"}:${line.slice(22, 27).trim()}`),
-  )
+  const residues = new Set(atoms.map((line) => `${line.slice(21, 22).trim() || "_"}:${line.slice(22, 27).trim()}`))
   const declaredModels = lines.filter((line) => line.startsWith("MODEL ")).length
   return {
     format: "pdb",
@@ -171,7 +169,13 @@ function molRecord(raw: string): MolRecord | undefined {
 }
 
 function analyzeMol(raw: string, source: MolecularSummary["source"], target: "sdf" | "mol"): MolecularSummary {
-  const chunks = target === "sdf" ? raw.split(/\$\$\$\$/).map((item) => item.trim()).filter(Boolean) : [raw]
+  const chunks =
+    target === "sdf"
+      ? raw
+          .split(/\$\$\$\$/)
+          .map((item) => item.trim())
+          .filter(Boolean)
+      : [raw]
   const records = chunks.flatMap((chunk) => {
     const value = molRecord(chunk)
     return value ? [value] : []

From 57b93a52a638f416fcac243ae2d7716729611062 Mon Sep 17 00:00:00 2001
From: Aayam Bansal <aayambansal@gmail.com>
Date: Wed, 29 Jul 2026 14:50:07 +0800
Subject: [PATCH 29/40] feat: version artifact review annotations

---
 backend/cli/src/file/annotations.ts           | 135 ++++++++++++++++--
 backend/cli/src/server/routes/file.ts         |  31 +++-
 backend/cli/test/server/file-research.test.ts |  94 +++++++++++-
 .../workspace/e2e/artifact-inspector.spec.ts  |  19 ++-
 .../src/artifacts/ArtifactInspector.tsx       |  90 +++++++++++-
 5 files changed, 346 insertions(+), 23 deletions(-)

diff --git a/backend/cli/src/file/annotations.ts b/backend/cli/src/file/annotations.ts
index b95d99d1..91340271 100644
--- a/backend/cli/src/file/annotations.ts
+++ b/backend/cli/src/file/annotations.ts
@@ -43,17 +43,33 @@ export namespace ArtifactAnnotation {
   })
   export type Message = z.infer<typeof Message>
 
+  export const Revision = z.object({
+    version: z.number().int().positive(),
+    event: z.enum(["created", "edited", "replied", "resolved", "reopened", "deleted"]),
+    actor: z.string(),
+    at: z.number(),
+    status: z.enum(["open", "resolved"]),
+    messages: Message.array(),
+    deletedAt: z.number().optional(),
+  })
+  export type Revision = z.infer<typeof Revision>
+
   export const Info = z.object({
     id: z.string(),
     projectID: z.string(),
     path: z.string(),
+    artifactHash: z.string().regex(/^[a-f0-9]{64}$/),
     anchor: Anchor,
     messages: Message.array(),
     status: z.enum(["open", "resolved"]),
+    version: z.number().int().positive(),
+    revisions: Revision.array(),
     createdAt: z.number(),
     updatedAt: z.number(),
+    deletedAt: z.number().optional(),
   })
   export type Info = z.infer<typeof Info>
+  const Legacy = Info.omit({ artifactHash: true, version: true, revisions: true, deletedAt: true })
 
   export const Create = z.object({
     path: z.string().trim().min(1).max(10_000),
@@ -66,10 +82,14 @@ export namespace ArtifactAnnotation {
   export const Update = z
     .object({
       status: z.enum(["open", "resolved"]).optional(),
+      body: z.string().trim().min(1).max(100_000).optional(),
       reply: z.string().trim().min(1).max(100_000).optional(),
       author: z.string().trim().min(1).max(200).optional(),
     })
-    .refine((value) => value.status !== undefined || value.reply !== undefined, "No annotation update supplied")
+    .refine(
+      (value) => value.status !== undefined || value.body !== undefined || value.reply !== undefined,
+      "No annotation update supplied",
+    )
   export type Update = z.infer<typeof Update>
 
   const prefix = () => ["artifact_annotation", Instance.project.id]
@@ -80,23 +100,84 @@ export namespace ArtifactAnnotation {
     if (!(await Instance.containsCanonicalPath(absolute))) {
       throw new Error(`Annotation target is outside the project: ${value}`)
     }
-    return path.relative(Instance.directory, absolute).replaceAll("\\", "/")
+    return {
+      absolute,
+      relative: path.relative(Instance.directory, absolute).replaceAll("\\", "/"),
+    }
+  }
+
+  async function digest(file: string) {
+    const hasher = new Bun.CryptoHasher("sha256")
+    const reader = Bun.file(file).stream().getReader()
+    const feed = async (): Promise<void> => {
+      const chunk = await reader.read()
+      if (chunk.done) return
+      hasher.update(chunk.value)
+      return feed()
+    }
+    await feed()
+    return hasher.digest("hex")
+  }
+
+  function hash(value: string) {
+    const hasher = new Bun.CryptoHasher("sha256")
+    hasher.update(value)
+    return hasher.digest("hex")
+  }
+
+  function revision(record: Info, event: Revision["event"], actor: string, at: number): Revision {
+    return {
+      version: record.version,
+      event,
+      actor,
+      at,
+      status: record.status,
+      messages: record.messages.map((message) => ({ ...message })),
+      ...(record.deletedAt ? { deletedAt: record.deletedAt } : {}),
+    }
+  }
+
+  async function read(id: string) {
+    const stored = await Storage.read<unknown>(key(id))
+    const current = Info.safeParse(stored)
+    if (current.success) return current.data
+    const legacy = Legacy.parse(stored)
+    const location = await target(legacy.path)
+    const artifactHash = (await Bun.file(location.absolute).exists())
+      ? await digest(location.absolute)
+      : hash(`missing:${legacy.path}`)
+    const record: Info = {
+      ...legacy,
+      artifactHash,
+      version: 1,
+      revisions: [],
+    }
+    record.revisions.push(revision(record, "created", record.messages[0]?.author ?? "You", record.createdAt))
+    await Storage.write(key(id), record)
+    return record
   }
 
   export async function list(filepath: string) {
-    const relative = await target(filepath)
+    const location = await target(filepath)
     const keys = await Storage.list(prefix())
-    const records = await Promise.all(keys.map((item) => Storage.read<Info>(item)))
-    return records.filter((item) => item.path === relative).toSorted((a, b) => a.createdAt - b.createdAt)
+    const records = await Promise.all(keys.map((item) => read(item.at(-1)!)))
+    return records
+      .filter((item) => item.path === location.relative && !item.deletedAt)
+      .toSorted((a, b) => a.createdAt - b.createdAt)
   }
 
   export async function create(input: Create) {
     const now = Date.now()
     const id = `ann_${ulid()}`
+    const location = await target(input.path)
+    if (!(await Bun.file(location.absolute).exists())) {
+      throw new Error(`Annotation target does not exist: ${input.path}`)
+    }
     const record: Info = {
       id,
       projectID: Instance.project.id,
-      path: await target(input.path),
+      path: location.relative,
+      artifactHash: await digest(location.absolute),
       anchor: input.anchor,
       messages: [
         {
@@ -107,30 +188,62 @@ export namespace ArtifactAnnotation {
         },
       ],
       status: "open",
+      version: 1,
+      revisions: [],
       createdAt: now,
       updatedAt: now,
     }
+    record.revisions.push(revision(record, "created", input.author ?? "You", now))
     await Storage.write(key(id), record)
     return record
   }
 
   export async function update(id: string, input: Update) {
+    await read(id)
     return Storage.update<Info>(key(id), (record) => {
+      if (record.deletedAt) throw new Error(`Annotation ${id} has been deleted`)
+      const now = Date.now()
+      const actor = input.author ?? "You"
+      const event: Revision["event"] = input.body
+        ? "edited"
+        : input.reply
+          ? "replied"
+          : input.status === "resolved"
+            ? "resolved"
+            : "reopened"
       if (input.status) record.status = input.status
+      if (input.body && record.messages[0]) {
+        record.messages[0].body = input.body
+        record.messages[0].author = actor
+      }
       if (input.reply) {
         record.messages.push({
           id: `msg_${ulid()}`,
           body: input.reply,
-          author: input.author ?? "You",
-          createdAt: Date.now(),
+          author: actor,
+          createdAt: now,
         })
       }
-      record.updatedAt = Date.now()
+      record.version += 1
+      record.updatedAt = now
+      record.revisions.push(revision(record, event, actor, now))
     })
   }
 
   export async function remove(id: string) {
-    await Storage.remove(key(id))
-    return { deleted: true as const }
+    await read(id)
+    const record = await Storage.update<Info>(key(id), (record) => {
+      if (record.deletedAt) return
+      const now = Date.now()
+      record.deletedAt = now
+      record.updatedAt = now
+      record.version += 1
+      record.revisions.push(revision(record, "deleted", "You", now))
+    })
+    return { deleted: true as const, version: record.version }
+  }
+
+  export async function history(id: string) {
+    return read(id)
   }
 }
diff --git a/backend/cli/src/server/routes/file.ts b/backend/cli/src/server/routes/file.ts
index 59436219..13545f51 100644
--- a/backend/cli/src/server/routes/file.ts
+++ b/backend/cli/src/server/routes/file.ts
@@ -345,7 +345,8 @@ export const FileRoutes = lazy(() =>
       "/file/annotations",
       describeRoute({
         summary: "Create an artifact annotation",
-        description: "Create a durable review thread anchored to an artifact, text range, notebook cell, molecule, or locus.",
+        description:
+          "Create a durable review thread anchored to an artifact, text range, notebook cell, molecule, or locus.",
         operationId: "file.annotations.create",
         responses: {
           200: {
@@ -357,6 +358,22 @@ export const FileRoutes = lazy(() =>
       validator("json", ArtifactAnnotation.Create),
       async (c) => c.json(await ArtifactAnnotation.create(c.req.valid("json"))),
     )
+    .get(
+      "/file/annotations/:id/history",
+      describeRoute({
+        summary: "Read artifact annotation history",
+        description: "Read every immutable revision of an artifact review thread, including a recoverable tombstone.",
+        operationId: "file.annotations.history",
+        responses: {
+          200: {
+            description: "Versioned artifact annotation",
+            content: { "application/json": { schema: resolver(ArtifactAnnotation.Info) } },
+          },
+        },
+      }),
+      validator("param", z.object({ id: z.string().startsWith("ann_") })),
+      async (c) => c.json(await ArtifactAnnotation.history(c.req.valid("param").id)),
+    )
     .patch(
       "/file/annotations/:id",
       describeRoute({
@@ -377,13 +394,17 @@ export const FileRoutes = lazy(() =>
     .delete(
       "/file/annotations/:id",
       describeRoute({
-        summary: "Delete an artifact annotation",
-        description: "Permanently remove an artifact review thread.",
+        summary: "Tombstone an artifact annotation",
+        description: "Hide an artifact review thread while retaining its recoverable revision history.",
         operationId: "file.annotations.delete",
         responses: {
           200: {
-            description: "Deleted annotation",
-            content: { "application/json": { schema: resolver(z.object({ deleted: z.literal(true) })) } },
+            description: "Tombstoned annotation",
+            content: {
+              "application/json": {
+                schema: resolver(z.object({ deleted: z.literal(true), version: z.number().int().positive() })),
+              },
+            },
           },
         },
       }),
diff --git a/backend/cli/test/server/file-research.test.ts b/backend/cli/test/server/file-research.test.ts
index 5fffe6f0..8859df53 100644
--- a/backend/cli/test/server/file-research.test.ts
+++ b/backend/cli/test/server/file-research.test.ts
@@ -2,6 +2,7 @@ import { describe, expect, test } from "bun:test"
 import path from "node:path"
 import { Instance } from "../../src/project/instance"
 import { FileRoutes } from "../../src/server/routes/file"
+import { Storage } from "../../src/storage/storage"
 import { tmpdir } from "../fixture/fixture"
 
 describe("/file research routes", () => {
@@ -68,7 +69,7 @@ describe("/file research routes", () => {
     })
   })
 
-  test("creates, resolves, and deletes durable artifact annotations", async () => {
+  test("versions, resolves, edits, and tombstones durable artifact annotations", async () => {
     await using tmp = await tmpdir({
       init: async (directory) => {
         await Bun.write(path.join(directory, "results.csv"), "metric,value\naccuracy,0.9\n")
@@ -87,10 +88,20 @@ describe("/file research routes", () => {
           }),
         })
         expect(created.status).toBe(200)
-        const note = (await created.json()) as { id: string; status: string; anchor: { kind: string } }
+        const note = (await created.json()) as {
+          id: string
+          status: string
+          anchor: { kind: string }
+          artifactHash: string
+          version: number
+          revisions: Array<{ event: string }>
+        }
         expect(note.id).toStartWith("ann_")
         expect(note.status).toBe("open")
         expect(note.anchor.kind).toBe("text")
+        expect(note.artifactHash).toMatch(/^[a-f0-9]{64}$/)
+        expect(note.version).toBe(1)
+        expect(note.revisions.map((item) => item.event)).toEqual(["created"])
 
         const listed = await FileRoutes().request("/file/annotations?path=results.csv")
         expect(listed.status).toBe(200)
@@ -102,12 +113,87 @@ describe("/file research routes", () => {
           body: JSON.stringify({ status: "resolved" }),
         })
         expect(resolved.status).toBe(200)
-        expect(((await resolved.json()) as { status: string }).status).toBe("resolved")
+        const resolvedNote = (await resolved.json()) as {
+          status: string
+          version: number
+          revisions: Array<{ event: string }>
+        }
+        expect(resolvedNote.status).toBe("resolved")
+        expect(resolvedNote.version).toBe(2)
+        expect(resolvedNote.revisions.map((item) => item.event)).toEqual(["created", "resolved"])
+
+        const edited = await FileRoutes().request(`/file/annotations/${note.id}`, {
+          method: "PATCH",
+          headers: { "Content-Type": "application/json" },
+          body: JSON.stringify({ body: "Verified against the held-out split." }),
+        })
+        expect(edited.status).toBe(200)
+        const editedNote = (await edited.json()) as {
+          version: number
+          messages: Array<{ body: string }>
+          revisions: Array<{ event: string }>
+        }
+        expect(editedNote.version).toBe(3)
+        expect(editedNote.messages[0]?.body).toBe("Verified against the held-out split.")
+        expect(editedNote.revisions.at(-1)?.event).toBe("edited")
 
         const removed = await FileRoutes().request(`/file/annotations/${note.id}`, { method: "DELETE" })
         expect(removed.status).toBe(200)
-        expect(await removed.json()).toEqual({ deleted: true })
+        expect(await removed.json()).toMatchObject({ deleted: true, version: 4 })
         expect(await (await FileRoutes().request("/file/annotations?path=results.csv")).json()).toEqual([])
+
+        const history = await FileRoutes().request(`/file/annotations/${note.id}/history`)
+        expect(history.status).toBe(200)
+        const tombstone = (await history.json()) as {
+          deletedAt: number
+          version: number
+          revisions: Array<{ version: number; event: string }>
+        }
+        expect(tombstone.deletedAt).toBeNumber()
+        expect(tombstone.version).toBe(4)
+        expect(tombstone.revisions).toEqual([
+          expect.objectContaining({ version: 1, event: "created" }),
+          expect.objectContaining({ version: 2, event: "resolved" }),
+          expect.objectContaining({ version: 3, event: "edited" }),
+          expect.objectContaining({ version: 4, event: "deleted" }),
+        ])
+      },
+    })
+  })
+
+  test("upgrades legacy annotations without losing their review thread", async () => {
+    await using tmp = await tmpdir({
+      init: async (directory) => {
+        await Bun.write(path.join(directory, "legacy.csv"), "metric,value\naccuracy,0.9\n")
+      },
+    })
+    await Instance.provide({
+      directory: tmp.path,
+      fn: async () => {
+        const id = "ann_legacy_review"
+        await Storage.write(["artifact_annotation", Instance.project.id, id], {
+          id,
+          projectID: Instance.project.id,
+          path: "legacy.csv",
+          anchor: { kind: "artifact", label: "legacy.csv" },
+          messages: [{ id: "msg_legacy", body: "Preserve this note.", author: "You", createdAt: 1 }],
+          status: "open",
+          createdAt: 1,
+          updatedAt: 1,
+        })
+
+        const listed = await FileRoutes().request("/file/annotations?path=legacy.csv")
+        expect(listed.status).toBe(200)
+        const notes = (await listed.json()) as Array<{
+          id: string
+          artifactHash: string
+          version: number
+          revisions: Array<{ event: string }>
+        }>
+        expect(notes).toHaveLength(1)
+        expect(notes[0]).toMatchObject({ id, version: 1 })
+        expect(notes[0]?.artifactHash).toMatch(/^[a-f0-9]{64}$/)
+        expect(notes[0]?.revisions.map((item) => item.event)).toEqual(["created"])
       },
     })
   })
diff --git a/frontend/workspace/e2e/artifact-inspector.spec.ts b/frontend/workspace/e2e/artifact-inspector.spec.ts
index 73e19f35..c9a47f0a 100644
--- a/frontend/workspace/e2e/artifact-inspector.spec.ts
+++ b/frontend/workspace/e2e/artifact-inspector.spec.ts
@@ -91,13 +91,30 @@ test("artifact review threads persist and can be resolved", async ({ page, direc
   const thread = inspector.locator('[data-component="artifact-annotation"]').filter({ hasText: "Confirm the O–H" })
   await expect(thread).toBeVisible()
   await expect(inspector.getByText("1 open", { exact: true })).toBeVisible()
+  await expect(thread.getByText("v1", { exact: true })).toBeVisible()
+  await expect(thread.getByText("History · 1 revisions", { exact: true })).toBeVisible()
 
   await thread.getByRole("button", { name: "Resolve", exact: true }).click()
   await expect(thread.getByText("Resolved", { exact: true })).toBeVisible()
+  await expect(thread.getByText("v2", { exact: true })).toBeVisible()
+
+  await thread.getByRole("button", { name: "Edit", exact: true }).click()
+  await inspector.getByLabel(/Edit annotation/).fill("O–H bond length verified against the source structure.")
+  await inspector.getByRole("button", { name: "Save edit", exact: true }).click()
+  const updated = inspector
+    .locator('[data-component="artifact-annotation"]')
+    .filter({ hasText: "O–H bond length verified against the source structure." })
+  await expect(
+    updated.getByText("O–H bond length verified against the source structure.", { exact: true }),
+  ).toBeVisible()
+  await expect(updated.getByText("v3", { exact: true })).toBeVisible()
+  await expect(updated.getByText("History · 3 revisions", { exact: true })).toBeVisible()
 
   await openFile(page, directory, "frontend/workspace/e2e/science/alignment.fasta")
   await openFile(page, directory, "frontend/workspace/e2e/science/water.xyz")
   await inspector.getByRole("tab", { name: "Review", exact: true }).click()
-  await expect(inspector.getByText("Confirm the O–H bond length before publication.", { exact: true })).toBeVisible()
+  await expect(
+    inspector.getByText("O–H bond length verified against the source structure.", { exact: true }),
+  ).toBeVisible()
   await expect(inspector.getByText("0 open", { exact: true })).toBeVisible()
 })
diff --git a/frontend/workspace/src/artifacts/ArtifactInspector.tsx b/frontend/workspace/src/artifacts/ArtifactInspector.tsx
index ddaf9d8a..f368d291 100644
--- a/frontend/workspace/src/artifacts/ArtifactInspector.tsx
+++ b/frontend/workspace/src/artifacts/ArtifactInspector.tsx
@@ -46,6 +46,7 @@ interface AnnotationMessage {
 interface Annotation {
   id: string
   path: string
+  artifactHash: string
   anchor: {
     kind: "artifact" | "text" | "notebook" | "molecule" | "genome"
     label?: string
@@ -59,6 +60,14 @@ interface Annotation {
   }
   messages: AnnotationMessage[]
   status: "open" | "resolved"
+  version: number
+  revisions: Array<{
+    version: number
+    event: "created" | "edited" | "replied" | "resolved" | "reopened" | "deleted"
+    actor: string
+    at: number
+    status: "open" | "resolved"
+  }>
   createdAt: number
   updatedAt: number
 }
@@ -71,6 +80,8 @@ function annotations(value: unknown): Annotation[] {
     return (
       typeof row.id === "string" &&
       (row.status === "open" || row.status === "resolved") &&
+      typeof row.version === "number" &&
+      Array.isArray(row.revisions) &&
       Array.isArray(row.messages) &&
       !!row.anchor &&
       typeof row.anchor.kind === "string"
@@ -425,6 +436,8 @@ function AnnotationThread(props: {
   onUpdate(id: string, body: Record<string, unknown>): Promise<boolean>
 }): JSX.Element {
   const [reply, setReply] = createSignal("")
+  const [edit, setEdit] = createSignal("")
+  const [editing, setEditing] = createSignal(false)
   const [busy, setBusy] = createSignal(false)
   const update = async (body: Record<string, unknown>) => {
     if (busy()) return
@@ -432,6 +445,7 @@ function AnnotationThread(props: {
     const ok = await props.onUpdate(props.annotation.id, body)
     setBusy(false)
     if (ok && typeof body.reply === "string") setReply("")
+    if (ok && typeof body.body === "string") setEditing(false)
   }
   const anchor = () => {
     const value = props.annotation.anchor
@@ -473,6 +487,20 @@ function AnnotationThread(props: {
         >
           {anchor()}
         </span>
+        <span style={{ "font-family": FONT_MONO, "font-size": "9px", color: "var(--color-text-faint)" }}>
+          v{props.annotation.version}
+        </span>
+        <button
+          type="button"
+          disabled={busy()}
+          style={quietButton()}
+          onClick={() => {
+            setEdit(props.annotation.messages[0]?.body ?? "")
+            setEditing(true)
+          }}
+        >
+          Edit
+        </button>
         <button
           type="button"
           disabled={busy()}
@@ -483,15 +511,73 @@ function AnnotationThread(props: {
         </button>
       </div>
       <For each={props.annotation.messages}>
-        {(message) => (
+        {(message, index) => (
           <div style={{ display: "grid", gap: "4px", padding: "8px 0", "border-top": "1px solid var(--color-border)" }}>
-            <p style={{ ...copyStyle(), color: "var(--color-text)" }}>{message.body}</p>
+            <Show
+              when={index() === 0 && editing()}
+              fallback={<p style={{ ...copyStyle(), color: "var(--color-text)" }}>{message.body}</p>}
+            >
+              <textarea
+                aria-label={`Edit annotation ${props.annotation.id}`}
+                value={edit()}
+                rows={3}
+                onInput={(event) => setEdit(event.currentTarget.value)}
+                style={{
+                  width: "100%",
+                  resize: "vertical",
+                  "box-sizing": "border-box",
+                  padding: "8px",
+                  border: "1px solid var(--color-border)",
+                  "border-radius": "5px",
+                  outline: "none",
+                  background: "var(--color-bg)",
+                  color: "var(--color-text)",
+                  "font-family": FONT_SANS,
+                  "font-size": "10px",
+                  "line-height": 1.5,
+                }}
+              />
+              <div style={{ display: "flex", gap: "6px" }}>
+                <button
+                  type="button"
+                  disabled={!edit().trim() || busy()}
+                  style={{ ...quietButton(), border: "1px solid var(--color-border)" }}
+                  onClick={() => void update({ body: edit().trim() })}
+                >
+                  Save edit
+                </button>
+                <button type="button" disabled={busy()} style={quietButton()} onClick={() => setEditing(false)}>
+                  Cancel
+                </button>
+              </div>
+            </Show>
             <span style={{ "font-family": FONT_MONO, "font-size": "9px", color: "var(--color-text-faint)" }}>
               {message.author} · {new Date(message.createdAt).toLocaleString()}
             </span>
           </div>
         )}
       </For>
+      <details>
+        <summary
+          style={{
+            cursor: "pointer",
+            "font-family": FONT_SANS,
+            "font-size": "10px",
+            color: "var(--color-text-muted)",
+          }}
+        >
+          History · {props.annotation.revisions.length} revisions
+        </summary>
+        <ol style={{ margin: "8px 0 0", padding: "0 0 0 20px", display: "grid", gap: "5px" }}>
+          <For each={props.annotation.revisions}>
+            {(item) => (
+              <li style={{ "font-family": FONT_MONO, "font-size": "9px", color: "var(--color-text-faint)" }}>
+                v{item.version} · {item.event} · {item.actor} · {new Date(item.at).toLocaleString()}
+              </li>
+            )}
+          </For>
+        </ol>
+      </details>
       <div style={{ display: "flex", gap: "6px" }}>
         <input
           aria-label={`Reply to ${props.annotation.id}`}

From db9cbfd3a425503647600835474fe088eb1c9a11 Mon Sep 17 00:00:00 2001
From: Aayam Bansal <aayambansal@gmail.com>
Date: Wed, 29 Jul 2026 14:57:38 +0800
Subject: [PATCH 30/40] feat: audit publication readiness

---
 backend/cli/src/file/review.ts                | 582 ++++++++++++++++++
 backend/cli/test/file/review.test.ts          | 185 ++++++
 .../2026-07-29-publication-review-gate.md     | 221 +++++++
 3 files changed, 988 insertions(+)
 create mode 100644 backend/cli/src/file/review.ts
 create mode 100644 backend/cli/test/file/review.test.ts
 create mode 100644 docs/superpowers/plans/2026-07-29-publication-review-gate.md

diff --git a/backend/cli/src/file/review.ts b/backend/cli/src/file/review.ts
new file mode 100644
index 00000000..8662af4d
--- /dev/null
+++ b/backend/cli/src/file/review.ts
@@ -0,0 +1,582 @@
+import path from "node:path"
+import { ulid } from "ulid"
+import z from "zod"
+import { Instance } from "../project/instance"
+import { Provenance } from "../science/provenance/store"
+import { Storage } from "../storage/storage"
+import { ArtifactFile } from "./artifacts"
+
+export namespace PublicationReview {
+  export const Check = z.enum(["citation", "numeric", "figure", "provenance"])
+  export type Check = z.infer<typeof Check>
+
+  export const Severity = z.enum(["blocking", "major", "minor", "info"])
+  export type Severity = z.infer<typeof Severity>
+
+  export const FindingStatus = z.enum(["open", "resolved", "overridden"])
+  export type FindingStatus = z.infer<typeof FindingStatus>
+
+  export const Location = z.object({
+    path: z.string(),
+    line: z.number().int().positive().optional(),
+  })
+  export type Location = z.infer<typeof Location>
+
+  export const Resolution = z.object({
+    kind: z.enum(["resolved", "overridden"]),
+    actor: z.string(),
+    reason: z.string(),
+    at: z.number(),
+  })
+  export type Resolution = z.infer<typeof Resolution>
+
+  export const Finding = z.object({
+    id: z.string(),
+    check: Check,
+    severity: Severity,
+    status: FindingStatus,
+    title: z.string(),
+    detail: z.string(),
+    evidence: z.string().array(),
+    location: Location,
+    resolution: Resolution.optional(),
+  })
+  export type Finding = z.infer<typeof Finding>
+
+  export const Event = z.object({
+    version: z.number().int().positive(),
+    type: z.enum(["generated", "resolved", "overridden", "finalized"]),
+    actor: z.string(),
+    at: z.number(),
+    findingID: z.string().optional(),
+    reason: z.string().optional(),
+  })
+  export type Event = z.infer<typeof Event>
+
+  export const Finalization = z.object({
+    actor: z.string(),
+    at: z.number(),
+    artifactHash: z.string().regex(/^[a-f0-9]{64}$/),
+  })
+  export type Finalization = z.infer<typeof Finalization>
+
+  export const Summary = z.object({
+    total: z.number().int().nonnegative(),
+    open: z.number().int().nonnegative(),
+    blocking: z.number().int().nonnegative(),
+    major: z.number().int().nonnegative(),
+    minor: z.number().int().nonnegative(),
+    info: z.number().int().nonnegative(),
+    resolved: z.number().int().nonnegative(),
+    overridden: z.number().int().nonnegative(),
+  })
+  export type Summary = z.infer<typeof Summary>
+
+  export const Report = z.object({
+    format: z.literal("openscience.publication-review.v1"),
+    id: z.string(),
+    projectID: z.string(),
+    path: z.string(),
+    artifactHash: z.string().regex(/^[a-f0-9]{64}$/),
+    version: z.number().int().positive(),
+    status: z.enum(["blocked", "warnings", "ready"]),
+    summary: Summary,
+    findings: Finding.array(),
+    events: Event.array(),
+    finalized: Finalization.optional(),
+    createdAt: z.number(),
+    updatedAt: z.number(),
+  })
+  export type Report = z.infer<typeof Report>
+
+  export const RunInput = z.object({
+    path: z.string().trim().min(1).max(10_000),
+    actor: z.string().trim().min(1).max(200).default("OpenScience"),
+  })
+  export type RunInput = z.infer<typeof RunInput>
+
+  export const ResolveInput = z.object({
+    status: z.enum(["resolved", "overridden"]),
+    actor: z.string().trim().min(1).max(200),
+    reason: z.string().trim().min(1).max(20_000),
+  })
+  export type ResolveInput = z.infer<typeof ResolveInput>
+
+  export const FinalizeInput = z.object({
+    actor: z.string().trim().min(1).max(200),
+  })
+  export type FinalizeInput = z.infer<typeof FinalizeInput>
+
+  const prefix = () => ["publication_review", Instance.project.id]
+  const key = (id: string) => [...prefix(), id]
+
+  export async function run(input: RunInput): Promise<Report> {
+    const parsed = RunInput.parse(input)
+    const source = await target(parsed.path)
+    if (![".md", ".markdown"].includes(path.extname(source.absolute).toLowerCase())) {
+      throw new Error("Publication review currently requires a Markdown manuscript")
+    }
+    if (!(await Bun.file(source.absolute).exists())) {
+      throw new Error(`Publication manuscript not found: ${parsed.path}`)
+    }
+    const [text, artifactHash, graph, provenance, audit] = await Promise.all([
+      Bun.file(source.absolute).text(),
+      digest(source.absolute),
+      Provenance.project(Instance.directory),
+      ArtifactFile.provenance(Instance.directory, source.relative),
+      ArtifactFile.audit(Instance.directory),
+    ])
+    const findings = [
+      ...(await citations(text, source)),
+      ...(await numbers(text, source)),
+      ...(await figures(text, source, graph.nodes)),
+      ...(await reproducibility(source, provenance, audit)),
+    ]
+    const now = Date.now()
+    const report: Report = {
+      format: "openscience.publication-review.v1",
+      id: `review_${ulid()}`,
+      projectID: Instance.project.id,
+      path: source.relative,
+      artifactHash,
+      version: 1,
+      status: status(findings),
+      summary: summary(findings),
+      findings: findings.toSorted(compare),
+      events: [{ version: 1, type: "generated", actor: parsed.actor, at: now }],
+      createdAt: now,
+      updatedAt: now,
+    }
+    await Storage.write(key(report.id), report)
+    return Report.parse(report)
+  }
+
+  export async function latest(filepath: string): Promise<Report | undefined> {
+    return (await history(filepath)).at(-1)
+  }
+
+  export async function history(filepath: string): Promise<Report[]> {
+    const source = await target(filepath)
+    const keys = await Storage.list(prefix())
+    const reports = await Promise.all(
+      keys.map((item) => Storage.read<unknown>(item).then((value) => Report.parse(value))),
+    )
+    return reports
+      .filter((report) => report.path === source.relative)
+      .toSorted((a, b) => a.createdAt - b.createdAt || a.id.localeCompare(b.id))
+  }
+
+  export async function get(id: string): Promise<Report> {
+    return Report.parse(await Storage.read<unknown>(key(id)))
+  }
+
+  export async function resolve(id: string, findingID: string, input: ResolveInput): Promise<Report> {
+    const parsed = ResolveInput.parse(input)
+    return Report.parse(
+      await Storage.update<Report>(key(id), (report) => {
+        if (report.finalized) throw new Error("A finalized publication review cannot be changed")
+        const finding = report.findings.find((item) => item.id === findingID)
+        if (!finding) throw new Error(`Review finding ${findingID} was not found`)
+        const now = Date.now()
+        finding.status = parsed.status
+        finding.resolution = {
+          kind: parsed.status,
+          actor: parsed.actor,
+          reason: parsed.reason,
+          at: now,
+        }
+        report.version += 1
+        report.updatedAt = now
+        report.status = status(report.findings)
+        report.summary = summary(report.findings)
+        report.events.push({
+          version: report.version,
+          type: parsed.status,
+          actor: parsed.actor,
+          at: now,
+          findingID,
+          reason: parsed.reason,
+        })
+      }),
+    )
+  }
+
+  export async function finalize(id: string, input: FinalizeInput): Promise<Report> {
+    const parsed = FinalizeInput.parse(input)
+    const current = await get(id)
+    await assertCurrent(current)
+    if (current.findings.some((finding) => finding.severity === "blocking" && finding.status === "open")) {
+      throw new Error("Resolve or explicitly override all blocking findings before finalization")
+    }
+    return Report.parse(
+      await Storage.update<Report>(key(id), (report) => {
+        if (report.finalized) return
+        const now = Date.now()
+        report.version += 1
+        report.updatedAt = now
+        report.finalized = {
+          actor: parsed.actor,
+          at: now,
+          artifactHash: report.artifactHash,
+        }
+        report.events.push({
+          version: report.version,
+          type: "finalized",
+          actor: parsed.actor,
+          at: now,
+        })
+      }),
+    )
+  }
+
+  export async function assertReady(filepath: string, id: string): Promise<Report> {
+    const report = await get(id)
+    const source = await target(filepath)
+    if (report.path !== source.relative) throw new Error("The publication review belongs to a different manuscript")
+    await assertCurrent(report)
+    if (!report.finalized) throw new Error("The publication review has not been finalized")
+    if (report.findings.some((finding) => finding.severity === "blocking" && finding.status === "open")) {
+      throw new Error("The publication review still has open blocking findings")
+    }
+    return report
+  }
+
+  async function citations(text: string, source: Awaited<ReturnType<typeof target>>): Promise<Finding[]> {
+    const lines = text.split(/\r?\n/)
+    const definitions = new Set(
+      lines.map((line) => /^\s*\[\^([^\]]+)\]:/.exec(line)?.[1]).filter((value): value is string => Boolean(value)),
+    )
+    const references = new Set<string>()
+    for (const [index, line] of lines.entries()) {
+      for (const match of line.matchAll(/\[\^([^\]]+)\](?!:)/g)) {
+        if (definitions.has(match[1]!)) continue
+        references.add(`${match[1]}\0${index + 1}`)
+      }
+    }
+    const bib = await bibliography(text, source)
+    const keys = new Set<string>()
+    for (const file of bib) {
+      const value = await Bun.file(file)
+        .text()
+        .catch(() => "")
+      for (const match of value.matchAll(/@\w+\s*\{\s*([^,\s]+)\s*,/g)) keys.add(match[1]!)
+    }
+    const cites = new Map<string, number>()
+    for (const [index, line] of lines.entries()) {
+      for (const match of line.matchAll(/@([A-Za-z][A-Za-z0-9_.:+/-]*)/g)) {
+        if (!cites.has(match[1]!)) cites.set(match[1]!, index + 1)
+      }
+    }
+    const missing = await Promise.all(
+      [...cites]
+        .filter(([key]) => !keys.has(key))
+        .map(([key, line]) =>
+          finding({
+            check: "citation",
+            severity: "blocking",
+            title: `Bibliography key @${key} is unresolved`,
+            detail: "The manuscript cites a key that is absent from its local bibliography files.",
+            evidence: bib.length
+              ? bib.map((file) => path.relative(Instance.directory, file).replaceAll("\\", "/"))
+              : ["No local bibliography file was found."],
+            location: { path: source.relative, line },
+          }),
+        ),
+    )
+    const footnotes = await Promise.all(
+      [...references].map((value) => {
+        const [label, line] = value.split("\0")
+        return finding({
+          check: "citation",
+          severity: "blocking",
+          title: `Footnote [^${label}] has no definition`,
+          detail: "Add a matching footnote definition or remove the unresolved reference.",
+          evidence: [`Referenced at ${source.relative}:${line}`],
+          location: { path: source.relative, line: Number(line) },
+        })
+      }),
+    )
+    const placeholders = await Promise.all(
+      lines.flatMap((line, index) => {
+        if (!/\[(?:citation needed|cite|reference needed)\]|\bTODO\s*:?\s*cite\b/i.test(line)) return []
+        return [
+          finding({
+            check: "citation",
+            severity: "blocking",
+            title: "Citation placeholder remains in the manuscript",
+            detail: "Replace the placeholder with a resolvable source before publication.",
+            evidence: [line.trim()],
+            location: { path: source.relative, line: index + 1 },
+          }),
+        ]
+      }),
+    )
+    return [...missing, ...footnotes, ...placeholders]
+  }
+
+  async function numbers(text: string, source: Awaited<ReturnType<typeof target>>): Promise<Finding[]> {
+    const lines = text.split(/\r?\n/)
+    return Promise.all(
+      lines.flatMap((line, index) => {
+        const claim =
+          /\b\d+(?:\.\d+)?\s*%/.test(line) ||
+          /\bp\s*(?:<|>|=|≤|≥)\s*0?\.\d+/i.test(line) ||
+          /\b(?:confidence interval|CI)\b/i.test(line) ||
+          /\b\d+(?:\.\d+)?\s*(?:mg|µg|μg|ng|kg|mL|µL|μL|mm|cm|nm|µm|μm|Hz|kDa)\b/.test(line)
+        if (!claim) return []
+        const traced =
+          /@[A-Za-z][A-Za-z0-9_.:+/-]*/.test(line) ||
+          /\b(?:figure|fig\.?|table|supplement(?:ary)?)\s*[A-Za-z0-9]/i.test(line) ||
+          /\[[^\]]+\]\([^)]*\.(?:csv|tsv|json|jsonl|parquet|arrow|xlsx?|ipynb)(?:[?#][^)]*)?\)/i.test(line)
+        if (traced) return []
+        return [
+          finding({
+            check: "numeric",
+            severity: "major",
+            title: "Numeric claim has no inline evidence trace",
+            detail:
+              "Link this reported value to a citation, table, figure, notebook, or local data artifact so it can be independently checked.",
+            evidence: [line.trim()],
+            location: { path: source.relative, line: index + 1 },
+          }),
+        ]
+      }),
+    )
+  }
+
+  async function figures(
+    text: string,
+    source: Awaited<ReturnType<typeof target>>,
+    nodes: Awaited<ReturnType<typeof Provenance.project>>["nodes"],
+  ): Promise<Finding[]> {
+    const lines = text.split(/\r?\n/)
+    const output: Finding[] = []
+    for (const [index, line] of lines.entries()) {
+      for (const match of line.matchAll(/!\[([^\]]*)\]\(\s*(?:<([^>]+)>|([^\s)]+))(?:\s+["'][^"']*["'])?\s*\)/g)) {
+        const alt = match[1]!.trim()
+        const value = (match[2] ?? match[3]!).trim()
+        if (/^(?:https?:|data:)/i.test(value)) continue
+        const absolute = path.resolve(path.dirname(source.absolute), decodeURIComponent(value.split(/[?#]/)[0]!))
+        const relative = path.relative(Instance.directory, absolute).replaceAll("\\", "/")
+        const inside = await Instance.containsCanonicalPath(absolute)
+        const exists = inside && (await Bun.file(absolute).exists())
+        if (!exists) {
+          output.push(
+            await finding({
+              check: "figure",
+              severity: "blocking",
+              title: `Figure ${value} is missing`,
+              detail: inside
+                ? "The local figure referenced by this manuscript does not exist."
+                : "The figure reference resolves outside the opened project.",
+              evidence: [relative],
+              location: { path: source.relative, line: index + 1 },
+            }),
+          )
+          continue
+        }
+        if (!alt) {
+          output.push(
+            await finding({
+              check: "figure",
+              severity: "minor",
+              title: `Figure ${value} has no alternative text`,
+              detail: "Add concise alternative text describing the scientific content of the figure.",
+              evidence: [relative],
+              location: { path: source.relative, line: index + 1 },
+            }),
+          )
+        }
+        const recorded = nodes.some((node) => {
+          if (node.kind !== "artifact" || !("path" in node) || !node.path) return false
+          const nodePath = path.isAbsolute(node.path)
+            ? path.relative(Instance.directory, node.path).replaceAll("\\", "/")
+            : node.path.replaceAll("\\", "/").replace(/^\.\//, "")
+          return nodePath === relative
+        })
+        if (recorded) continue
+        output.push(
+          await finding({
+            check: "figure",
+            severity: "major",
+            title: `Figure ${value} has no recorded provenance`,
+            detail: "Record the generating run, code, and source inputs for this local figure.",
+            evidence: [relative, "No matching artifact node exists in the project provenance graph."],
+            location: { path: source.relative, line: index + 1 },
+          }),
+        )
+      }
+    }
+    return output
+  }
+
+  async function reproducibility(
+    source: Awaited<ReturnType<typeof target>>,
+    provenance: ArtifactFile.Provenance,
+    audit: ArtifactFile.Audit,
+  ): Promise<Finding[]> {
+    const output: Finding[] = []
+    if (!provenance.tracked || !provenance.commit) {
+      output.push(
+        await finding({
+          check: "provenance",
+          severity: "blocking",
+          title: "Manuscript has no reachable Git snapshot",
+          detail: "Track and commit the manuscript so the reviewed source can be recovered.",
+          evidence: [`Git status: ${provenance.status}`],
+          location: { path: source.relative },
+        }),
+      )
+    } else if (provenance.dirty) {
+      output.push(
+        await finding({
+          check: "provenance",
+          severity: "blocking",
+          title: "Manuscript differs from its recorded Git snapshot",
+          detail: "Commit the reviewed manuscript bytes before marking the publication ready.",
+          evidence: [`Git status: ${provenance.status}`, `Latest commit: ${provenance.commit.sha}`],
+          location: { path: source.relative },
+        }),
+      )
+    }
+    const failures = audit.checks.filter((check) => check.status === "fail")
+    for (const check of failures) {
+      if (check.id === "git-repository" || check.id === "git-commit") continue
+      output.push(
+        await finding({
+          check: "provenance",
+          severity: "blocking",
+          title: check.label,
+          detail: check.detail,
+          evidence: [`Project reproducibility check: ${check.id}`],
+          location: { path: source.relative },
+        }),
+      )
+    }
+    const warnings = audit.checks.filter((check) => check.status === "warn")
+    for (const check of warnings) {
+      if (check.id === "git-clean" && provenance.dirty) continue
+      output.push(
+        await finding({
+          check: "provenance",
+          severity: "minor",
+          title: check.label,
+          detail: check.detail,
+          evidence: [`Project reproducibility check: ${check.id}`],
+          location: { path: source.relative },
+        }),
+      )
+    }
+    return output
+  }
+
+  async function bibliography(text: string, source: Awaited<ReturnType<typeof target>>): Promise<string[]> {
+    const frontmatter = /^---\s*\n([\s\S]*?)\n---/m.exec(text)?.[1] ?? ""
+    const declared = frontmatter.split(/\r?\n/).flatMap((line) => {
+      const value = /^\s*bibliography\s*:\s*(.+)\s*$/i.exec(line)?.[1]
+      if (!value) return []
+      return value
+        .replace(/^\[|\]$/g, "")
+        .split(",")
+        .map((item) => item.trim().replace(/^["']|["']$/g, ""))
+        .filter(Boolean)
+    })
+    const candidates = [
+      ...declared.map((file) => path.resolve(path.dirname(source.absolute), file)),
+      path.join(path.dirname(source.absolute), "references.bib"),
+      path.join(path.dirname(source.absolute), "bibliography.bib"),
+      path.join(path.dirname(source.absolute), "refs.bib"),
+      path.join(Instance.directory, "references.bib"),
+      path.join(Instance.directory, "bibliography.bib"),
+      path.join(Instance.directory, "refs.bib"),
+    ]
+    const unique = [...new Set(candidates)]
+    const safe = await Promise.all(
+      unique.map(async (file) =>
+        (await Instance.containsCanonicalPath(file)) && (await Bun.file(file).exists()) ? file : undefined,
+      ),
+    )
+    return safe.filter((file): file is string => Boolean(file))
+  }
+
+  async function target(value: string) {
+    const absolute = path.resolve(Instance.directory, value)
+    if (!(await Instance.containsCanonicalPath(absolute))) {
+      throw new Error(`Publication review target is outside the project: ${value}`)
+    }
+    return {
+      absolute,
+      relative: path.relative(Instance.directory, absolute).replaceAll("\\", "/"),
+    }
+  }
+
+  async function assertCurrent(report: Report) {
+    const source = await target(report.path)
+    if (!(await Bun.file(source.absolute).exists())) throw new Error("The reviewed manuscript no longer exists")
+    if ((await digest(source.absolute)) !== report.artifactHash) {
+      throw new Error("The manuscript changed after this publication review was generated")
+    }
+  }
+
+  async function finding(input: Omit<Finding, "id" | "status">): Promise<Finding> {
+    return {
+      ...input,
+      id: `finding_${(await hash(JSON.stringify(stable(input)))).slice(0, 20)}`,
+      status: "open",
+    }
+  }
+
+  function summary(findings: Finding[]): Summary {
+    return {
+      total: findings.length,
+      open: findings.filter((finding) => finding.status === "open").length,
+      blocking: findings.filter((finding) => finding.severity === "blocking").length,
+      major: findings.filter((finding) => finding.severity === "major").length,
+      minor: findings.filter((finding) => finding.severity === "minor").length,
+      info: findings.filter((finding) => finding.severity === "info").length,
+      resolved: findings.filter((finding) => finding.status === "resolved").length,
+      overridden: findings.filter((finding) => finding.status === "overridden").length,
+    }
+  }
+
+  function status(findings: Finding[]): Report["status"] {
+    if (findings.some((finding) => finding.severity === "blocking" && finding.status === "open")) return "blocked"
+    if (findings.some((finding) => finding.status === "open")) return "warnings"
+    return "ready"
+  }
+
+  function compare(a: Finding, b: Finding) {
+    const rank: Record<Severity, number> = { blocking: 0, major: 1, minor: 2, info: 3 }
+    return (
+      rank[a.severity] - rank[b.severity] || (a.location.line ?? 0) - (b.location.line ?? 0) || a.id.localeCompare(b.id)
+    )
+  }
+
+  function stable(value: unknown): unknown {
+    if (Array.isArray(value)) return value.map(stable)
+    if (!value || typeof value !== "object") return value
+    return Object.fromEntries(
+      Object.entries(value as Record<string, unknown>)
+        .toSorted(([a], [b]) => a.localeCompare(b))
+        .map(([key, item]) => [key, stable(item)]),
+    )
+  }
+
+  async function digest(file: string) {
+    const hasher = new Bun.CryptoHasher("sha256")
+    const reader = Bun.file(file).stream().getReader()
+    const feed = async (): Promise<void> => {
+      const chunk = await reader.read()
+      if (chunk.done) return
+      hasher.update(chunk.value)
+      return feed()
+    }
+    await feed()
+    return hasher.digest("hex")
+  }
+
+  async function hash(value: string) {
+    const digest = await crypto.subtle.digest("SHA-256", new TextEncoder().encode(value))
+    return [...new Uint8Array(digest)].map((byte) => byte.toString(16).padStart(2, "0")).join("")
+  }
+}
diff --git a/backend/cli/test/file/review.test.ts b/backend/cli/test/file/review.test.ts
new file mode 100644
index 00000000..acdcdeeb
--- /dev/null
+++ b/backend/cli/test/file/review.test.ts
@@ -0,0 +1,185 @@
+import { $ } from "bun"
+import { describe, expect, test } from "bun:test"
+import path from "node:path"
+import { PublicationReview } from "../../src/file/review"
+import { Instance } from "../../src/project/instance"
+import { Provenance } from "../../src/science/provenance/store"
+import { tmpdir } from "../fixture/fixture"
+
+describe("PublicationReview", () => {
+  test("records concrete citation, numeric, figure, and provenance findings", async () => {
+    await using tmp = await tmpdir({
+      git: true,
+      init: async (directory) => {
+        await Bun.write(path.join(directory, "references.bib"), "@article{known2024, title={Known result}}\n")
+        await Bun.write(path.join(directory, "figures", "observed.png"), "not-a-real-image")
+        await Bun.write(
+          path.join(directory, "report.md"),
+          [
+            "---",
+            "bibliography: references.bib",
+            "---",
+            "# Treatment response",
+            "",
+            "The response improved by 42% (p = 0.01).",
+            "",
+            "Prior work supports the mechanism [@missing2024].",
+            "",
+            "The secondary endpoint remained stable[^missing].",
+            "",
+            "![Observed response](figures/observed.png)",
+            "",
+            "![Missing panel](figures/missing.png)",
+            "",
+            "[citation needed]",
+            "",
+          ].join("\n"),
+        )
+      },
+    })
+
+    await Instance.provide({
+      directory: tmp.path,
+      fn: async () => {
+        const report = await PublicationReview.run({
+          path: "report.md",
+          actor: "Aayam Bansal",
+        })
+        expect(report.format).toBe("openscience.publication-review.v1")
+        expect(report.artifactHash).toMatch(/^[a-f0-9]{64}$/)
+        expect(report.status).toBe("blocked")
+        const checks = new Set(report.findings.map((finding) => finding.check))
+        expect(checks.has("citation")).toBe(true)
+        expect(checks.has("numeric")).toBe(true)
+        expect(checks.has("figure")).toBe(true)
+        expect(checks.has("provenance")).toBe(true)
+        expect(report.findings.find((finding) => finding.title.includes("missing2024"))).toMatchObject({
+          severity: "blocking",
+          status: "open",
+          location: { path: "report.md", line: 8 },
+        })
+        expect(report.findings.find((finding) => finding.title.includes("missing.png"))).toMatchObject({
+          severity: "blocking",
+          status: "open",
+        })
+        expect(report.findings.find((finding) => finding.title.includes("observed.png"))).toMatchObject({
+          severity: "major",
+          status: "open",
+        })
+        expect(report.events).toEqual([
+          expect.objectContaining({ type: "generated", actor: "Aayam Bansal", version: 1 }),
+        ])
+        expect(report.summary.blocking).toBeGreaterThanOrEqual(2)
+      },
+    })
+  })
+
+  test("finalizes the exact reviewed bytes after attributed resolutions and overrides", async () => {
+    await using tmp = await tmpdir({
+      git: true,
+      init: async (directory) => {
+        await Bun.write(path.join(directory, "README.md"), "# Review fixture\n")
+        await Bun.write(path.join(directory, "uv.lock"), "version = 1\n")
+        await Bun.write(path.join(directory, "pyproject.toml"), '[project]\nname = "review-fixture"\n')
+        await Bun.write(
+          path.join(directory, "report.md"),
+          "# Result\n\nThe response was 42% [citation needed] and differs from prior work [@missing2024].\n",
+        )
+        await $`git add README.md uv.lock pyproject.toml report.md`.cwd(directory).quiet()
+        await $`git -c user.name=OpenScience -c user.email=test@openscience.local commit -m "review fixture"`
+          .cwd(directory)
+          .quiet()
+      },
+    })
+
+    await Instance.provide({
+      directory: tmp.path,
+      fn: async () => {
+        const report = await PublicationReview.run({ path: "report.md", actor: "Reviewer" })
+        await expect(PublicationReview.finalize(report.id, { actor: "Reviewer" })).rejects.toThrow("blocking findings")
+        const blockers = report.findings.filter((finding) => finding.severity === "blocking")
+        for (const [index, finding] of blockers.entries()) {
+          await PublicationReview.resolve(report.id, finding.id, {
+            status: index ? "overridden" : "resolved",
+            actor: "Aayam Bansal",
+            reason: index ? "Accepted for this exploratory release." : "Verified against the source record.",
+          })
+        }
+        const finalized = await PublicationReview.finalize(report.id, { actor: "Aayam Bansal" })
+        expect(finalized.finalized).toMatchObject({
+          actor: "Aayam Bansal",
+          artifactHash: report.artifactHash,
+        })
+        const events = finalized.events.map((event) => event.type)
+        expect(events).toContain("resolved")
+        expect(events).toContain("overridden")
+        expect(events).toContain("finalized")
+        expect(await PublicationReview.assertReady("report.md", report.id)).toMatchObject({
+          id: report.id,
+          artifactHash: report.artifactHash,
+        })
+
+        await Bun.write(path.join(tmp.path, "report.md"), "# Result\n\nThe response changed.\n")
+        await expect(PublicationReview.assertReady("report.md", report.id)).rejects.toThrow("changed")
+      },
+    })
+  })
+
+  test("recognizes a traced manuscript and keeps report history across source versions", async () => {
+    await using tmp = await tmpdir({
+      git: true,
+      init: async (directory) => {
+        await Bun.write(path.join(directory, "README.md"), "# Ready fixture\n")
+        await Bun.write(path.join(directory, "uv.lock"), "version = 1\n")
+        await Bun.write(path.join(directory, "pyproject.toml"), '[project]\nname = "ready-fixture"\n')
+        await Bun.write(path.join(directory, "references.bib"), "@article{known2024, title={Known result}}\n")
+        await Bun.write(path.join(directory, "figures", "response.svg"), "<svg></svg>")
+        await Bun.write(
+          path.join(directory, "report.md"),
+          [
+            "---",
+            "bibliography: references.bib",
+            "---",
+            "# Result",
+            "",
+            "The response was 42% (Figure 1; @known2024).",
+            "",
+            "![Response](figures/response.svg)",
+            "",
+          ].join("\n"),
+        )
+        await $`git add .`.cwd(directory).quiet()
+        await $`git -c user.name=OpenScience -c user.email=test@openscience.local commit -m "ready fixture"`
+          .cwd(directory)
+          .quiet()
+      },
+    })
+
+    await Provenance.record(
+      {
+        kind: "artifact",
+        label: "Response figure",
+        artifactType: "figure",
+        path: "figures/response.svg",
+        meta: { directory: tmp.path },
+      } as Parameters<typeof Provenance.record>[0],
+    )
+    await Instance.provide({
+      directory: tmp.path,
+      fn: async () => {
+        const first = await PublicationReview.run({ path: "report.md", actor: "Reviewer" })
+        expect(first.findings.filter((finding) => finding.severity === "blocking")).toEqual([])
+        expect(first.status).not.toBe("blocked")
+
+        await Bun.write(
+          path.join(tmp.path, "report.md"),
+          `${await Bun.file(path.join(tmp.path, "report.md")).text()}\n`,
+        )
+        const second = await PublicationReview.run({ path: "report.md", actor: "Reviewer" })
+        expect(second.id).not.toBe(first.id)
+        expect(second.artifactHash).not.toBe(first.artifactHash)
+        expect((await PublicationReview.history("report.md")).map((report) => report.id)).toEqual([first.id, second.id])
+      },
+    })
+  })
+})
diff --git a/docs/superpowers/plans/2026-07-29-publication-review-gate.md b/docs/superpowers/plans/2026-07-29-publication-review-gate.md
new file mode 100644
index 00000000..35d2ef27
--- /dev/null
+++ b/docs/superpowers/plans/2026-07-29-publication-review-gate.md
@@ -0,0 +1,221 @@
+# Deterministic Publication Review Gate Implementation Plan
+
+> **Execution mode:** single-agent implementation on `openscience/aayam-new`.
+> Keep the review engine local, deterministic, version-bound, and independently
+> testable before connecting any optional model reviewer.
+
+**Goal:** Turn OpenScience’s existing publication export and advisory review
+prompts into a real readiness workflow. A scientist can run structural checks
+against a Markdown manuscript, inspect exact findings, resolve or explicitly
+override them with an attributed reason, finalize the exact reviewed bytes, and
+request a reviewed export that cannot silently use stale or unreviewed content.
+
+**Architecture:** Add one file-scoped `PublicationReview` service beside
+`PublicationFile`. It composes the existing canonical path boundary,
+`ArtifactFile.provenance`, project reproducibility audit, and provenance graph.
+Reports live in project-scoped Storage as version-bound sidecars. Findings have
+stable deterministic IDs; report events are append-only. Publication export
+remains available in draft mode and gains an explicit `reviewed` mode that
+requires a finalized report for the current source hash. The artifact
+inspector’s Review tab composes deterministic findings and manual annotation
+threads instead of replacing either.
+
+**Tech stack:** TypeScript, Bun, Zod, Hono, SolidJS, Playwright, existing
+OpenScience Storage and project APIs.
+
+## Global Constraints
+
+- Work only on `openscience/aayam-new`.
+- Preserve the user-owned untracked `AUDIT.md`.
+- Do not modify Atlas unless OpenScience cannot express a required contract.
+- Never push either repository’s `main`.
+- Never run the production npm workflow.
+- Keep `Aayam Bansal <aayambansal@gmail.com>` as author and committer.
+- A review is valid only for the exact SHA-256 of the reviewed manuscript.
+- Deterministic checks must cite a file location or concrete project evidence.
+- Missing evidence is reported as missing; it is never inferred.
+- An override requires actor, reason, timestamp, and an immutable event.
+- Existing draft exports keep working. Only `readiness: "reviewed"` is gated.
+
+---
+
+### Task 1: Review Report Contract and Deterministic Checks
+
+**Files:**
+
+- Create: `backend/cli/src/file/review.ts`
+- Create: `backend/cli/test/file/review.test.ts`
+
+**Contract:**
+
+- Reports include source path/hash, version, timestamps, status, counts,
+  findings, finalization state, and append-only events.
+- Findings cover `citation`, `numeric`, `figure`, and `provenance`.
+- Citation checks detect unresolved citation placeholders, bibliography keys
+  absent from local `.bib` files, and undefined footnotes.
+- Numeric checks identify statistical/numeric claims without a nearby citation,
+  table/figure reference, or linked project data source.
+- Figure checks reject missing local figures, flag empty alt text, and require a
+  matching provenance artifact node for local figures.
+- Provenance checks bind the manuscript to Git state and the existing project
+  reproducibility audit.
+- Re-running after source bytes change creates a new report rather than
+  carrying resolutions across versions.
+
+**Verification:**
+
+- Start with a failing fixture containing one broken citation, undefined
+  footnote, untraced numeric claim, missing figure, unprovenanced figure, and
+  dirty/untracked manuscript.
+- Add a clean fixture whose citations, numeric trace, figure file, provenance
+  node, Git state, environment, and lockfile pass.
+- Run:
+
+  ```bash
+  cd backend/cli
+  bun test test/file/review.test.ts
+  ```
+
+- Commit:
+
+  ```bash
+  git add backend/cli/src/file/review.ts backend/cli/test/file/review.test.ts
+  git commit -m "feat: audit publication readiness"
+  ```
+
+### Task 2: Resolution, Override, Finalization, and Reviewed Export
+
+**Files:**
+
+- Modify: `backend/cli/src/file/review.ts`
+- Modify: `backend/cli/src/file/publication.ts`
+- Modify: `backend/cli/src/file/index.ts`
+- Modify: `backend/cli/test/file/review.test.ts`
+- Modify: `backend/cli/test/file/publication.test.ts`
+
+**Contract:**
+
+- Resolve records actor, reason, time, finding ID, and next report version.
+- Override has the same audit fields plus `kind: "overridden"` and can never be
+  created without a non-empty reason.
+- Finalize fails while a blocking finding is open.
+- Finalize stores actor, time, report ID, and reviewed artifact hash.
+- A finalized report becomes stale immediately when the manuscript changes.
+- `PublicationFile.Input` adds `readiness: "draft" | "reviewed"` with `draft`
+  as the backwards-compatible default.
+- Reviewed export rejects missing, open-blocked, unfinalized, or stale reports.
+- Export results identify draft/reviewed mode and the bound review report.
+
+**Verification:**
+
+- Test open-blocked finalization, resolution, attributed override, successful
+  finalization, stale-source rejection, and ordinary draft export.
+- Re-run publication security tests.
+- Commit:
+
+  ```bash
+  git add backend/cli/src/file/review.ts \
+    backend/cli/src/file/publication.ts \
+    backend/cli/src/file/index.ts \
+    backend/cli/test/file/review.test.ts \
+    backend/cli/test/file/publication.test.ts
+  git commit -m "feat: gate reviewed publication exports"
+  ```
+
+### Task 3: File API
+
+**Files:**
+
+- Modify: `backend/cli/src/server/routes/file.ts`
+- Modify: `backend/cli/test/server/file-research.test.ts`
+
+**Routes:**
+
+- `GET /file/reviews?path=…` — latest report for the current source path.
+- `GET /file/reviews/history?path=…` — prior reports for source versions.
+- `POST /file/reviews` — run deterministic checks.
+- `PATCH /file/reviews/:id/findings/:finding` — resolve or override.
+- `POST /file/reviews/:id/finalize` — finalize the exact reviewed bytes.
+
+**Verification:**
+
+- Exercise routes against actual temporary files and Storage.
+- Verify current report, history, resolution events, failed blocked
+  finalization, successful finalization, and stale state after a file edit.
+- Run the file research and review suites.
+- Regenerate the JavaScript SDK with `./tooling/repo/generate.ts` only if the
+  generated SDK is used by this UI slice; otherwise keep the direct local API
+  pattern already used by the artifact inspector.
+- Commit:
+
+  ```bash
+  git add backend/cli/src/server/routes/file.ts \
+    backend/cli/test/server/file-research.test.ts
+  git commit -m "feat: expose publication review workflow"
+  ```
+
+### Task 4: Artifact Inspector Readiness UI
+
+**Files:**
+
+- Modify: `frontend/workspace/src/artifacts/ArtifactInspector.tsx`
+- Modify: `frontend/workspace/src/artifacts/inspector.ts`
+- Modify: `frontend/workspace/src/artifacts/inspector.test.ts`
+- Modify: `frontend/workspace/e2e/artifact-inspector.spec.ts`
+- Add: `frontend/workspace/e2e/science/review-report.md`
+
+**Contract:**
+
+- Review tab shows a compact readiness header before manual threads.
+- For report formats, “Run checks” loads the exact current manuscript.
+- Findings are grouped by severity and show check type, evidence/location,
+  status, and resolution record.
+- Resolve is a deliberate one-click acknowledgement with an attributed reason.
+- Override opens a reason field and cannot submit empty text.
+- Finalize is disabled while blocking findings are open.
+- Stale state is explicit after the file changes.
+- Non-report artifacts retain annotation threads and show that publication
+  checks apply to Markdown manuscripts.
+
+**Verification:**
+
+- Pure normalization tests cover unknown, blocked, warnings, ready, stale, and
+  finalized states.
+- Browser coverage runs checks on the fixture, resolves/overrides blockers,
+  finalizes the reviewed bytes, and proves state persists after switching
+  files.
+- Run:
+
+  ```bash
+  cd frontend/workspace
+  bun run test:e2e -- e2e/artifact-inspector.spec.ts --workers=1
+  cd ../..
+  bun run typecheck
+  bun run format:check
+  ```
+
+- Commit:
+
+  ```bash
+  git add frontend/workspace/src/artifacts/ArtifactInspector.tsx \
+    frontend/workspace/src/artifacts/inspector.ts \
+    frontend/workspace/src/artifacts/inspector.test.ts \
+    frontend/workspace/e2e/artifact-inspector.spec.ts \
+    frontend/workspace/e2e/science/review-report.md
+  git commit -m "feat: review manuscripts in the artifact inspector"
+  ```
+
+### Task 5: Batch Verification and Publication
+
+- Run the full backend suite from `backend/cli`.
+- Run root typecheck and formatting.
+- Run the serial browser pack and production workspace build.
+- Inspect the review UI at wide and narrow desktop breakpoints.
+- Push only `openscience/aayam-new`.
+- Run branch CI and repair failures on the branch.
+- Trigger `.github/workflows/npm-test.yml` once for this coherent batch.
+- Install `@synsci/openscience@test` and `synsci@test` in a fresh temporary npm
+  prefix, serve with isolated state, and exercise health, review, finalization,
+  and reviewed export through the packaged binary.
+- Record the exact branch SHA, test package version, workflow result, and
+  remaining launch-critical gaps before starting the manuscript authoring slice.

From 0f0d0473ecc29a4c52fcace1bbdfb3374a07631c Mon Sep 17 00:00:00 2001
From: Aayam Bansal <aayambansal@gmail.com>
Date: Wed, 29 Jul 2026 14:58:43 +0800
Subject: [PATCH 31/40] feat: gate reviewed publication exports

---
 backend/cli/src/file/publication.ts       | 30 +++++++++--
 backend/cli/test/file/publication.test.ts | 66 +++++++++++++++++++++++
 2 files changed, 91 insertions(+), 5 deletions(-)

diff --git a/backend/cli/src/file/publication.ts b/backend/cli/src/file/publication.ts
index 85cbe6d2..3c98b629 100644
--- a/backend/cli/src/file/publication.ts
+++ b/backend/cli/src/file/publication.ts
@@ -4,16 +4,28 @@ import { marked, Renderer } from "marked"
 import z from "zod"
 import { OpenScience } from "../openscience"
 import { escapeHtml } from "../util/html"
+import { PublicationReview } from "./review"
 
 export namespace PublicationFile {
   export const Format = z.enum(["html", "pdf", "docx", "latex", "pptx"])
   export type Format = z.infer<typeof Format>
 
-  export const Input = z.object({
-    path: z.string().trim().min(1).max(4_000),
-    format: Format,
-  })
-  export type Input = z.infer<typeof Input>
+  export const Input = z
+    .object({
+      path: z.string().trim().min(1).max(4_000),
+      format: Format,
+      readiness: z.enum(["draft", "reviewed"]).default("draft"),
+      review_id: z.string().startsWith("review_").optional(),
+    })
+    .superRefine((input, context) => {
+      if (input.readiness !== "reviewed" || input.review_id) return
+      context.addIssue({
+        code: "custom",
+        path: ["review_id"],
+        message: "A reviewed publication export requires a finalized review report",
+      })
+    })
+  export type Input = z.input<typeof Input>
 
   export const Capabilities = z.object({
     pandoc: z.boolean(),
@@ -28,6 +40,8 @@ export namespace PublicationFile {
     size: z.number().int().nonnegative(),
     created_at: z.string(),
     engine: z.string(),
+    readiness: z.enum(["draft", "reviewed"]),
+    review_id: z.string().optional(),
   })
   export type Result = z.infer<typeof Result>
 
@@ -62,6 +76,8 @@ export namespace PublicationFile {
       throw new Error("Publication export currently requires a Markdown report")
     }
     if (!(await Bun.file(source).exists())) throw new Error(`Report not found: ${parsed.path}`)
+    const review =
+      parsed.readiness === "reviewed" ? await PublicationReview.assertReady(parsed.path, parsed.review_id!) : undefined
     const support = await capabilities()
     if (!support.formats[parsed.format]) {
       throw new Error(
@@ -150,6 +166,8 @@ ${body}
         size: stat.size,
         created_at: new Date().toISOString(),
         engine: "OpenScience Markdown",
+        readiness: parsed.readiness,
+        ...(review ? { review_id: review.id } : {}),
       })
     }
     const args = [
@@ -184,6 +202,8 @@ ${body}
       size: stat.size,
       created_at: new Date().toISOString(),
       engine: parsed.format === "pdf" ? `pandoc + ${support.pdf_engine}` : "pandoc",
+      readiness: parsed.readiness,
+      ...(review ? { review_id: review.id } : {}),
     })
   }
 
diff --git a/backend/cli/test/file/publication.test.ts b/backend/cli/test/file/publication.test.ts
index aa233d35..39d7b806 100644
--- a/backend/cli/test/file/publication.test.ts
+++ b/backend/cli/test/file/publication.test.ts
@@ -1,6 +1,9 @@
+import { $ } from "bun"
 import { describe, expect, test } from "bun:test"
 import path from "node:path"
 import { PublicationFile } from "../../src/file/publication"
+import { PublicationReview } from "../../src/file/review"
+import { Instance } from "../../src/project/instance"
 import { tmpdir } from "../fixture/fixture"
 
 describe("PublicationFile", () => {
@@ -25,6 +28,7 @@ describe("PublicationFile", () => {
     expect(result.path).toMatch(/^exports\/report-\d{8}-\d{9}-[a-f0-9]{8}\.html$/)
     expect(result.size).toBeGreaterThan(100)
     expect(result.engine).toBe("OpenScience Markdown")
+    expect(result.readiness).toBe("draft")
     const html = await Bun.file(path.join(tmp.path, result.path)).text()
     expect(html).toContain("Treatment response")
     expect(html).toContain("Content-Security-Policy")
@@ -56,4 +60,66 @@ describe("PublicationFile", () => {
     await expect(PublicationFile.render(tmp.path, { path: "data.csv", format: "html" })).rejects.toThrow("Markdown")
     await expect(PublicationFile.render(tmp.path, { path: "../report.md", format: "html" })).rejects.toThrow("escapes")
   })
+
+  test("gates reviewed exports on a finalized report for the exact source bytes", async () => {
+    await using tmp = await tmpdir({
+      git: true,
+      init: async (directory) => {
+        await Bun.write(path.join(directory, "README.md"), "# Publication fixture\n")
+        await Bun.write(path.join(directory, "uv.lock"), "version = 1\n")
+        await Bun.write(path.join(directory, "pyproject.toml"), '[project]\nname = "publication-fixture"\n')
+        await Bun.write(path.join(directory, "report.md"), "# Stable result\n\nAll structural checks pass.\n")
+        await $`git add README.md uv.lock pyproject.toml report.md`.cwd(directory).quiet()
+        await $`git -c user.name=OpenScience -c user.email=test@openscience.local commit -m "publication fixture"`
+          .cwd(directory)
+          .quiet()
+      },
+    })
+
+    await Instance.provide({
+      directory: tmp.path,
+      fn: async () => {
+        const review = await PublicationReview.run({ path: "report.md", actor: "Reviewer" })
+        await expect(
+          PublicationFile.render(tmp.path, {
+            path: "report.md",
+            format: "html",
+            readiness: "reviewed",
+            review_id: review.id,
+          }),
+        ).rejects.toThrow("finalized")
+
+        const finalized = await PublicationReview.finalize(review.id, { actor: "Aayam Bansal" })
+        const result = await PublicationFile.render(tmp.path, {
+          path: "report.md",
+          format: "html",
+          readiness: "reviewed",
+          review_id: finalized.id,
+        })
+        expect(result).toMatchObject({
+          readiness: "reviewed",
+          review_id: finalized.id,
+        })
+
+        await Bun.write(path.join(tmp.path, "report.md"), "# Changed after review\n")
+        await expect(
+          PublicationFile.render(tmp.path, {
+            path: "report.md",
+            format: "html",
+            readiness: "reviewed",
+            review_id: finalized.id,
+          }),
+        ).rejects.toThrow("changed")
+        expect(
+          (
+            await PublicationFile.render(tmp.path, {
+              path: "report.md",
+              format: "html",
+              readiness: "draft",
+            })
+          ).readiness,
+        ).toBe("draft")
+      },
+    })
+  })
 })

From 99bd491401a5702d6c724fa147e8decc980c1dae Mon Sep 17 00:00:00 2001
From: Aayam Bansal <aayambansal@gmail.com>
Date: Wed, 29 Jul 2026 15:01:08 +0800
Subject: [PATCH 32/40] feat: expose publication review workflow

---
 backend/cli/src/file/index.ts                 |   28 +
 backend/cli/src/file/review.ts                |   15 +
 backend/cli/src/server/routes/file.ts         |  114 +
 backend/cli/test/file/review.test.ts          |   16 +-
 backend/cli/test/server/file-research.test.ts |   77 +
 tooling/sdk/js/src/v2/gen/sdk.gen.ts          |  410 ++
 tooling/sdk/js/src/v2/gen/types.gen.ts        |  756 ++++
 tooling/sdk/openapi.json                      | 3497 ++++++++++++++++-
 8 files changed, 4744 insertions(+), 169 deletions(-)

diff --git a/backend/cli/src/file/index.ts b/backend/cli/src/file/index.ts
index 5d3cef2d..eb6a7928 100644
--- a/backend/cli/src/file/index.ts
+++ b/backend/cli/src/file/index.ts
@@ -19,6 +19,7 @@ import { ScienceFile } from "./science"
 import { ArtifactFile } from "./artifacts"
 import { StarterFile } from "./starters"
 import { PublicationFile } from "./publication"
+import { PublicationReview } from "./review"
 
 export namespace File {
   const log = Log.create({ service: "file" })
@@ -390,6 +391,33 @@ export namespace File {
     return PublicationFile.render(Instance.directory, input)
   }
 
+  export async function review(input: PublicationReview.RunInput): Promise<PublicationReview.Report> {
+    return PublicationReview.run(input)
+  }
+
+  export async function reviewCurrent(file: string): Promise<PublicationReview.State | undefined> {
+    return PublicationReview.current(file)
+  }
+
+  export async function reviewHistory(file: string): Promise<PublicationReview.Report[]> {
+    return PublicationReview.history(file)
+  }
+
+  export async function reviewResolve(
+    id: string,
+    finding: string,
+    input: PublicationReview.ResolveInput,
+  ): Promise<PublicationReview.Report> {
+    return PublicationReview.resolve(id, finding, input)
+  }
+
+  export async function reviewFinalize(
+    id: string,
+    input: PublicationReview.FinalizeInput,
+  ): Promise<PublicationReview.Report> {
+    return PublicationReview.finalize(id, input)
+  }
+
   export async function write(file: string, content: string): Promise<Content> {
     using _ = log.time("write", { file })
     const full = await contained(file)
diff --git a/backend/cli/src/file/review.ts b/backend/cli/src/file/review.ts
index 8662af4d..51ecc360 100644
--- a/backend/cli/src/file/review.ts
+++ b/backend/cli/src/file/review.ts
@@ -89,6 +89,11 @@ export namespace PublicationReview {
   })
   export type Report = z.infer<typeof Report>
 
+  export const State = Report.extend({
+    stale: z.boolean(),
+  })
+  export type State = z.infer<typeof State>
+
   export const RunInput = z.object({
     path: z.string().trim().min(1).max(10_000),
     actor: z.string().trim().min(1).max(200).default("OpenScience"),
@@ -155,6 +160,16 @@ export namespace PublicationReview {
     return (await history(filepath)).at(-1)
   }
 
+  export async function current(filepath: string): Promise<State | undefined> {
+    const report = await latest(filepath)
+    if (!report) return
+    const source = await target(filepath)
+    const stale =
+      !(await Bun.file(source.absolute).exists()) ||
+      (await digest(source.absolute).catch(() => "")) !== report.artifactHash
+    return State.parse({ ...report, stale })
+  }
+
   export async function history(filepath: string): Promise<Report[]> {
     const source = await target(filepath)
     const keys = await Storage.list(prefix())
diff --git a/backend/cli/src/server/routes/file.ts b/backend/cli/src/server/routes/file.ts
index 13545f51..418b393d 100644
--- a/backend/cli/src/server/routes/file.ts
+++ b/backend/cli/src/server/routes/file.ts
@@ -11,6 +11,7 @@ import { ArtifactFile } from "../../file/artifacts"
 import { StarterFile } from "../../file/starters"
 import { PublicationFile } from "../../file/publication"
 import { ArtifactAnnotation } from "../../file/annotations"
+import { PublicationReview } from "../../file/review"
 
 export const FileRoutes = lazy(() =>
   new Hono()
@@ -476,6 +477,119 @@ export const FileRoutes = lazy(() =>
       validator("json", PublicationFile.Input),
       async (c) => c.json(await File.publication(c.req.valid("json"))),
     )
+    .get(
+      "/file/reviews",
+      describeRoute({
+        summary: "Read the current publication review",
+        description:
+          "Return the latest deterministic review report and whether it is stale for the current source bytes.",
+        operationId: "file.reviews.current",
+        responses: {
+          200: {
+            description: "Current publication review",
+            content: { "application/json": { schema: resolver(PublicationReview.State) } },
+          },
+          404: { description: "No publication review exists for this manuscript" },
+        },
+      }),
+      validator("query", z.object({ path: z.string().trim().min(1).max(10_000) })),
+      async (c) => {
+        const report = await File.reviewCurrent(c.req.valid("query").path)
+        if (!report) return c.json({ error: "No publication review exists for this manuscript" }, 404)
+        return c.json(report)
+      },
+    )
+    .get(
+      "/file/reviews/history",
+      describeRoute({
+        summary: "List publication review history",
+        description: "List prior deterministic review reports for every reviewed version of a manuscript.",
+        operationId: "file.reviews.history",
+        responses: {
+          200: {
+            description: "Publication review history",
+            content: { "application/json": { schema: resolver(PublicationReview.Report.array()) } },
+          },
+        },
+      }),
+      validator("query", z.object({ path: z.string().trim().min(1).max(10_000) })),
+      async (c) => c.json(await File.reviewHistory(c.req.valid("query").path)),
+    )
+    .post(
+      "/file/reviews",
+      describeRoute({
+        summary: "Run deterministic publication checks",
+        description:
+          "Check citations, numeric traces, figures, and provenance for the exact Markdown manuscript bytes.",
+        operationId: "file.reviews.run",
+        responses: {
+          200: {
+            description: "Generated publication review",
+            content: { "application/json": { schema: resolver(PublicationReview.Report) } },
+          },
+        },
+      }),
+      validator("json", PublicationReview.RunInput),
+      async (c) => c.json(await File.review(c.req.valid("json"))),
+    )
+    .patch(
+      "/file/reviews/:id/findings/:finding",
+      describeRoute({
+        summary: "Resolve or override a publication finding",
+        description: "Record an attributed reason and close one deterministic review finding.",
+        operationId: "file.reviews.resolve",
+        responses: {
+          200: {
+            description: "Updated publication review",
+            content: { "application/json": { schema: resolver(PublicationReview.Report) } },
+          },
+          409: { description: "Finding cannot be updated" },
+        },
+      }),
+      validator(
+        "param",
+        z.object({
+          id: z.string().startsWith("review_"),
+          finding: z.string().startsWith("finding_"),
+        }),
+      ),
+      validator("json", PublicationReview.ResolveInput),
+      async (c) => {
+        const params = c.req.valid("param")
+        const result = await File.reviewResolve(params.id, params.finding, c.req.valid("json")).then(
+          (value) => ({ value }),
+          (error) => ({ error: error instanceof Error ? error.message : String(error) }),
+        )
+        if ("error" in result) return c.json({ error: result.error }, 409)
+        return c.json(result.value)
+      },
+    )
+    .post(
+      "/file/reviews/:id/finalize",
+      describeRoute({
+        summary: "Finalize a publication review",
+        description:
+          "Bind publication-ready state to the exact reviewed source hash after all blocking findings close.",
+        operationId: "file.reviews.finalize",
+        responses: {
+          200: {
+            description: "Finalized publication review",
+            content: { "application/json": { schema: resolver(PublicationReview.Report) } },
+          },
+          409: { description: "Review is blocked, stale, or already invalid" },
+        },
+      }),
+      validator("param", z.object({ id: z.string().startsWith("review_") })),
+      validator("json", PublicationReview.FinalizeInput),
+      async (c) => {
+        const result = await File.reviewFinalize(c.req.valid("param").id, c.req.valid("json")).then(
+          (value) => ({ value }),
+          (error) => ({ error: error instanceof Error ? error.message : String(error) }),
+        )
+        if ("error" in result) return c.json({ error: result.error }, 409)
+        return c.json(result.value)
+      },
+    )
     .get(
       "/file/status",
       describeRoute({
diff --git a/backend/cli/test/file/review.test.ts b/backend/cli/test/file/review.test.ts
index acdcdeeb..e8049ebd 100644
--- a/backend/cli/test/file/review.test.ts
+++ b/backend/cli/test/file/review.test.ts
@@ -155,15 +155,13 @@ describe("PublicationReview", () => {
       },
     })
 
-    await Provenance.record(
-      {
-        kind: "artifact",
-        label: "Response figure",
-        artifactType: "figure",
-        path: "figures/response.svg",
-        meta: { directory: tmp.path },
-      } as Parameters<typeof Provenance.record>[0],
-    )
+    await Provenance.record({
+      kind: "artifact",
+      label: "Response figure",
+      artifactType: "figure",
+      path: "figures/response.svg",
+      meta: { directory: tmp.path },
+    } as Parameters<typeof Provenance.record>[0])
     await Instance.provide({
       directory: tmp.path,
       fn: async () => {
diff --git a/backend/cli/test/server/file-research.test.ts b/backend/cli/test/server/file-research.test.ts
index 8859df53..becb7000 100644
--- a/backend/cli/test/server/file-research.test.ts
+++ b/backend/cli/test/server/file-research.test.ts
@@ -69,6 +69,83 @@ describe("/file research routes", () => {
     })
   })
 
+  test("runs, resolves, finalizes, and detects stale publication reviews", async () => {
+    await using tmp = await tmpdir({
+      git: true,
+      init: async (directory) => {
+        await Bun.write(path.join(directory, "README.md"), "# Review API fixture\n")
+        await Bun.write(path.join(directory, "uv.lock"), "version = 1\n")
+        await Bun.write(path.join(directory, "pyproject.toml"), '[project]\nname = "review-api"\n')
+        await Bun.write(path.join(directory, "report.md"), "# Result\n\nPrior evidence is unresolved [@missing2024].\n")
+        await Bun.$`git add README.md uv.lock pyproject.toml report.md`.cwd(directory).quiet()
+        await Bun.$`git -c user.name=OpenScience -c user.email=test@openscience.local commit -m "review API fixture"`
+          .cwd(directory)
+          .quiet()
+      },
+    })
+    await Instance.provide({
+      directory: tmp.path,
+      fn: async () => {
+        const created = await FileRoutes().request("/file/reviews", {
+          method: "POST",
+          headers: { "Content-Type": "application/json" },
+          body: JSON.stringify({ path: "report.md", actor: "Aayam Bansal" }),
+        })
+        expect(created.status).toBe(200)
+        const report = (await created.json()) as {
+          id: string
+          status: string
+          findings: Array<{ id: string; severity: string; status: string }>
+        }
+        expect(report.status).toBe("blocked")
+
+        const current = await FileRoutes().request("/file/reviews?path=report.md")
+        expect(current.status).toBe(200)
+        expect(await current.json()).toMatchObject({ id: report.id, stale: false })
+
+        const blocked = await FileRoutes().request(`/file/reviews/${report.id}/finalize`, {
+          method: "POST",
+          headers: { "Content-Type": "application/json" },
+          body: JSON.stringify({ actor: "Aayam Bansal" }),
+        })
+        expect(blocked.status).toBe(409)
+
+        for (const finding of report.findings.filter((item) => item.severity === "blocking")) {
+          const resolved = await FileRoutes().request(`/file/reviews/${report.id}/findings/${finding.id}`, {
+            method: "PATCH",
+            headers: { "Content-Type": "application/json" },
+            body: JSON.stringify({
+              status: "overridden",
+              actor: "Aayam Bansal",
+              reason: "Accepted for the internal preview with an explicit audit record.",
+            }),
+          })
+          expect(resolved.status).toBe(200)
+        }
+
+        const finalized = await FileRoutes().request(`/file/reviews/${report.id}/finalize`, {
+          method: "POST",
+          headers: { "Content-Type": "application/json" },
+          body: JSON.stringify({ actor: "Aayam Bansal" }),
+        })
+        expect(finalized.status).toBe(200)
+        expect(await finalized.json()).toMatchObject({
+          id: report.id,
+          finalized: { actor: "Aayam Bansal" },
+        })
+
+        await Bun.write(path.join(tmp.path, "report.md"), "# Changed result\n")
+        expect(await (await FileRoutes().request("/file/reviews?path=report.md")).json()).toMatchObject({
+          id: report.id,
+          stale: true,
+        })
+        const history = await FileRoutes().request("/file/reviews/history?path=report.md")
+        expect(history.status).toBe(200)
+        expect((await history.json()) as unknown[]).toHaveLength(1)
+      },
+    })
+  })
+
   test("versions, resolves, edits, and tombstones durable artifact annotations", async () => {
     await using tmp = await tmpdir({
       init: async (directory) => {
diff --git a/tooling/sdk/js/src/v2/gen/sdk.gen.ts b/tooling/sdk/js/src/v2/gen/sdk.gen.ts
index be1bab45..55b22e47 100644
--- a/tooling/sdk/js/src/v2/gen/sdk.gen.ts
+++ b/tooling/sdk/js/src/v2/gen/sdk.gen.ts
@@ -32,6 +32,11 @@ import type {
   ConfigUpdateResponses,
   EventSubscribeResponses,
   ExperimentalResourceListResponses,
+  FileAnnotationsCreateResponses,
+  FileAnnotationsDeleteResponses,
+  FileAnnotationsHistoryResponses,
+  FileAnnotationsListResponses,
+  FileAnnotationsUpdateResponses,
   FileArtifactsResponses,
   FileInspectResponses,
   FileListResponses,
@@ -44,6 +49,14 @@ import type {
   FileRawResponses,
   FileReadResponses,
   FileReproducibilityResponses,
+  FileReviewsCurrentErrors,
+  FileReviewsCurrentResponses,
+  FileReviewsFinalizeErrors,
+  FileReviewsFinalizeResponses,
+  FileReviewsHistoryResponses,
+  FileReviewsResolveErrors,
+  FileReviewsResolveResponses,
+  FileReviewsRunResponses,
   FileStarterResponses,
   FileStatusResponses,
   FileWriteResponses,
@@ -3401,6 +3414,389 @@ export class Find extends HeyApiClient {
   }
 }
 
+export class Annotations extends HeyApiClient {
+  /**
+   * List artifact annotations
+   *
+   * List durable review threads anchored to a project artifact.
+   */
+  public list<ThrowOnError extends boolean = false>(
+    parameters: {
+      directory?: string
+      path: string
+    },
+    options?: Options<never, ThrowOnError>,
+  ) {
+    const params = buildClientParams(
+      [parameters],
+      [
+        {
+          args: [
+            { in: "query", key: "directory" },
+            { in: "query", key: "path" },
+          ],
+        },
+      ],
+    )
+    return (options?.client ?? this.client).get<FileAnnotationsListResponses, unknown, ThrowOnError>({
+      url: "/file/annotations",
+      ...options,
+      ...params,
+    })
+  }
+
+  /**
+   * Create an artifact annotation
+   *
+   * Create a durable review thread anchored to an artifact, text range, notebook cell, molecule, or locus.
+   */
+  public create<ThrowOnError extends boolean = false>(
+    parameters?: {
+      directory?: string
+      path?: string
+      body?: string
+      author?: string
+      anchor?:
+        | {
+            kind: "artifact"
+            label?: string
+          }
+        | {
+            kind: "text"
+            startLine: number
+            endLine: number
+            quote?: string
+          }
+        | {
+            kind: "notebook"
+            cellId: string
+            line?: number
+          }
+        | {
+            kind: "molecule"
+            selection: string
+            count?: number
+          }
+        | {
+            kind: "genome"
+            chromosome: string
+            start: number
+            end: number
+          }
+    },
+    options?: Options<never, ThrowOnError>,
+  ) {
+    const params = buildClientParams(
+      [parameters],
+      [
+        {
+          args: [
+            { in: "query", key: "directory" },
+            { in: "body", key: "path" },
+            { in: "body", key: "body" },
+            { in: "body", key: "author" },
+            { in: "body", key: "anchor" },
+          ],
+        },
+      ],
+    )
+    return (options?.client ?? this.client).post<FileAnnotationsCreateResponses, unknown, ThrowOnError>({
+      url: "/file/annotations",
+      ...options,
+      ...params,
+      headers: {
+        "Content-Type": "application/json",
+        ...options?.headers,
+        ...params.headers,
+      },
+    })
+  }
+
+  /**
+   * Read artifact annotation history
+   *
+   * Read every immutable revision of an artifact review thread, including a recoverable tombstone.
+   */
+  public history<ThrowOnError extends boolean = false>(
+    parameters: {
+      id: string
+      directory?: string
+    },
+    options?: Options<never, ThrowOnError>,
+  ) {
+    const params = buildClientParams(
+      [parameters],
+      [
+        {
+          args: [
+            { in: "path", key: "id" },
+            { in: "query", key: "directory" },
+          ],
+        },
+      ],
+    )
+    return (options?.client ?? this.client).get<FileAnnotationsHistoryResponses, unknown, ThrowOnError>({
+      url: "/file/annotations/{id}/history",
+      ...options,
+      ...params,
+    })
+  }
+
+  /**
+   * Tombstone an artifact annotation
+   *
+   * Hide an artifact review thread while retaining its recoverable revision history.
+   */
+  public delete<ThrowOnError extends boolean = false>(
+    parameters: {
+      id: string
+      directory?: string
+    },
+    options?: Options<never, ThrowOnError>,
+  ) {
+    const params = buildClientParams(
+      [parameters],
+      [
+        {
+          args: [
+            { in: "path", key: "id" },
+            { in: "query", key: "directory" },
+          ],
+        },
+      ],
+    )
+    return (options?.client ?? this.client).delete<FileAnnotationsDeleteResponses, unknown, ThrowOnError>({
+      url: "/file/annotations/{id}",
+      ...options,
+      ...params,
+    })
+  }
+
+  /**
+   * Update an artifact annotation
+   *
+   * Reply to, resolve, or reopen an artifact review thread.
+   */
+  public update<ThrowOnError extends boolean = false>(
+    parameters: {
+      id: string
+      directory?: string
+      status?: "open" | "resolved"
+      body?: string
+      reply?: string
+      author?: string
+    },
+    options?: Options<never, ThrowOnError>,
+  ) {
+    const params = buildClientParams(
+      [parameters],
+      [
+        {
+          args: [
+            { in: "path", key: "id" },
+            { in: "query", key: "directory" },
+            { in: "body", key: "status" },
+            { in: "body", key: "body" },
+            { in: "body", key: "reply" },
+            { in: "body", key: "author" },
+          ],
+        },
+      ],
+    )
+    return (options?.client ?? this.client).patch<FileAnnotationsUpdateResponses, unknown, ThrowOnError>({
+      url: "/file/annotations/{id}",
+      ...options,
+      ...params,
+      headers: {
+        "Content-Type": "application/json",
+        ...options?.headers,
+        ...params.headers,
+      },
+    })
+  }
+}
+
+export class Reviews extends HeyApiClient {
+  /**
+   * Read the current publication review
+   *
+   * Return the latest deterministic review report and whether it is stale for the current source bytes.
+   */
+  public current<ThrowOnError extends boolean = false>(
+    parameters: {
+      directory?: string
+      path: string
+    },
+    options?: Options<never, ThrowOnError>,
+  ) {
+    const params = buildClientParams(
+      [parameters],
+      [
+        {
+          args: [
+            { in: "query", key: "directory" },
+            { in: "query", key: "path" },
+          ],
+        },
+      ],
+    )
+    return (options?.client ?? this.client).get<FileReviewsCurrentResponses, FileReviewsCurrentErrors, ThrowOnError>({
+      url: "/file/reviews",
+      ...options,
+      ...params,
+    })
+  }
+
+  /**
+   * Run deterministic publication checks
+   *
+   * Check citations, numeric traces, figures, and provenance for the exact Markdown manuscript bytes.
+   */
+  public run<ThrowOnError extends boolean = false>(
+    parameters?: {
+      directory?: string
+      path?: string
+      actor?: string
+    },
+    options?: Options<never, ThrowOnError>,
+  ) {
+    const params = buildClientParams(
+      [parameters],
+      [
+        {
+          args: [
+            { in: "query", key: "directory" },
+            { in: "body", key: "path" },
+            { in: "body", key: "actor" },
+          ],
+        },
+      ],
+    )
+    return (options?.client ?? this.client).post<FileReviewsRunResponses, unknown, ThrowOnError>({
+      url: "/file/reviews",
+      ...options,
+      ...params,
+      headers: {
+        "Content-Type": "application/json",
+        ...options?.headers,
+        ...params.headers,
+      },
+    })
+  }
+
+  /**
+   * List publication review history
+   *
+   * List prior deterministic review reports for every reviewed version of a manuscript.
+   */
+  public history<ThrowOnError extends boolean = false>(
+    parameters: {
+      directory?: string
+      path: string
+    },
+    options?: Options<never, ThrowOnError>,
+  ) {
+    const params = buildClientParams(
+      [parameters],
+      [
+        {
+          args: [
+            { in: "query", key: "directory" },
+            { in: "query", key: "path" },
+          ],
+        },
+      ],
+    )
+    return (options?.client ?? this.client).get<FileReviewsHistoryResponses, unknown, ThrowOnError>({
+      url: "/file/reviews/history",
+      ...options,
+      ...params,
+    })
+  }
+
+  /**
+   * Resolve or override a publication finding
+   *
+   * Record an attributed reason and close one deterministic review finding.
+   */
+  public resolve<ThrowOnError extends boolean = false>(
+    parameters: {
+      id: string
+      finding: string
+      directory?: string
+      status?: "resolved" | "overridden"
+      actor?: string
+      reason?: string
+    },
+    options?: Options<never, ThrowOnError>,
+  ) {
+    const params = buildClientParams(
+      [parameters],
+      [
+        {
+          args: [
+            { in: "path", key: "id" },
+            { in: "path", key: "finding" },
+            { in: "query", key: "directory" },
+            { in: "body", key: "status" },
+            { in: "body", key: "actor" },
+            { in: "body", key: "reason" },
+          ],
+        },
+      ],
+    )
+    return (options?.client ?? this.client).patch<FileReviewsResolveResponses, FileReviewsResolveErrors, ThrowOnError>({
+      url: "/file/reviews/{id}/findings/{finding}",
+      ...options,
+      ...params,
+      headers: {
+        "Content-Type": "application/json",
+        ...options?.headers,
+        ...params.headers,
+      },
+    })
+  }
+
+  /**
+   * Finalize a publication review
+   *
+   * Bind publication-ready state to the exact reviewed source hash after all blocking findings close.
+   */
+  public finalize<ThrowOnError extends boolean = false>(
+    parameters: {
+      id: string
+      directory?: string
+      actor?: string
+    },
+    options?: Options<never, ThrowOnError>,
+  ) {
+    const params = buildClientParams(
+      [parameters],
+      [
+        {
+          args: [
+            { in: "path", key: "id" },
+            { in: "query", key: "directory" },
+            { in: "body", key: "actor" },
+          ],
+        },
+      ],
+    )
+    return (options?.client ?? this.client).post<FileReviewsFinalizeResponses, FileReviewsFinalizeErrors, ThrowOnError>(
+      {
+        url: "/file/reviews/{id}/finalize",
+        ...options,
+        ...params,
+        headers: {
+          "Content-Type": "application/json",
+          ...options?.headers,
+          ...params.headers,
+        },
+      },
+    )
+  }
+}
+
 export class File extends HeyApiClient {
   /**
    * List files
@@ -3710,6 +4106,8 @@ export class File extends HeyApiClient {
       directory?: string
       path?: string
       format?: "html" | "pdf" | "docx" | "latex" | "pptx"
+      readiness?: "draft" | "reviewed"
+      review_id?: string
     },
     options?: Options<never, ThrowOnError>,
   ) {
@@ -3721,6 +4119,8 @@ export class File extends HeyApiClient {
             { in: "query", key: "directory" },
             { in: "body", key: "path" },
             { in: "body", key: "format" },
+            { in: "body", key: "readiness" },
+            { in: "body", key: "review_id" },
           ],
         },
       ],
@@ -3755,6 +4155,16 @@ export class File extends HeyApiClient {
       ...params,
     })
   }
+
+  private _annotations?: Annotations
+  get annotations(): Annotations {
+    return (this._annotations ??= new Annotations({ client: this.client }))
+  }
+
+  private _reviews?: Reviews
+  get reviews(): Reviews {
+    return (this._reviews ??= new Reviews({ client: this.client }))
+  }
 }
 
 export class Notebook extends HeyApiClient {
diff --git a/tooling/sdk/js/src/v2/gen/types.gen.ts b/tooling/sdk/js/src/v2/gen/types.gen.ts
index 4f0872a5..710cb283 100644
--- a/tooling/sdk/js/src/v2/gen/types.gen.ts
+++ b/tooling/sdk/js/src/v2/gen/types.gen.ts
@@ -5871,6 +5871,370 @@ export type FileReproducibilityResponses = {
 
 export type FileReproducibilityResponse = FileReproducibilityResponses[keyof FileReproducibilityResponses]
 
+export type FileAnnotationsListData = {
+  body?: never
+  path?: never
+  query: {
+    directory?: string
+    path: string
+  }
+  url: "/file/annotations"
+}
+
+export type FileAnnotationsListResponses = {
+  /**
+   * Artifact annotations
+   */
+  200: Array<{
+    id: string
+    projectID: string
+    path: string
+    artifactHash: string
+    anchor:
+      | {
+          kind: "artifact"
+          label?: string
+        }
+      | {
+          kind: "text"
+          startLine: number
+          endLine: number
+          quote?: string
+        }
+      | {
+          kind: "notebook"
+          cellId: string
+          line?: number
+        }
+      | {
+          kind: "molecule"
+          selection: string
+          count?: number
+        }
+      | {
+          kind: "genome"
+          chromosome: string
+          start: number
+          end: number
+        }
+    messages: Array<{
+      id: string
+      body: string
+      author: string
+      createdAt: number
+    }>
+    status: "open" | "resolved"
+    version: number
+    revisions: Array<{
+      version: number
+      event: "created" | "edited" | "replied" | "resolved" | "reopened" | "deleted"
+      actor: string
+      at: number
+      status: "open" | "resolved"
+      messages: Array<{
+        id: string
+        body: string
+        author: string
+        createdAt: number
+      }>
+      deletedAt?: number
+    }>
+    createdAt: number
+    updatedAt: number
+    deletedAt?: number
+  }>
+}
+
+export type FileAnnotationsListResponse = FileAnnotationsListResponses[keyof FileAnnotationsListResponses]
+
+export type FileAnnotationsCreateData = {
+  body?: {
+    path: string
+    body: string
+    author?: string
+    anchor?:
+      | {
+          kind: "artifact"
+          label?: string
+        }
+      | {
+          kind: "text"
+          startLine: number
+          endLine: number
+          quote?: string
+        }
+      | {
+          kind: "notebook"
+          cellId: string
+          line?: number
+        }
+      | {
+          kind: "molecule"
+          selection: string
+          count?: number
+        }
+      | {
+          kind: "genome"
+          chromosome: string
+          start: number
+          end: number
+        }
+  }
+  path?: never
+  query?: {
+    directory?: string
+  }
+  url: "/file/annotations"
+}
+
+export type FileAnnotationsCreateResponses = {
+  /**
+   * Created annotation
+   */
+  200: {
+    id: string
+    projectID: string
+    path: string
+    artifactHash: string
+    anchor:
+      | {
+          kind: "artifact"
+          label?: string
+        }
+      | {
+          kind: "text"
+          startLine: number
+          endLine: number
+          quote?: string
+        }
+      | {
+          kind: "notebook"
+          cellId: string
+          line?: number
+        }
+      | {
+          kind: "molecule"
+          selection: string
+          count?: number
+        }
+      | {
+          kind: "genome"
+          chromosome: string
+          start: number
+          end: number
+        }
+    messages: Array<{
+      id: string
+      body: string
+      author: string
+      createdAt: number
+    }>
+    status: "open" | "resolved"
+    version: number
+    revisions: Array<{
+      version: number
+      event: "created" | "edited" | "replied" | "resolved" | "reopened" | "deleted"
+      actor: string
+      at: number
+      status: "open" | "resolved"
+      messages: Array<{
+        id: string
+        body: string
+        author: string
+        createdAt: number
+      }>
+      deletedAt?: number
+    }>
+    createdAt: number
+    updatedAt: number
+    deletedAt?: number
+  }
+}
+
+export type FileAnnotationsCreateResponse = FileAnnotationsCreateResponses[keyof FileAnnotationsCreateResponses]
+
+export type FileAnnotationsHistoryData = {
+  body?: never
+  path: {
+    id: string
+  }
+  query?: {
+    directory?: string
+  }
+  url: "/file/annotations/{id}/history"
+}
+
+export type FileAnnotationsHistoryResponses = {
+  /**
+   * Versioned artifact annotation
+   */
+  200: {
+    id: string
+    projectID: string
+    path: string
+    artifactHash: string
+    anchor:
+      | {
+          kind: "artifact"
+          label?: string
+        }
+      | {
+          kind: "text"
+          startLine: number
+          endLine: number
+          quote?: string
+        }
+      | {
+          kind: "notebook"
+          cellId: string
+          line?: number
+        }
+      | {
+          kind: "molecule"
+          selection: string
+          count?: number
+        }
+      | {
+          kind: "genome"
+          chromosome: string
+          start: number
+          end: number
+        }
+    messages: Array<{
+      id: string
+      body: string
+      author: string
+      createdAt: number
+    }>
+    status: "open" | "resolved"
+    version: number
+    revisions: Array<{
+      version: number
+      event: "created" | "edited" | "replied" | "resolved" | "reopened" | "deleted"
+      actor: string
+      at: number
+      status: "open" | "resolved"
+      messages: Array<{
+        id: string
+        body: string
+        author: string
+        createdAt: number
+      }>
+      deletedAt?: number
+    }>
+    createdAt: number
+    updatedAt: number
+    deletedAt?: number
+  }
+}
+
+export type FileAnnotationsHistoryResponse = FileAnnotationsHistoryResponses[keyof FileAnnotationsHistoryResponses]
+
+export type FileAnnotationsDeleteData = {
+  body?: never
+  path: {
+    id: string
+  }
+  query?: {
+    directory?: string
+  }
+  url: "/file/annotations/{id}"
+}
+
+export type FileAnnotationsDeleteResponses = {
+  /**
+   * Tombstoned annotation
+   */
+  200: {
+    deleted: true
+    version: number
+  }
+}
+
+export type FileAnnotationsDeleteResponse = FileAnnotationsDeleteResponses[keyof FileAnnotationsDeleteResponses]
+
+export type FileAnnotationsUpdateData = {
+  body?: {
+    status?: "open" | "resolved"
+    body?: string
+    reply?: string
+    author?: string
+  }
+  path: {
+    id: string
+  }
+  query?: {
+    directory?: string
+  }
+  url: "/file/annotations/{id}"
+}
+
+export type FileAnnotationsUpdateResponses = {
+  /**
+   * Updated annotation
+   */
+  200: {
+    id: string
+    projectID: string
+    path: string
+    artifactHash: string
+    anchor:
+      | {
+          kind: "artifact"
+          label?: string
+        }
+      | {
+          kind: "text"
+          startLine: number
+          endLine: number
+          quote?: string
+        }
+      | {
+          kind: "notebook"
+          cellId: string
+          line?: number
+        }
+      | {
+          kind: "molecule"
+          selection: string
+          count?: number
+        }
+      | {
+          kind: "genome"
+          chromosome: string
+          start: number
+          end: number
+        }
+    messages: Array<{
+      id: string
+      body: string
+      author: string
+      createdAt: number
+    }>
+    status: "open" | "resolved"
+    version: number
+    revisions: Array<{
+      version: number
+      event: "created" | "edited" | "replied" | "resolved" | "reopened" | "deleted"
+      actor: string
+      at: number
+      status: "open" | "resolved"
+      messages: Array<{
+        id: string
+        body: string
+        author: string
+        createdAt: number
+      }>
+      deletedAt?: number
+    }>
+    createdAt: number
+    updatedAt: number
+    deletedAt?: number
+  }
+}
+
+export type FileAnnotationsUpdateResponse = FileAnnotationsUpdateResponses[keyof FileAnnotationsUpdateResponses]
+
 export type FileManifestData = {
   body?: never
   path?: never
@@ -5967,6 +6331,8 @@ export type FilePublicationData = {
   body?: {
     path: string
     format: "html" | "pdf" | "docx" | "latex" | "pptx"
+    readiness?: "draft" | "reviewed"
+    review_id?: string
   }
   path?: never
   query?: {
@@ -5985,11 +6351,401 @@ export type FilePublicationResponses = {
     size: number
     created_at: string
     engine: string
+    readiness: "draft" | "reviewed"
+    review_id?: string
   }
 }
 
 export type FilePublicationResponse = FilePublicationResponses[keyof FilePublicationResponses]
 
+export type FileReviewsCurrentData = {
+  body?: never
+  path?: never
+  query: {
+    directory?: string
+    path: string
+  }
+  url: "/file/reviews"
+}
+
+export type FileReviewsCurrentErrors = {
+  /**
+   * No publication review exists for this manuscript
+   */
+  404: unknown
+}
+
+export type FileReviewsCurrentResponses = {
+  /**
+   * Current publication review
+   */
+  200: {
+    format: "openscience.publication-review.v1"
+    id: string
+    projectID: string
+    path: string
+    artifactHash: string
+    version: number
+    status: "blocked" | "warnings" | "ready"
+    summary: {
+      total: number
+      open: number
+      blocking: number
+      major: number
+      minor: number
+      info: number
+      resolved: number
+      overridden: number
+    }
+    findings: Array<{
+      id: string
+      check: "citation" | "numeric" | "figure" | "provenance"
+      severity: "blocking" | "major" | "minor" | "info"
+      status: "open" | "resolved" | "overridden"
+      title: string
+      detail: string
+      evidence: Array<string>
+      location: {
+        path: string
+        line?: number
+      }
+      resolution?: {
+        kind: "resolved" | "overridden"
+        actor: string
+        reason: string
+        at: number
+      }
+    }>
+    events: Array<{
+      version: number
+      type: "generated" | "resolved" | "overridden" | "finalized"
+      actor: string
+      at: number
+      findingID?: string
+      reason?: string
+    }>
+    finalized?: {
+      actor: string
+      at: number
+      artifactHash: string
+    }
+    createdAt: number
+    updatedAt: number
+    stale: boolean
+  }
+}
+
+export type FileReviewsCurrentResponse = FileReviewsCurrentResponses[keyof FileReviewsCurrentResponses]
+
+export type FileReviewsRunData = {
+  body?: {
+    path: string
+    actor?: string
+  }
+  path?: never
+  query?: {
+    directory?: string
+  }
+  url: "/file/reviews"
+}
+
+export type FileReviewsRunResponses = {
+  /**
+   * Generated publication review
+   */
+  200: {
+    format: "openscience.publication-review.v1"
+    id: string
+    projectID: string
+    path: string
+    artifactHash: string
+    version: number
+    status: "blocked" | "warnings" | "ready"
+    summary: {
+      total: number
+      open: number
+      blocking: number
+      major: number
+      minor: number
+      info: number
+      resolved: number
+      overridden: number
+    }
+    findings: Array<{
+      id: string
+      check: "citation" | "numeric" | "figure" | "provenance"
+      severity: "blocking" | "major" | "minor" | "info"
+      status: "open" | "resolved" | "overridden"
+      title: string
+      detail: string
+      evidence: Array<string>
+      location: {
+        path: string
+        line?: number
+      }
+      resolution?: {
+        kind: "resolved" | "overridden"
+        actor: string
+        reason: string
+        at: number
+      }
+    }>
+    events: Array<{
+      version: number
+      type: "generated" | "resolved" | "overridden" | "finalized"
+      actor: string
+      at: number
+      findingID?: string
+      reason?: string
+    }>
+    finalized?: {
+      actor: string
+      at: number
+      artifactHash: string
+    }
+    createdAt: number
+    updatedAt: number
+  }
+}
+
+export type FileReviewsRunResponse = FileReviewsRunResponses[keyof FileReviewsRunResponses]
+
+export type FileReviewsHistoryData = {
+  body?: never
+  path?: never
+  query: {
+    directory?: string
+    path: string
+  }
+  url: "/file/reviews/history"
+}
+
+export type FileReviewsHistoryResponses = {
+  /**
+   * Publication review history
+   */
+  200: Array<{
+    format: "openscience.publication-review.v1"
+    id: string
+    projectID: string
+    path: string
+    artifactHash: string
+    version: number
+    status: "blocked" | "warnings" | "ready"
+    summary: {
+      total: number
+      open: number
+      blocking: number
+      major: number
+      minor: number
+      info: number
+      resolved: number
+      overridden: number
+    }
+    findings: Array<{
+      id: string
+      check: "citation" | "numeric" | "figure" | "provenance"
+      severity: "blocking" | "major" | "minor" | "info"
+      status: "open" | "resolved" | "overridden"
+      title: string
+      detail: string
+      evidence: Array<string>
+      location: {
+        path: string
+        line?: number
+      }
+      resolution?: {
+        kind: "resolved" | "overridden"
+        actor: string
+        reason: string
+        at: number
+      }
+    }>
+    events: Array<{
+      version: number
+      type: "generated" | "resolved" | "overridden" | "finalized"
+      actor: string
+      at: number
+      findingID?: string
+      reason?: string
+    }>
+    finalized?: {
+      actor: string
+      at: number
+      artifactHash: string
+    }
+    createdAt: number
+    updatedAt: number
+  }>
+}
+
+export type FileReviewsHistoryResponse = FileReviewsHistoryResponses[keyof FileReviewsHistoryResponses]
+
+export type FileReviewsResolveData = {
+  body?: {
+    status: "resolved" | "overridden"
+    actor: string
+    reason: string
+  }
+  path: {
+    id: string
+    finding: string
+  }
+  query?: {
+    directory?: string
+  }
+  url: "/file/reviews/{id}/findings/{finding}"
+}
+
+export type FileReviewsResolveErrors = {
+  /**
+   * Finding cannot be updated
+   */
+  409: unknown
+}
+
+export type FileReviewsResolveResponses = {
+  /**
+   * Updated publication review
+   */
+  200: {
+    format: "openscience.publication-review.v1"
+    id: string
+    projectID: string
+    path: string
+    artifactHash: string
+    version: number
+    status: "blocked" | "warnings" | "ready"
+    summary: {
+      total: number
+      open: number
+      blocking: number
+      major: number
+      minor: number
+      info: number
+      resolved: number
+      overridden: number
+    }
+    findings: Array<{
+      id: string
+      check: "citation" | "numeric" | "figure" | "provenance"
+      severity: "blocking" | "major" | "minor" | "info"
+      status: "open" | "resolved" | "overridden"
+      title: string
+      detail: string
+      evidence: Array<string>
+      location: {
+        path: string
+        line?: number
+      }
+      resolution?: {
+        kind: "resolved" | "overridden"
+        actor: string
+        reason: string
+        at: number
+      }
+    }>
+    events: Array<{
+      version: number
+      type: "generated" | "resolved" | "overridden" | "finalized"
+      actor: string
+      at: number
+      findingID?: string
+      reason?: string
+    }>
+    finalized?: {
+      actor: string
+      at: number
+      artifactHash: string
+    }
+    createdAt: number
+    updatedAt: number
+  }
+}
+
+export type FileReviewsResolveResponse = FileReviewsResolveResponses[keyof FileReviewsResolveResponses]
+
+export type FileReviewsFinalizeData = {
+  body?: {
+    actor: string
+  }
+  path: {
+    id: string
+  }
+  query?: {
+    directory?: string
+  }
+  url: "/file/reviews/{id}/finalize"
+}
+
+export type FileReviewsFinalizeErrors = {
+  /**
+   * Review is blocked, stale, or already invalid
+   */
+  409: unknown
+}
+
+export type FileReviewsFinalizeResponses = {
+  /**
+   * Finalized publication review
+   */
+  200: {
+    format: "openscience.publication-review.v1"
+    id: string
+    projectID: string
+    path: string
+    artifactHash: string
+    version: number
+    status: "blocked" | "warnings" | "ready"
+    summary: {
+      total: number
+      open: number
+      blocking: number
+      major: number
+      minor: number
+      info: number
+      resolved: number
+      overridden: number
+    }
+    findings: Array<{
+      id: string
+      check: "citation" | "numeric" | "figure" | "provenance"
+      severity: "blocking" | "major" | "minor" | "info"
+      status: "open" | "resolved" | "overridden"
+      title: string
+      detail: string
+      evidence: Array<string>
+      location: {
+        path: string
+        line?: number
+      }
+      resolution?: {
+        kind: "resolved" | "overridden"
+        actor: string
+        reason: string
+        at: number
+      }
+    }>
+    events: Array<{
+      version: number
+      type: "generated" | "resolved" | "overridden" | "finalized"
+      actor: string
+      at: number
+      findingID?: string
+      reason?: string
+    }>
+    finalized?: {
+      actor: string
+      at: number
+      artifactHash: string
+    }
+    createdAt: number
+    updatedAt: number
+  }
+}
+
+export type FileReviewsFinalizeResponse = FileReviewsFinalizeResponses[keyof FileReviewsFinalizeResponses]
+
 export type FileStatusData = {
   body?: never
   path?: never
diff --git a/tooling/sdk/openapi.json b/tooling/sdk/openapi.json
index 5bb6170d..c9f16bd3 100644
--- a/tooling/sdk/openapi.json
+++ b/tooling/sdk/openapi.json
@@ -9244,9 +9244,2202 @@
         ]
       }
     },
+    "/file/annotations": {
+      "get": {
+        "operationId": "file.annotations.list",
+        "parameters": [
+          {
+            "in": "query",
+            "name": "directory",
+            "schema": {
+              "type": "string"
+            }
+          },
+          {
+            "in": "query",
+            "name": "path",
+            "schema": {
+              "type": "string"
+            },
+            "required": true
+          }
+        ],
+        "summary": "List artifact annotations",
+        "description": "List durable review threads anchored to a project artifact.",
+        "responses": {
+          "200": {
+            "description": "Artifact annotations",
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "type": "object",
+                    "properties": {
+                      "id": {
+                        "type": "string"
+                      },
+                      "projectID": {
+                        "type": "string"
+                      },
+                      "path": {
+                        "type": "string"
+                      },
+                      "artifactHash": {
+                        "type": "string",
+                        "pattern": "^[a-f0-9]{64}$"
+                      },
+                      "anchor": {
+                        "anyOf": [
+                          {
+                            "type": "object",
+                            "properties": {
+                              "kind": {
+                                "type": "string",
+                                "const": "artifact"
+                              },
+                              "label": {
+                                "type": "string",
+                                "maxLength": 500
+                              }
+                            },
+                            "required": [
+                              "kind"
+                            ]
+                          },
+                          {
+                            "type": "object",
+                            "properties": {
+                              "kind": {
+                                "type": "string",
+                                "const": "text"
+                              },
+                              "startLine": {
+                                "type": "integer",
+                                "minimum": 1,
+                                "maximum": 9007199254740991
+                              },
+                              "endLine": {
+                                "type": "integer",
+                                "minimum": 1,
+                                "maximum": 9007199254740991
+                              },
+                              "quote": {
+                                "type": "string",
+                                "maxLength": 10000
+                              }
+                            },
+                            "required": [
+                              "kind",
+                              "startLine",
+                              "endLine"
+                            ]
+                          },
+                          {
+                            "type": "object",
+                            "properties": {
+                              "kind": {
+                                "type": "string",
+                                "const": "notebook"
+                              },
+                              "cellId": {
+                                "type": "string",
+                                "minLength": 1,
+                                "maxLength": 500
+                              },
+                              "line": {
+                                "type": "integer",
+                                "minimum": 1,
+                                "maximum": 9007199254740991
+                              }
+                            },
+                            "required": [
+                              "kind",
+                              "cellId"
+                            ]
+                          },
+                          {
+                            "type": "object",
+                            "properties": {
+                              "kind": {
+                                "type": "string",
+                                "const": "molecule"
+                              },
+                              "selection": {
+                                "type": "string",
+                                "minLength": 1,
+                                "maxLength": 2000
+                              },
+                              "count": {
+                                "type": "integer",
+                                "minimum": 1,
+                                "maximum": 9007199254740991
+                              }
+                            },
+                            "required": [
+                              "kind",
+                              "selection"
+                            ]
+                          },
+                          {
+                            "type": "object",
+                            "properties": {
+                              "kind": {
+                                "type": "string",
+                                "const": "genome"
+                              },
+                              "chromosome": {
+                                "type": "string",
+                                "minLength": 1,
+                                "maxLength": 200
+                              },
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+            "name": "directory",
+            "schema": {
+              "type": "string"
+            }
+          },
+          {
+            "in": "path",
+            "name": "id",
+            "schema": {
+              "type": "string",
+              "pattern": "^ann_.*"
+            },
+            "required": true
+          }
+        ],
+        "summary": "Update an artifact annotation",
+        "description": "Reply to, resolve, or reopen an artifact review thread.",
+        "responses": {
+          "200": {
+            "description": "Updated annotation",
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "object",
+                  "properties": {
+                    "id": {
+                      "type": "string"
+                    },
+                    "projectID": {
+                      "type": "string"
+                    },
+                    "path": {
+                      "type": "string"
+                    },
+                    "artifactHash": {
+                      "type": "string",
+                      "pattern": "^[a-f0-9]{64}$"
+                    },
+                    "anchor": {
+                      "anyOf": [
+                        {
+                          "type": "object",
+                          "properties": {
+                            "kind": {
+                              "type": "string",
+                              "const": "artifact"
+                            },
+                            "label": {
+                              "type": "string",
+                              "maxLength": 500
+                            }
+                          },
+                          "required": [
+                            "kind"
+                          ]
+                        },
+                        {
+                          "type": "object",
+                          "properties": {
+                            "kind": {
+                              "type": "string",
+                              "const": "text"
+                            },
+                            "startLine": {
+                              "type": "integer",
+                              "minimum": 1,
+                              "maximum": 9007199254740991
+                            },
+                            "endLine": {
+                              "type": "integer",
+                              "minimum": 1,
+                              "maximum": 9007199254740991
+                            },
+                            "quote": {
+                              "type": "string",
+                              "maxLength": 10000
+                            }
+                          },
+                          "required": [
+                            "kind",
+                            "startLine",
+                            "endLine"
+                          ]
+                        },
+                        {
+                          "type": "object",
+                          "properties": {
+                            "kind": {
+                              "type": "string",
+                              "const": "notebook"
+                            },
+                            "cellId": {
+                              "type": "string",
+                              "minLength": 1,
+                              "maxLength": 500
+                            },
+                            "line": {
+                              "type": "integer",
+                              "minimum": 1,
+                              "maximum": 9007199254740991
+                            }
+                          },
+                          "required": [
+                            "kind",
+                            "cellId"
+                          ]
+                        },
+                        {
+                          "type": "object",
+                          "properties": {
+                            "kind": {
+                              "type": "string",
+                              "const": "molecule"
+                            },
+                            "selection": {
+                              "type": "string",
+                              "minLength": 1,
+                              "maxLength": 2000
+                            },
+                            "count": {
+                              "type": "integer",
+                              "minimum": 1,
+                              "maximum": 9007199254740991
+                            }
+                          },
+                          "required": [
+                            "kind",
+                            "selection"
+                          ]
+                        },
+                        {
+                          "type": "object",
+                          "properties": {
+                            "kind": {
+                              "type": "string",
+                              "const": "genome"
+                            },
+                            "chromosome": {
+                              "type": "string",
+                              "minLength": 1,
+                              "maxLength": 200
+                            },
+                            "start": {
+                              "type": "integer",
+                              "minimum": 0,
+                              "maximum": 9007199254740991
+                            },
+                            "end": {
+                              "type": "integer",
+                              "minimum": 0,
+                              "maximum": 9007199254740991
+                            }
+                          },
+                          "required": [
+                            "kind",
+                            "chromosome",
+                            "start",
+                            "end"
+                          ]
+                        }
+                      ]
+                    },
+                    "messages": {
+                      "type": "array",
+                      "items": {
+                        "type": "object",
+                        "properties": {
+                          "id": {
+                            "type": "string"
+                          },
+                          "body": {
+                            "type": "string"
+                          },
+                          "author": {
+                            "type": "string"
+                          },
+                          "createdAt": {
+                            "type": "number"
+                          }
+                        },
+                        "required": [
+                          "id",
+                          "body",
+                          "author",
+                          "createdAt"
+                        ]
+                      }
+                    },
+                    "status": {
+                      "type": "string",
+                      "enum": [
+                        "open",
+                        "resolved"
+                      ]
+                    },
+                    "version": {
+                      "type": "integer",
+                      "exclusiveMinimum": 0,
+                      "maximum": 9007199254740991
+                    },
+                    "revisions": {
+                      "type": "array",
+                      "items": {
+                        "type": "object",
+                        "properties": {
+                          "version": {
+                            "type": "integer",
+                            "exclusiveMinimum": 0,
+                            "maximum": 9007199254740991
+                          },
+                          "event": {
+                            "type": "string",
+                            "enum": [
+                              "created",
+                              "edited",
+                              "replied",
+                              "resolved",
+                              "reopened",
+                              "deleted"
+                            ]
+                          },
+                          "actor": {
+                            "type": "string"
+                          },
+                          "at": {
+                            "type": "number"
+                          },
+                          "status": {
+                            "type": "string",
+                            "enum": [
+                              "open",
+                              "resolved"
+                            ]
+                          },
+                          "messages": {
+                            "type": "array",
+                            "items": {
+                              "type": "object",
+                              "properties": {
+                                "id": {
+                                  "type": "string"
+                                },
+                                "body": {
+                                  "type": "string"
+                                },
+                                "author": {
+                                  "type": "string"
+                                },
+                                "createdAt": {
+                                  "type": "number"
+                                }
+                              },
+                              "required": [
+                                "id",
+                                "body",
+                                "author",
+                                "createdAt"
+                              ]
+                            }
+                          },
+                          "deletedAt": {
+                            "type": "number"
+                          }
+                        },
+                        "required": [
+                          "version",
+                          "event",
+                          "actor",
+                          "at",
+                          "status",
+                          "messages"
+                        ]
+                      }
+                    },
+                    "createdAt": {
+                      "type": "number"
+                    },
+                    "updatedAt": {
+                      "type": "number"
+                    },
+                    "deletedAt": {
+                      "type": "number"
+                    }
+                  },
+                  "required": [
+                    "id",
+                    "projectID",
+                    "path",
+                    "artifactHash",
+                    "anchor",
+                    "messages",
+                    "status",
+                    "version",
+                    "revisions",
+                    "createdAt",
+                    "updatedAt"
+                  ]
+                }
+              }
+            }
+          }
+        },
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "type": "object",
+                "properties": {
+                  "status": {
+                    "type": "string",
+                    "enum": [
+                      "open",
+                      "resolved"
+                    ]
+                  },
+                  "body": {
+                    "type": "string",
+                    "minLength": 1,
+                    "maxLength": 100000
+                  },
+                  "reply": {
+                    "type": "string",
+                    "minLength": 1,
+                    "maxLength": 100000
+                  },
+                  "author": {
+                    "type": "string",
+                    "minLength": 1,
+                    "maxLength": 200
+                  }
+                }
+              }
+            }
+          }
+        },
+        "x-codeSamples": [
+          {
+            "lang": "js",
+            "source": "import { createOpenScienceClient } from \"@synsci/sdk\"\n\nconst client = createOpenScienceClient()\nawait client.file.annotations.update({\n  ...\n})"
+          }
+        ]
+      },
+      "delete": {
+        "operationId": "file.annotations.delete",
+        "parameters": [
+          {
+            "in": "query",
+            "name": "directory",
+            "schema": {
+              "type": "string"
+            }
+          },
+          {
+            "in": "path",
+            "name": "id",
+            "schema": {
+              "type": "string",
+              "pattern": "^ann_.*"
+            },
+            "required": true
+          }
+        ],
+        "summary": "Tombstone an artifact annotation",
+        "description": "Hide an artifact review thread while retaining its recoverable revision history.",
+        "responses": {
+          "200": {
+            "description": "Tombstoned annotation",
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "object",
+                  "properties": {
+                    "deleted": {
+                      "type": "boolean",
+                      "const": true
+                    },
+                    "version": {
+                      "type": "integer",
+                      "exclusiveMinimum": 0,
+                      "maximum": 9007199254740991
+                    }
+                  },
+                  "required": [
+                    "deleted",
+                    "version"
+                  ]
+                }
+              }
+            }
+          }
+        },
+        "x-codeSamples": [
+          {
+            "lang": "js",
+            "source": "import { createOpenScienceClient } from \"@synsci/sdk\"\n\nconst client = createOpenScienceClient()\nawait client.file.annotations.delete({\n  ...\n})"
+          }
+        ]
+      }
+    },
     "/file/manifest": {
       "get": {
-        "operationId": "file.manifest",
+        "operationId": "file.manifest",
+        "parameters": [
+          {
+            "in": "query",
+            "name": "directory",
+            "schema": {
+              "type": "string"
+            }
+          }
+        ],
+        "summary": "Create an artifact integrity manifest",
+        "description": "Hash every discovered research artifact and return a portable, deterministic manifest.",
+        "responses": {
+          "200": {
+            "description": "Artifact checksum manifest",
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "object",
+                  "properties": {
+                    "format": {
+                      "type": "string",
+                      "const": "openscience.artifact-manifest.v1"
+                    },
+                    "generated_at": {
+                      "type": "string"
+                    },
+                    "digest": {
+                      "type": "string",
+                      "pattern": "^[a-f0-9]{64}$"
+                    },
+                    "artifacts": {
+                      "type": "array",
+                      "items": {
+                        "type": "object",
+                        "properties": {
+                          "name": {
+                            "type": "string"
+                          },
+                          "path": {
+                            "type": "string"
+                          },
+                          "kind": {
+                            "type": "string",
+                            "enum": [
+                              "notebook",
+                              "dataset",
+                              "figure",
+                              "report",
+                              "structure",
+                              "sequence",
+                              "genomics",
+                              "spectrum",
+                              "model",
+                              "archive"
+                            ]
+                          },
+                          "format": {
+                            "type": "string"
+                          },
+                          "size": {
+                            "type": "number"
+                          },
+                          "modified": {
+                            "type": "number"
+                          },
+                          "sha256": {
+                            "type": "string",
+                            "pattern": "^[a-f0-9]{64}$"
+                          }
+                        },
+                        "required": [
+                          "name",
+                          "path",
+                          "kind",
+                          "format",
+                          "size",
+                          "modified",
+                          "sha256"
+                        ]
+                      }
+                    }
+                  },
+                  "required": [
+                    "format",
+                    "generated_at",
+                    "digest",
+                    "artifacts"
+                  ]
+                }
+              }
+            }
+          }
+        },
+        "x-codeSamples": [
+          {
+            "lang": "js",
+            "source": "import { createOpenScienceClient } from \"@synsci/sdk\"\n\nconst client = createOpenScienceClient()\nawait client.file.manifest({\n  ...\n})"
+          }
+        ]
+      }
+    },
+    "/file/starters": {
+      "post": {
+        "operationId": "file.starter",
+        "parameters": [
+          {
+            "in": "query",
+            "name": "directory",
+            "schema": {
+              "type": "string"
+            }
+          }
+        ],
+        "summary": "Create a local scientific starter project",
+        "description": "Materialize a valid notebook, sample data, and README without external downloads.",
+        "responses": {
+          "200": {
+            "description": "Created starter files",
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "object",
+                  "properties": {
+                    "template": {
+                      "type": "string",
+                      "enum": [
+                        "single-cell",
+                        "dose-response",
+                        "protein-structure"
+                      ]
+                    },
+                    "directory": {
+                      "type": "string"
+                    },
+                    "files": {
+                      "type": "array",
+                      "items": {
+                        "type": "string"
+                      }
+                    },
+                    "notebook": {
+                      "type": "string"
+                    },
+                    "readme": {
+                      "type": "string"
+                    }
+                  },
+                  "required": [
+                    "template",
+                    "directory",
+                    "files",
+                    "notebook",
+                    "readme"
+                  ]
+                }
+              }
+            }
+          }
+        },
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "type": "object",
+                "properties": {
+                  "template": {
+                    "type": "string",
+                    "enum": [
+                      "single-cell",
+                      "dose-response",
+                      "protein-structure"
+                    ]
+                  }
+                },
+                "required": [
+                  "template"
+                ]
+              }
+            }
+          }
+        },
+        "x-codeSamples": [
+          {
+            "lang": "js",
+            "source": "import { createOpenScienceClient } from \"@synsci/sdk\"\n\nconst client = createOpenScienceClient()\nawait client.file.starter({\n  ...\n})"
+          }
+        ]
+      }
+    },
+    "/file/publication/capabilities": {
+      "get": {
+        "operationId": "file.publicationCapabilities",
+        "parameters": [
+          {
+            "in": "query",
+            "name": "directory",
+            "schema": {
+              "type": "string"
+            }
+          }
+        ],
+        "summary": "Inspect local publication export support",
+        "description": "Detect Pandoc and a PDF engine before offering report export formats.",
+        "responses": {
+          "200": {
+            "description": "Available local publication formats",
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "object",
+                  "properties": {
+                    "pandoc": {
+                      "type": "boolean"
+                    },
+                    "pdf_engine": {
+                      "type": "string"
+                    },
+                    "formats": {
+                      "type": "object",
+                      "propertyNames": {
+                        "type": "string",
+                        "enum": [
+                          "html",
+                          "pdf",
+                          "docx",
+                          "latex",
+                          "pptx"
+                        ]
+                      },
+                      "additionalProperties": {
+                        "type": "boolean"
+                      }
+                    }
+                  },
+                  "required": [
+                    "pandoc",
+                    "formats"
+                  ]
+                }
+              }
+            }
+          }
+        },
+        "x-codeSamples": [
+          {
+            "lang": "js",
+            "source": "import { createOpenScienceClient } from \"@synsci/sdk\"\n\nconst client = createOpenScienceClient()\nawait client.file.publicationCapabilities({\n  ...\n})"
+          }
+        ]
+      }
+    },
+    "/file/publication": {
+      "post": {
+        "operationId": "file.publication",
+        "parameters": [
+          {
+            "in": "query",
+            "name": "directory",
+            "schema": {
+              "type": "string"
+            }
+          }
+        ],
+        "summary": "Export a Markdown research report",
+        "description": "Create a timestamped HTML, PDF, DOCX, LaTeX, or PowerPoint publication artifact locally.",
+        "responses": {
+          "200": {
+            "description": "Created publication artifact",
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "object",
+                  "properties": {
+                    "path": {
+                      "type": "string"
+                    },
+                    "format": {
+                      "type": "string",
+                      "enum": [
+                        "html",
+                        "pdf",
+                        "docx",
+                        "latex",
+                        "pptx"
+                      ]
+                    },
+                    "size": {
+                      "type": "integer",
+                      "minimum": 0,
+                      "maximum": 9007199254740991
+                    },
+                    "created_at": {
+                      "type": "string"
+                    },
+                    "engine": {
+                      "type": "string"
+                    },
+                    "readiness": {
+                      "type": "string",
+                      "enum": [
+                        "draft",
+                        "reviewed"
+                      ]
+                    },
+                    "review_id": {
+                      "type": "string"
+                    }
+                  },
+                  "required": [
+                    "path",
+                    "format",
+                    "size",
+                    "created_at",
+                    "engine",
+                    "readiness"
+                  ]
+                }
+              }
+            }
+          }
+        },
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "type": "object",
+                "properties": {
+                  "path": {
+                    "type": "string",
+                    "minLength": 1,
+                    "maxLength": 4000
+                  },
+                  "format": {
+                    "type": "string",
+                    "enum": [
+                      "html",
+                      "pdf",
+                      "docx",
+                      "latex",
+                      "pptx"
+                    ]
+                  },
+                  "readiness": {
+                    "default": "draft",
+                    "type": "string",
+                    "enum": [
+                      "draft",
+                      "reviewed"
+                    ]
+                  },
+                  "review_id": {
+                    "type": "string",
+                    "pattern": "^review_.*"
+                  }
+                },
+                "required": [
+                  "path",
+                  "format"
+                ]
+              }
+            }
+          }
+        },
+        "x-codeSamples": [
+          {
+            "lang": "js",
+            "source": "import { createOpenScienceClient } from \"@synsci/sdk\"\n\nconst client = createOpenScienceClient()\nawait client.file.publication({\n  ...\n})"
+          }
+        ]
+      }
+    },
+    "/file/reviews": {
+      "get": {
+        "operationId": "file.reviews.current",
+        "parameters": [
+          {
+            "in": "query",
+            "name": "directory",
+            "schema": {
+              "type": "string"
+            }
+          },
+          {
+            "in": "query",
+            "name": "path",
+            "schema": {
+              "type": "string",
+              "minLength": 1,
+              "maxLength": 10000
+            },
+            "required": true
+          }
+        ],
+        "summary": "Read the current publication review",
+        "description": "Return the latest deterministic review report and whether it is stale for the current source bytes.",
+        "responses": {
+          "200": {
+            "description": "Current publication review",
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "object",
+                  "properties": {
+                    "format": {
+                      "type": "string",
+                      "const": "openscience.publication-review.v1"
+                    },
+                    "id": {
+                      "type": "string"
+                    },
+                    "projectID": {
+                      "type": "string"
+                    },
+                    "path": {
+                      "type": "string"
+                    },
+                    "artifactHash": {
+                      "type": "string",
+                      "pattern": "^[a-f0-9]{64}$"
+                    },
+                    "version": {
+                      "type": "integer",
+                      "exclusiveMinimum": 0,
+                      "maximum": 9007199254740991
+                    },
+                    "status": {
+                      "type": "string",
+                      "enum": [
+                        "blocked",
+                        "warnings",
+                        "ready"
+                      ]
+                    },
+                    "summary": {
+                      "type": "object",
+                      "properties": {
+                        "total": {
+                          "type": "integer",
+                          "minimum": 0,
+                          "maximum": 9007199254740991
+                        },
+                        "open": {
+                          "type": "integer",
+                          "minimum": 0,
+                          "maximum": 9007199254740991
+                        },
+                        "blocking": {
+                          "type": "integer",
+                          "minimum": 0,
+                          "maximum": 9007199254740991
+                        },
+                        "major": {
+                          "type": "integer",
+                          "minimum": 0,
+                          "maximum": 9007199254740991
+                        },
+                        "minor": {
+                          "type": "integer",
+                          "minimum": 0,
+                          "maximum": 9007199254740991
+                        },
+                        "info": {
+                          "type": "integer",
+                          "minimum": 0,
+                          "maximum": 9007199254740991
+                        },
+                        "resolved": {
+                          "type": "integer",
+                          "minimum": 0,
+                          "maximum": 9007199254740991
+                        },
+                        "overridden": {
+                          "type": "integer",
+                          "minimum": 0,
+                          "maximum": 9007199254740991
+                        }
+                      },
+                      "required": [
+                        "total",
+                        "open",
+                        "blocking",
+                        "major",
+                        "minor",
+                        "info",
+                        "resolved",
+                        "overridden"
+                      ]
+                    },
+                    "findings": {
+                      "type": "array",
+                      "items": {
+                        "type": "object",
+                        "properties": {
+                          "id": {
+                            "type": "string"
+                          },
+                          "check": {
+                            "type": "string",
+                            "enum": [
+                              "citation",
+                              "numeric",
+                              "figure",
+                              "provenance"
+                            ]
+                          },
+                          "severity": {
+                            "type": "string",
+                            "enum": [
+                              "blocking",
+                              "major",
+                              "minor",
+                              "info"
+                            ]
+                          },
+                          "status": {
+                            "type": "string",
+                            "enum": [
+                              "open",
+                              "resolved",
+                              "overridden"
+                            ]
+                          },
+                          "title": {
+                            "type": "string"
+                          },
+                          "detail": {
+                            "type": "string"
+                          },
+                          "evidence": {
+                            "type": "array",
+                            "items": {
+                              "type": "string"
+                            }
+                          },
+                          "location": {
+                            "type": "object",
+                            "properties": {
+                              "path": {
+                                "type": "string"
+                              },
+                              "line": {
+                                "type": "integer",
+                                "exclusiveMinimum": 0,
+                                "maximum": 9007199254740991
+                              }
+                            },
+                            "required": [
+                              "path"
+                            ]
+                          },
+                          "resolution": {
+                            "type": "object",
+                            "properties": {
+                              "kind": {
+                                "type": "string",
+                                "enum": [
+                                  "resolved",
+                                  "overridden"
+                                ]
+                              },
+                              "actor": {
+                                "type": "string"
+                              },
+                              "reason": {
+                                "type": "string"
+                              },
+                              "at": {
+                                "type": "number"
+                              }
+                            },
+                            "required": [
+                              "kind",
+                              "actor",
+                              "reason",
+                              "at"
+                            ]
+                          }
+                        },
+                        "required": [
+                          "id",
+                          "check",
+                          "severity",
+                          "status",
+                          "title",
+                          "detail",
+                          "evidence",
+                          "location"
+                        ]
+                      }
+                    },
+                    "events": {
+                      "type": "array",
+                      "items": {
+                        "type": "object",
+                        "properties": {
+                          "version": {
+                            "type": "integer",
+                            "exclusiveMinimum": 0,
+                            "maximum": 9007199254740991
+                          },
+                          "type": {
+                            "type": "string",
+                            "enum": [
+                              "generated",
+                              "resolved",
+                              "overridden",
+                              "finalized"
+                            ]
+                          },
+                          "actor": {
+                            "type": "string"
+                          },
+                          "at": {
+                            "type": "number"
+                          },
+                          "findingID": {
+                            "type": "string"
+                          },
+                          "reason": {
+                            "type": "string"
+                          }
+                        },
+                        "required": [
+                          "version",
+                          "type",
+                          "actor",
+                          "at"
+                        ]
+                      }
+                    },
+                    "finalized": {
+                      "type": "object",
+                      "properties": {
+                        "actor": {
+                          "type": "string"
+                        },
+                        "at": {
+                          "type": "number"
+                        },
+                        "artifactHash": {
+                          "type": "string",
+                          "pattern": "^[a-f0-9]{64}$"
+                        }
+                      },
+                      "required": [
+                        "actor",
+                        "at",
+                        "artifactHash"
+                      ]
+                    },
+                    "createdAt": {
+                      "type": "number"
+                    },
+                    "updatedAt": {
+                      "type": "number"
+                    },
+                    "stale": {
+                      "type": "boolean"
+                    }
+                  },
+                  "required": [
+                    "format",
+                    "id",
+                    "projectID",
+                    "path",
+                    "artifactHash",
+                    "version",
+                    "status",
+                    "summary",
+                    "findings",
+                    "events",
+                    "createdAt",
+                    "updatedAt",
+                    "stale"
+                  ]
+                }
+              }
+            }
+          },
+          "404": {
+            "description": "No publication review exists for this manuscript"
+          }
+        },
+        "x-codeSamples": [
+          {
+            "lang": "js",
+            "source": "import { createOpenScienceClient } from \"@synsci/sdk\"\n\nconst client = createOpenScienceClient()\nawait client.file.reviews.current({\n  ...\n})"
+          }
+        ]
+      },
+      "post": {
+        "operationId": "file.reviews.run",
         "parameters": [
           {
             "in": "query",
@@ -9256,11 +11449,11 @@
             }
           }
         ],
-        "summary": "Create an artifact integrity manifest",
-        "description": "Hash every discovered research artifact and return a portable, deterministic manifest.",
+        "summary": "Run deterministic publication checks",
+        "description": "Check citations, numeric traces, figures, and provenance for the exact Markdown manuscript bytes.",
         "responses": {
           "200": {
-            "description": "Artifact checksum manifest",
+            "description": "Generated publication review",
             "content": {
               "application/json": {
                 "schema": {
@@ -9268,89 +11461,313 @@
                   "properties": {
                     "format": {
                       "type": "string",
-                      "const": "openscience.artifact-manifest.v1"
+                      "const": "openscience.publication-review.v1"
                     },
-                    "generated_at": {
+                    "id": {
                       "type": "string"
                     },
-                    "digest": {
+                    "projectID": {
+                      "type": "string"
+                    },
+                    "path": {
+                      "type": "string"
+                    },
+                    "artifactHash": {
                       "type": "string",
                       "pattern": "^[a-f0-9]{64}$"
                     },
-                    "artifacts": {
+                    "version": {
+                      "type": "integer",
+                      "exclusiveMinimum": 0,
+                      "maximum": 9007199254740991
+                    },
+                    "status": {
+                      "type": "string",
+                      "enum": [
+                        "blocked",
+                        "warnings",
+                        "ready"
+                      ]
+                    },
+                    "summary": {
+                      "type": "object",
+                      "properties": {
+                        "total": {
+                          "type": "integer",
+                          "minimum": 0,
+                          "maximum": 9007199254740991
+                        },
+                        "open": {
+                          "type": "integer",
+                          "minimum": 0,
+                          "maximum": 9007199254740991
+                        },
+                        "blocking": {
+                          "type": "integer",
+                          "minimum": 0,
+                          "maximum": 9007199254740991
+                        },
+                        "major": {
+                          "type": "integer",
+                          "minimum": 0,
+                          "maximum": 9007199254740991
+                        },
+                        "minor": {
+                          "type": "integer",
+                          "minimum": 0,
+                          "maximum": 9007199254740991
+                        },
+                        "info": {
+                          "type": "integer",
+                          "minimum": 0,
+                          "maximum": 9007199254740991
+                        },
+                        "resolved": {
+                          "type": "integer",
+                          "minimum": 0,
+                          "maximum": 9007199254740991
+                        },
+                        "overridden": {
+                          "type": "integer",
+                          "minimum": 0,
+                          "maximum": 9007199254740991
+                        }
+                      },
+                      "required": [
+                        "total",
+                        "open",
+                        "blocking",
+                        "major",
+                        "minor",
+                        "info",
+                        "resolved",
+                        "overridden"
+                      ]
+                    },
+                    "findings": {
                       "type": "array",
                       "items": {
                         "type": "object",
                         "properties": {
-                          "name": {
-                            "type": "string"
-                          },
-                          "path": {
+                          "id": {
                             "type": "string"
                           },
-                          "kind": {
+                          "check": {
                             "type": "string",
                             "enum": [
-                              "notebook",
-                              "dataset",
+                              "citation",
+                              "numeric",
                               "figure",
-                              "report",
-                              "structure",
-                              "sequence",
-                              "genomics",
-                              "spectrum",
-                              "model",
-                              "archive"
+                              "provenance"
+                            ]
+                          },
+                          "severity": {
+                            "type": "string",
+                            "enum": [
+                              "blocking",
+                              "major",
+                              "minor",
+                              "info"
+                            ]
+                          },
+                          "status": {
+                            "type": "string",
+                            "enum": [
+                              "open",
+                              "resolved",
+                              "overridden"
+                            ]
+                          },
+                          "title": {
+                            "type": "string"
+                          },
+                          "detail": {
+                            "type": "string"
+                          },
+                          "evidence": {
+                            "type": "array",
+                            "items": {
+                              "type": "string"
+                            }
+                          },
+                          "location": {
+                            "type": "object",
+                            "properties": {
+                              "path": {
+                                "type": "string"
+                              },
+                              "line": {
+                                "type": "integer",
+                                "exclusiveMinimum": 0,
+                                "maximum": 9007199254740991
+                              }
+                            },
+                            "required": [
+                              "path"
+                            ]
+                          },
+                          "resolution": {
+                            "type": "object",
+                            "properties": {
+                              "kind": {
+                                "type": "string",
+                                "enum": [
+                                  "resolved",
+                                  "overridden"
+                                ]
+                              },
+                              "actor": {
+                                "type": "string"
+                              },
+                              "reason": {
+                                "type": "string"
+                              },
+                              "at": {
+                                "type": "number"
+                              }
+                            },
+                            "required": [
+                              "kind",
+                              "actor",
+                              "reason",
+                              "at"
+                            ]
+                          }
+                        },
+                        "required": [
+                          "id",
+                          "check",
+                          "severity",
+                          "status",
+                          "title",
+                          "detail",
+                          "evidence",
+                          "location"
+                        ]
+                      }
+                    },
+                    "events": {
+                      "type": "array",
+                      "items": {
+                        "type": "object",
+                        "properties": {
+                          "version": {
+                            "type": "integer",
+                            "exclusiveMinimum": 0,
+                            "maximum": 9007199254740991
+                          },
+                          "type": {
+                            "type": "string",
+                            "enum": [
+                              "generated",
+                              "resolved",
+                              "overridden",
+                              "finalized"
                             ]
                           },
-                          "format": {
+                          "actor": {
                             "type": "string"
                           },
-                          "size": {
+                          "at": {
                             "type": "number"
                           },
-                          "modified": {
-                            "type": "number"
+                          "findingID": {
+                            "type": "string"
                           },
-                          "sha256": {
-                            "type": "string",
-                            "pattern": "^[a-f0-9]{64}$"
+                          "reason": {
+                            "type": "string"
                           }
                         },
                         "required": [
-                          "name",
-                          "path",
-                          "kind",
-                          "format",
-                          "size",
-                          "modified",
-                          "sha256"
+                          "version",
+                          "type",
+                          "actor",
+                          "at"
                         ]
                       }
+                    },
+                    "finalized": {
+                      "type": "object",
+                      "properties": {
+                        "actor": {
+                          "type": "string"
+                        },
+                        "at": {
+                          "type": "number"
+                        },
+                        "artifactHash": {
+                          "type": "string",
+                          "pattern": "^[a-f0-9]{64}$"
+                        }
+                      },
+                      "required": [
+                        "actor",
+                        "at",
+                        "artifactHash"
+                      ]
+                    },
+                    "createdAt": {
+                      "type": "number"
+                    },
+                    "updatedAt": {
+                      "type": "number"
                     }
                   },
                   "required": [
                     "format",
-                    "generated_at",
-                    "digest",
-                    "artifacts"
+                    "id",
+                    "projectID",
+                    "path",
+                    "artifactHash",
+                    "version",
+                    "status",
+                    "summary",
+                    "findings",
+                    "events",
+                    "createdAt",
+                    "updatedAt"
                   ]
                 }
               }
             }
           }
         },
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "type": "object",
+                "properties": {
+                  "path": {
+                    "type": "string",
+                    "minLength": 1,
+                    "maxLength": 10000
+                  },
+                  "actor": {
+                    "default": "OpenScience",
+                    "type": "string",
+                    "minLength": 1,
+                    "maxLength": 200
+                  }
+                },
+                "required": [
+                  "path"
+                ]
+              }
+            }
+          }
+        },
         "x-codeSamples": [
           {
             "lang": "js",
-            "source": "import { createOpenScienceClient } from \"@synsci/sdk\"\n\nconst client = createOpenScienceClient()\nawait client.file.manifest({\n  ...\n})"
+            "source": "import { createOpenScienceClient } from \"@synsci/sdk\"\n\nconst client = createOpenScienceClient()\nawait client.file.reviews.run({\n  ...\n})"
           }
         ]
       }
     },
-    "/file/starters": {
-      "post": {
-        "operationId": "file.starter",
+    "/file/reviews/history": {
+      "get": {
+        "operationId": "file.reviews.history",
         "parameters": [
           {
             "in": "query",
@@ -9358,72 +11775,300 @@
             "schema": {
               "type": "string"
             }
+          },
+          {
+            "in": "query",
+            "name": "path",
+            "schema": {
+              "type": "string",
+              "minLength": 1,
+              "maxLength": 10000
+            },
+            "required": true
           }
         ],
-        "summary": "Create a local scientific starter project",
-        "description": "Materialize a valid notebook, sample data, and README without external downloads.",
+        "summary": "List publication review history",
+        "description": "List prior deterministic review reports for every reviewed version of a manuscript.",
         "responses": {
           "200": {
-            "description": "Created starter files",
+            "description": "Publication review history",
             "content": {
               "application/json": {
                 "schema": {
-                  "type": "object",
-                  "properties": {
-                    "template": {
-                      "type": "string",
-                      "enum": [
-                        "single-cell",
-                        "dose-response",
-                        "protein-structure"
-                      ]
-                    },
-                    "directory": {
-                      "type": "string"
-                    },
-                    "files": {
-                      "type": "array",
-                      "items": {
+                  "type": "array",
+                  "items": {
+                    "type": "object",
+                    "properties": {
+                      "format": {
+                        "type": "string",
+                        "const": "openscience.publication-review.v1"
+                      },
+                      "id": {
+                        "type": "string"
+                      },
+                      "projectID": {
+                        "type": "string"
+                      },
+                      "path": {
                         "type": "string"
+                      },
+                      "artifactHash": {
+                        "type": "string",
+                        "pattern": "^[a-f0-9]{64}$"
+                      },
+                      "version": {
+                        "type": "integer",
+                        "exclusiveMinimum": 0,
+                        "maximum": 9007199254740991
+                      },
+                      "status": {
+                        "type": "string",
+                        "enum": [
+                          "blocked",
+                          "warnings",
+                          "ready"
+                        ]
+                      },
+                      "summary": {
+                        "type": "object",
+                        "properties": {
+                          "total": {
+                            "type": "integer",
+                            "minimum": 0,
+                            "maximum": 9007199254740991
+                          },
+                          "open": {
+                            "type": "integer",
+                            "minimum": 0,
+                            "maximum": 9007199254740991
+                          },
+                          "blocking": {
+                            "type": "integer",
+                            "minimum": 0,
+                            "maximum": 9007199254740991
+                          },
+                          "major": {
+                            "type": "integer",
+                            "minimum": 0,
+                            "maximum": 9007199254740991
+                          },
+                          "minor": {
+                            "type": "integer",
+                            "minimum": 0,
+                            "maximum": 9007199254740991
+                          },
+                          "info": {
+                            "type": "integer",
+                            "minimum": 0,
+                            "maximum": 9007199254740991
+                          },
+                          "resolved": {
+                            "type": "integer",
+                            "minimum": 0,
+                            "maximum": 9007199254740991
+                          },
+                          "overridden": {
+                            "type": "integer",
+                            "minimum": 0,
+                            "maximum": 9007199254740991
+                          }
+                        },
+                        "required": [
+                          "total",
+                          "open",
+                          "blocking",
+                          "major",
+                          "minor",
+                          "info",
+                          "resolved",
+                          "overridden"
+                        ]
+                      },
+                      "findings": {
+                        "type": "array",
+                        "items": {
+                          "type": "object",
+                          "properties": {
+                            "id": {
+                              "type": "string"
+                            },
+                            "check": {
+                              "type": "string",
+                              "enum": [
+                                "citation",
+                                "numeric",
+                                "figure",
+                                "provenance"
+                              ]
+                            },
+                            "severity": {
+                              "type": "string",
+                              "enum": [
+                                "blocking",
+                                "major",
+                                "minor",
+                                "info"
+                              ]
+                            },
+                            "status": {
+                              "type": "string",
+                              "enum": [
+                                "open",
+                                "resolved",
+                                "overridden"
+                              ]
+                            },
+                            "title": {
+                              "type": "string"
+                            },
+                            "detail": {
+                              "type": "string"
+                            },
+                            "evidence": {
+                              "type": "array",
+                              "items": {
+                                "type": "string"
+                              }
+                            },
+                            "location": {
+                              "type": "object",
+                              "properties": {
+                                "path": {
+                                  "type": "string"
+                                },
+                                "line": {
+                                  "type": "integer",
+                                  "exclusiveMinimum": 0,
+                                  "maximum": 9007199254740991
+                                }
+                              },
+                              "required": [
+                                "path"
+                              ]
+                            },
+                            "resolution": {
+                              "type": "object",
+                              "properties": {
+                                "kind": {
+                                  "type": "string",
+                                  "enum": [
+                                    "resolved",
+                                    "overridden"
+                                  ]
+                                },
+                                "actor": {
+                                  "type": "string"
+                                },
+                                "reason": {
+                                  "type": "string"
+                                },
+                                "at": {
+                                  "type": "number"
+                                }
+                              },
+                              "required": [
+                                "kind",
+                                "actor",
+                                "reason",
+                                "at"
+                              ]
+                            }
+                          },
+                          "required": [
+                            "id",
+                            "check",
+                            "severity",
+                            "status",
+                            "title",
+                            "detail",
+                            "evidence",
+                            "location"
+                          ]
+                        }
+                      },
+                      "events": {
+                        "type": "array",
+                        "items": {
+                          "type": "object",
+                          "properties": {
+                            "version": {
+                              "type": "integer",
+                              "exclusiveMinimum": 0,
+                              "maximum": 9007199254740991
+                            },
+                            "type": {
+                              "type": "string",
+                              "enum": [
+                                "generated",
+                                "resolved",
+                                "overridden",
+                                "finalized"
+                              ]
+                            },
+                            "actor": {
+                              "type": "string"
+                            },
+                            "at": {
+                              "type": "number"
+                            },
+                            "findingID": {
+                              "type": "string"
+                            },
+                            "reason": {
+                              "type": "string"
+                            }
+                          },
+                          "required": [
+                            "version",
+                            "type",
+                            "actor",
+                            "at"
+                          ]
+                        }
+                      },
+                      "finalized": {
+                        "type": "object",
+                        "properties": {
+                          "actor": {
+                            "type": "string"
+                          },
+                          "at": {
+                            "type": "number"
+                          },
+                          "artifactHash": {
+                            "type": "string",
+                            "pattern": "^[a-f0-9]{64}$"
+                          }
+                        },
+                        "required": [
+                          "actor",
+                          "at",
+                          "artifactHash"
+                        ]
+                      },
+                      "createdAt": {
+                        "type": "number"
+                      },
+                      "updatedAt": {
+                        "type": "number"
                       }
                     },
-                    "notebook": {
-                      "type": "string"
-                    },
-                    "readme": {
-                      "type": "string"
-                    }
-                  },
-                  "required": [
-                    "template",
-                    "directory",
-                    "files",
-                    "notebook",
-                    "readme"
-                  ]
-                }
-              }
-            }
-          }
-        },
-        "requestBody": {
-          "content": {
-            "application/json": {
-              "schema": {
-                "type": "object",
-                "properties": {
-                  "template": {
-                    "type": "string",
-                    "enum": [
-                      "single-cell",
-                      "dose-response",
-                      "protein-structure"
+                    "required": [
+                      "format",
+                      "id",
+                      "projectID",
+                      "path",
+                      "artifactHash",
+                      "version",
+                      "status",
+                      "summary",
+                      "findings",
+                      "events",
+                      "createdAt",
+                      "updatedAt"
                     ]
                   }
-                },
-                "required": [
-                  "template"
-                ]
+                }
               }
             }
           }
@@ -9431,14 +12076,14 @@
         "x-codeSamples": [
           {
             "lang": "js",
-            "source": "import { createOpenScienceClient } from \"@synsci/sdk\"\n\nconst client = createOpenScienceClient()\nawait client.file.starter({\n  ...\n})"
+            "source": "import { createOpenScienceClient } from \"@synsci/sdk\"\n\nconst client = createOpenScienceClient()\nawait client.file.reviews.history({\n  ...\n})"
           }
         ]
       }
     },
-    "/file/publication/capabilities": {
-      "get": {
-        "operationId": "file.publicationCapabilities",
+    "/file/reviews/{id}/findings/{finding}": {
+      "patch": {
+        "operationId": "file.reviews.resolve",
         "parameters": [
           {
             "in": "query",
@@ -9446,61 +12091,356 @@
             "schema": {
               "type": "string"
             }
+          },
+          {
+            "in": "path",
+            "name": "id",
+            "schema": {
+              "type": "string",
+              "pattern": "^review_.*"
+            },
+            "required": true
+          },
+          {
+            "in": "path",
+            "name": "finding",
+            "schema": {
+              "type": "string",
+              "pattern": "^finding_.*"
+            },
+            "required": true
           }
         ],
-        "summary": "Inspect local publication export support",
-        "description": "Detect Pandoc and a PDF engine before offering report export formats.",
+        "summary": "Resolve or override a publication finding",
+        "description": "Record an attributed reason and close one deterministic review finding.",
         "responses": {
           "200": {
-            "description": "Available local publication formats",
+            "description": "Updated publication review",
             "content": {
               "application/json": {
                 "schema": {
                   "type": "object",
                   "properties": {
-                    "pandoc": {
-                      "type": "boolean"
+                    "format": {
+                      "type": "string",
+                      "const": "openscience.publication-review.v1"
                     },
-                    "pdf_engine": {
+                    "id": {
                       "type": "string"
                     },
-                    "formats": {
+                    "projectID": {
+                      "type": "string"
+                    },
+                    "path": {
+                      "type": "string"
+                    },
+                    "artifactHash": {
+                      "type": "string",
+                      "pattern": "^[a-f0-9]{64}$"
+                    },
+                    "version": {
+                      "type": "integer",
+                      "exclusiveMinimum": 0,
+                      "maximum": 9007199254740991
+                    },
+                    "status": {
+                      "type": "string",
+                      "enum": [
+                        "blocked",
+                        "warnings",
+                        "ready"
+                      ]
+                    },
+                    "summary": {
                       "type": "object",
-                      "propertyNames": {
-                        "type": "string",
-                        "enum": [
-                          "html",
-                          "pdf",
-                          "docx",
-                          "latex",
-                          "pptx"
-                        ]
+                      "properties": {
+                        "total": {
+                          "type": "integer",
+                          "minimum": 0,
+                          "maximum": 9007199254740991
+                        },
+                        "open": {
+                          "type": "integer",
+                          "minimum": 0,
+                          "maximum": 9007199254740991
+                        },
+                        "blocking": {
+                          "type": "integer",
+                          "minimum": 0,
+                          "maximum": 9007199254740991
+                        },
+                        "major": {
+                          "type": "integer",
+                          "minimum": 0,
+                          "maximum": 9007199254740991
+                        },
+                        "minor": {
+                          "type": "integer",
+                          "minimum": 0,
+                          "maximum": 9007199254740991
+                        },
+                        "info": {
+                          "type": "integer",
+                          "minimum": 0,
+                          "maximum": 9007199254740991
+                        },
+                        "resolved": {
+                          "type": "integer",
+                          "minimum": 0,
+                          "maximum": 9007199254740991
+                        },
+                        "overridden": {
+                          "type": "integer",
+                          "minimum": 0,
+                          "maximum": 9007199254740991
+                        }
                       },
-                      "additionalProperties": {
-                        "type": "boolean"
+                      "required": [
+                        "total",
+                        "open",
+                        "blocking",
+                        "major",
+                        "minor",
+                        "info",
+                        "resolved",
+                        "overridden"
+                      ]
+                    },
+                    "findings": {
+                      "type": "array",
+                      "items": {
+                        "type": "object",
+                        "properties": {
+                          "id": {
+                            "type": "string"
+                          },
+                          "check": {
+                            "type": "string",
+                            "enum": [
+                              "citation",
+                              "numeric",
+                              "figure",
+                              "provenance"
+                            ]
+                          },
+                          "severity": {
+                            "type": "string",
+                            "enum": [
+                              "blocking",
+                              "major",
+                              "minor",
+                              "info"
+                            ]
+                          },
+                          "status": {
+                            "type": "string",
+                            "enum": [
+                              "open",
+                              "resolved",
+                              "overridden"
+                            ]
+                          },
+                          "title": {
+                            "type": "string"
+                          },
+                          "detail": {
+                            "type": "string"
+                          },
+                          "evidence": {
+                            "type": "array",
+                            "items": {
+                              "type": "string"
+                            }
+                          },
+                          "location": {
+                            "type": "object",
+                            "properties": {
+                              "path": {
+                                "type": "string"
+                              },
+                              "line": {
+                                "type": "integer",
+                                "exclusiveMinimum": 0,
+                                "maximum": 9007199254740991
+                              }
+                            },
+                            "required": [
+                              "path"
+                            ]
+                          },
+                          "resolution": {
+                            "type": "object",
+                            "properties": {
+                              "kind": {
+                                "type": "string",
+                                "enum": [
+                                  "resolved",
+                                  "overridden"
+                                ]
+                              },
+                              "actor": {
+                                "type": "string"
+                              },
+                              "reason": {
+                                "type": "string"
+                              },
+                              "at": {
+                                "type": "number"
+                              }
+                            },
+                            "required": [
+                              "kind",
+                              "actor",
+                              "reason",
+                              "at"
+                            ]
+                          }
+                        },
+                        "required": [
+                          "id",
+                          "check",
+                          "severity",
+                          "status",
+                          "title",
+                          "detail",
+                          "evidence",
+                          "location"
+                        ]
+                      }
+                    },
+                    "events": {
+                      "type": "array",
+                      "items": {
+                        "type": "object",
+                        "properties": {
+                          "version": {
+                            "type": "integer",
+                            "exclusiveMinimum": 0,
+                            "maximum": 9007199254740991
+                          },
+                          "type": {
+                            "type": "string",
+                            "enum": [
+                              "generated",
+                              "resolved",
+                              "overridden",
+                              "finalized"
+                            ]
+                          },
+                          "actor": {
+                            "type": "string"
+                          },
+                          "at": {
+                            "type": "number"
+                          },
+                          "findingID": {
+                            "type": "string"
+                          },
+                          "reason": {
+                            "type": "string"
+                          }
+                        },
+                        "required": [
+                          "version",
+                          "type",
+                          "actor",
+                          "at"
+                        ]
                       }
+                    },
+                    "finalized": {
+                      "type": "object",
+                      "properties": {
+                        "actor": {
+                          "type": "string"
+                        },
+                        "at": {
+                          "type": "number"
+                        },
+                        "artifactHash": {
+                          "type": "string",
+                          "pattern": "^[a-f0-9]{64}$"
+                        }
+                      },
+                      "required": [
+                        "actor",
+                        "at",
+                        "artifactHash"
+                      ]
+                    },
+                    "createdAt": {
+                      "type": "number"
+                    },
+                    "updatedAt": {
+                      "type": "number"
                     }
                   },
                   "required": [
-                    "pandoc",
-                    "formats"
+                    "format",
+                    "id",
+                    "projectID",
+                    "path",
+                    "artifactHash",
+                    "version",
+                    "status",
+                    "summary",
+                    "findings",
+                    "events",
+                    "createdAt",
+                    "updatedAt"
                   ]
                 }
               }
             }
+          },
+          "409": {
+            "description": "Finding cannot be updated"
+          }
+        },
+        "requestBody": {
+          "content": {
+            "application/json": {
+              "schema": {
+                "type": "object",
+                "properties": {
+                  "status": {
+                    "type": "string",
+                    "enum": [
+                      "resolved",
+                      "overridden"
+                    ]
+                  },
+                  "actor": {
+                    "type": "string",
+                    "minLength": 1,
+                    "maxLength": 200
+                  },
+                  "reason": {
+                    "type": "string",
+                    "minLength": 1,
+                    "maxLength": 20000
+                  }
+                },
+                "required": [
+                  "status",
+                  "actor",
+                  "reason"
+                ]
+              }
+            }
           }
         },
         "x-codeSamples": [
           {
             "lang": "js",
-            "source": "import { createOpenScienceClient } from \"@synsci/sdk\"\n\nconst client = createOpenScienceClient()\nawait client.file.publicationCapabilities({\n  ...\n})"
+            "source": "import { createOpenScienceClient } from \"@synsci/sdk\"\n\nconst client = createOpenScienceClient()\nawait client.file.reviews.resolve({\n  ...\n})"
           }
         ]
       }
     },
-    "/file/publication": {
+    "/file/reviews/{id}/finalize": {
       "post": {
-        "operationId": "file.publication",
+        "operationId": "file.reviews.finalize",
         "parameters": [
           {
             "in": "query",
@@ -9508,53 +12448,301 @@
             "schema": {
               "type": "string"
             }
+          },
+          {
+            "in": "path",
+            "name": "id",
+            "schema": {
+              "type": "string",
+              "pattern": "^review_.*"
+            },
+            "required": true
           }
         ],
-        "summary": "Export a Markdown research report",
-        "description": "Create a timestamped HTML, PDF, DOCX, LaTeX, or PowerPoint publication artifact locally.",
+        "summary": "Finalize a publication review",
+        "description": "Bind publication-ready state to the exact reviewed source hash after all blocking findings close.",
         "responses": {
           "200": {
-            "description": "Created publication artifact",
+            "description": "Finalized publication review",
             "content": {
               "application/json": {
                 "schema": {
                   "type": "object",
                   "properties": {
+                    "format": {
+                      "type": "string",
+                      "const": "openscience.publication-review.v1"
+                    },
+                    "id": {
+                      "type": "string"
+                    },
+                    "projectID": {
+                      "type": "string"
+                    },
                     "path": {
                       "type": "string"
                     },
-                    "format": {
+                    "artifactHash": {
                       "type": "string",
-                      "enum": [
-                        "html",
-                        "pdf",
-                        "docx",
-                        "latex",
-                        "pptx"
-                      ]
+                      "pattern": "^[a-f0-9]{64}$"
                     },
-                    "size": {
+                    "version": {
                       "type": "integer",
-                      "minimum": 0,
+                      "exclusiveMinimum": 0,
                       "maximum": 9007199254740991
                     },
-                    "created_at": {
-                      "type": "string"
+                    "status": {
+                      "type": "string",
+                      "enum": [
+                        "blocked",
+                        "warnings",
+                        "ready"
+                      ]
                     },
-                    "engine": {
-                      "type": "string"
+                    "summary": {
+                      "type": "object",
+                      "properties": {
+                        "total": {
+                          "type": "integer",
+                          "minimum": 0,
+                          "maximum": 9007199254740991
+                        },
+                        "open": {
+                          "type": "integer",
+                          "minimum": 0,
+                          "maximum": 9007199254740991
+                        },
+                        "blocking": {
+                          "type": "integer",
+                          "minimum": 0,
+                          "maximum": 9007199254740991
+                        },
+                        "major": {
+                          "type": "integer",
+                          "minimum": 0,
+                          "maximum": 9007199254740991
+                        },
+                        "minor": {
+                          "type": "integer",
+                          "minimum": 0,
+                          "maximum": 9007199254740991
+                        },
+                        "info": {
+                          "type": "integer",
+                          "minimum": 0,
+                          "maximum": 9007199254740991
+                        },
+                        "resolved": {
+                          "type": "integer",
+                          "minimum": 0,
+                          "maximum": 9007199254740991
+                        },
+                        "overridden": {
+                          "type": "integer",
+                          "minimum": 0,
+                          "maximum": 9007199254740991
+                        }
+                      },
+                      "required": [
+                        "total",
+                        "open",
+                        "blocking",
+                        "major",
+                        "minor",
+                        "info",
+                        "resolved",
+                        "overridden"
+                      ]
+                    },
+                    "findings": {
+                      "type": "array",
+                      "items": {
+                        "type": "object",
+                        "properties": {
+                          "id": {
+                            "type": "string"
+                          },
+                          "check": {
+                            "type": "string",
+                            "enum": [
+                              "citation",
+                              "numeric",
+                              "figure",
+                              "provenance"
+                            ]
+                          },
+                          "severity": {
+                            "type": "string",
+                            "enum": [
+                              "blocking",
+                              "major",
+                              "minor",
+                              "info"
+                            ]
+                          },
+                          "status": {
+                            "type": "string",
+                            "enum": [
+                              "open",
+                              "resolved",
+                              "overridden"
+                            ]
+                          },
+                          "title": {
+                            "type": "string"
+                          },
+                          "detail": {
+                            "type": "string"
+                          },
+                          "evidence": {
+                            "type": "array",
+                            "items": {
+                              "type": "string"
+                            }
+                          },
+                          "location": {
+                            "type": "object",
+                            "properties": {
+                              "path": {
+                                "type": "string"
+                              },
+                              "line": {
+                                "type": "integer",
+                                "exclusiveMinimum": 0,
+                                "maximum": 9007199254740991
+                              }
+                            },
+                            "required": [
+                              "path"
+                            ]
+                          },
+                          "resolution": {
+                            "type": "object",
+                            "properties": {
+                              "kind": {
+                                "type": "string",
+                                "enum": [
+                                  "resolved",
+                                  "overridden"
+                                ]
+                              },
+                              "actor": {
+                                "type": "string"
+                              },
+                              "reason": {
+                                "type": "string"
+                              },
+                              "at": {
+                                "type": "number"
+                              }
+                            },
+                            "required": [
+                              "kind",
+                              "actor",
+                              "reason",
+                              "at"
+                            ]
+                          }
+                        },
+                        "required": [
+                          "id",
+                          "check",
+                          "severity",
+                          "status",
+                          "title",
+                          "detail",
+                          "evidence",
+                          "location"
+                        ]
+                      }
+                    },
+                    "events": {
+                      "type": "array",
+                      "items": {
+                        "type": "object",
+                        "properties": {
+                          "version": {
+                            "type": "integer",
+                            "exclusiveMinimum": 0,
+                            "maximum": 9007199254740991
+                          },
+                          "type": {
+                            "type": "string",
+                            "enum": [
+                              "generated",
+                              "resolved",
+                              "overridden",
+                              "finalized"
+                            ]
+                          },
+                          "actor": {
+                            "type": "string"
+                          },
+                          "at": {
+                            "type": "number"
+                          },
+                          "findingID": {
+                            "type": "string"
+                          },
+                          "reason": {
+                            "type": "string"
+                          }
+                        },
+                        "required": [
+                          "version",
+                          "type",
+                          "actor",
+                          "at"
+                        ]
+                      }
+                    },
+                    "finalized": {
+                      "type": "object",
+                      "properties": {
+                        "actor": {
+                          "type": "string"
+                        },
+                        "at": {
+                          "type": "number"
+                        },
+                        "artifactHash": {
+                          "type": "string",
+                          "pattern": "^[a-f0-9]{64}$"
+                        }
+                      },
+                      "required": [
+                        "actor",
+                        "at",
+                        "artifactHash"
+                      ]
+                    },
+                    "createdAt": {
+                      "type": "number"
+                    },
+                    "updatedAt": {
+                      "type": "number"
                     }
                   },
                   "required": [
-                    "path",
                     "format",
-                    "size",
-                    "created_at",
-                    "engine"
+                    "id",
+                    "projectID",
+                    "path",
+                    "artifactHash",
+                    "version",
+                    "status",
+                    "summary",
+                    "findings",
+                    "events",
+                    "createdAt",
+                    "updatedAt"
                   ]
                 }
               }
             }
+          },
+          "409": {
+            "description": "Review is blocked, stale, or already invalid"
           }
         },
         "requestBody": {
@@ -9563,25 +12751,14 @@
               "schema": {
                 "type": "object",
                 "properties": {
-                  "path": {
+                  "actor": {
                     "type": "string",
                     "minLength": 1,
-                    "maxLength": 4000
-                  },
-                  "format": {
-                    "type": "string",
-                    "enum": [
-                      "html",
-                      "pdf",
-                      "docx",
-                      "latex",
-                      "pptx"
-                    ]
+                    "maxLength": 200
                   }
                 },
                 "required": [
-                  "path",
-                  "format"
+                  "actor"
                 ]
               }
             }
@@ -9590,7 +12767,7 @@
         "x-codeSamples": [
           {
             "lang": "js",
-            "source": "import { createOpenScienceClient } from \"@synsci/sdk\"\n\nconst client = createOpenScienceClient()\nawait client.file.publication({\n  ...\n})"
+            "source": "import { createOpenScienceClient } from \"@synsci/sdk\"\n\nconst client = createOpenScienceClient()\nawait client.file.reviews.finalize({\n  ...\n})"
           }
         ]
       }

From 5511e4524d1de9ab3531dd2931cb60598c31faa7 Mon Sep 17 00:00:00 2001
From: Aayam Bansal <aayambansal@gmail.com>
Date: Wed, 29 Jul 2026 15:10:57 +0800
Subject: [PATCH 33/40] fix: review nested manuscripts from project root

---
 backend/cli/src/file/review.ts       | 31 ++++++++++++++++------------
 backend/cli/test/file/review.test.ts | 18 +++++++++-------
 2 files changed, 29 insertions(+), 20 deletions(-)

diff --git a/backend/cli/src/file/review.ts b/backend/cli/src/file/review.ts
index 51ecc360..d6d67634 100644
--- a/backend/cli/src/file/review.ts
+++ b/backend/cli/src/file/review.ts
@@ -127,9 +127,9 @@ export namespace PublicationReview {
     const [text, artifactHash, graph, provenance, audit] = await Promise.all([
       Bun.file(source.absolute).text(),
       digest(source.absolute),
-      Provenance.project(Instance.directory),
-      ArtifactFile.provenance(Instance.directory, source.relative),
-      ArtifactFile.audit(Instance.directory),
+      Provenance.project(Instance.worktree),
+      ArtifactFile.provenance(Instance.worktree, source.relative),
+      ArtifactFile.audit(Instance.worktree),
     ])
     const findings = [
       ...(await citations(text, source)),
@@ -292,7 +292,7 @@ export namespace PublicationReview {
             title: `Bibliography key @${key} is unresolved`,
             detail: "The manuscript cites a key that is absent from its local bibliography files.",
             evidence: bib.length
-              ? bib.map((file) => path.relative(Instance.directory, file).replaceAll("\\", "/"))
+              ? bib.map((file) => path.relative(Instance.worktree, file).replaceAll("\\", "/"))
               : ["No local bibliography file was found."],
             location: { path: source.relative, line },
           }),
@@ -372,7 +372,7 @@ export namespace PublicationReview {
         const value = (match[2] ?? match[3]!).trim()
         if (/^(?:https?:|data:)/i.test(value)) continue
         const absolute = path.resolve(path.dirname(source.absolute), decodeURIComponent(value.split(/[?#]/)[0]!))
-        const relative = path.relative(Instance.directory, absolute).replaceAll("\\", "/")
+        const relative = path.relative(Instance.worktree, absolute).replaceAll("\\", "/")
         const inside = await Instance.containsCanonicalPath(absolute)
         const exists = inside && (await Bun.file(absolute).exists())
         if (!exists) {
@@ -404,10 +404,9 @@ export namespace PublicationReview {
         }
         const recorded = nodes.some((node) => {
           if (node.kind !== "artifact" || !("path" in node) || !node.path) return false
-          const nodePath = path.isAbsolute(node.path)
-            ? path.relative(Instance.directory, node.path).replaceAll("\\", "/")
-            : node.path.replaceAll("\\", "/").replace(/^\.\//, "")
-          return nodePath === relative
+          const owner = typeof node.meta?.directory === "string" ? node.meta.directory : Instance.worktree
+          const nodePath = path.isAbsolute(node.path) ? node.path : path.resolve(owner, node.path)
+          return path.resolve(nodePath) === path.resolve(absolute)
         })
         if (recorded) continue
         output.push(
@@ -504,6 +503,9 @@ export namespace PublicationReview {
       path.join(Instance.directory, "references.bib"),
       path.join(Instance.directory, "bibliography.bib"),
       path.join(Instance.directory, "refs.bib"),
+      path.join(Instance.worktree, "references.bib"),
+      path.join(Instance.worktree, "bibliography.bib"),
+      path.join(Instance.worktree, "refs.bib"),
     ]
     const unique = [...new Set(candidates)]
     const safe = await Promise.all(
@@ -521,14 +523,17 @@ export namespace PublicationReview {
     }
     return {
       absolute,
-      relative: path.relative(Instance.directory, absolute).replaceAll("\\", "/"),
+      relative: path.relative(Instance.worktree, absolute).replaceAll("\\", "/"),
     }
   }
 
   async function assertCurrent(report: Report) {
-    const source = await target(report.path)
-    if (!(await Bun.file(source.absolute).exists())) throw new Error("The reviewed manuscript no longer exists")
-    if ((await digest(source.absolute)) !== report.artifactHash) {
+    const absolute = path.resolve(Instance.worktree, report.path)
+    if (!(await Instance.containsCanonicalPath(absolute))) {
+      throw new Error("The reviewed manuscript is outside the current project")
+    }
+    if (!(await Bun.file(absolute).exists())) throw new Error("The reviewed manuscript no longer exists")
+    if ((await digest(absolute)) !== report.artifactHash) {
       throw new Error("The manuscript changed after this publication review was generated")
     }
   }
diff --git a/backend/cli/test/file/review.test.ts b/backend/cli/test/file/review.test.ts
index e8049ebd..b6c61e7f 100644
--- a/backend/cli/test/file/review.test.ts
+++ b/backend/cli/test/file/review.test.ts
@@ -132,10 +132,13 @@ describe("PublicationReview", () => {
         await Bun.write(path.join(directory, "README.md"), "# Ready fixture\n")
         await Bun.write(path.join(directory, "uv.lock"), "version = 1\n")
         await Bun.write(path.join(directory, "pyproject.toml"), '[project]\nname = "ready-fixture"\n')
-        await Bun.write(path.join(directory, "references.bib"), "@article{known2024, title={Known result}}\n")
-        await Bun.write(path.join(directory, "figures", "response.svg"), "<svg></svg>")
         await Bun.write(
-          path.join(directory, "report.md"),
+          path.join(directory, "manuscript", "references.bib"),
+          "@article{known2024, title={Known result}}\n",
+        )
+        await Bun.write(path.join(directory, "manuscript", "figures", "response.svg"), "<svg></svg>")
+        await Bun.write(
+          path.join(directory, "manuscript", "report.md"),
           [
             "---",
             "bibliography: references.bib",
@@ -159,19 +162,20 @@ describe("PublicationReview", () => {
       kind: "artifact",
       label: "Response figure",
       artifactType: "figure",
-      path: "figures/response.svg",
+      path: "manuscript/figures/response.svg",
       meta: { directory: tmp.path },
     } as Parameters<typeof Provenance.record>[0])
     await Instance.provide({
-      directory: tmp.path,
+      directory: path.join(tmp.path, "manuscript"),
       fn: async () => {
         const first = await PublicationReview.run({ path: "report.md", actor: "Reviewer" })
         expect(first.findings.filter((finding) => finding.severity === "blocking")).toEqual([])
         expect(first.status).not.toBe("blocked")
+        expect(first.path).toBe("manuscript/report.md")
 
         await Bun.write(
-          path.join(tmp.path, "report.md"),
-          `${await Bun.file(path.join(tmp.path, "report.md")).text()}\n`,
+          path.join(tmp.path, "manuscript", "report.md"),
+          `${await Bun.file(path.join(tmp.path, "manuscript", "report.md")).text()}\n`,
         )
         const second = await PublicationReview.run({ path: "report.md", actor: "Reviewer" })
         expect(second.id).not.toBe(first.id)

From 1bb2e9509170eb5d3a8259efad0b21451ff3284a Mon Sep 17 00:00:00 2001
From: Aayam Bansal <aayambansal@gmail.com>
Date: Wed, 29 Jul 2026 15:12:01 +0800
Subject: [PATCH 34/40] feat: review manuscripts in the artifact inspector

---
 .../workspace/e2e/artifact-inspector.spec.ts  |  44 ++
 .../workspace/e2e/science/review-report.md    |  11 +
 frontend/workspace/script/e2e-local.ts        |   7 +-
 .../src/artifacts/ArtifactInspector.tsx       | 379 +++++++++++++++++-
 .../workspace/src/artifacts/inspector.test.ts |  65 ++-
 frontend/workspace/src/artifacts/inspector.ts | 272 +++++++++++++
 6 files changed, 772 insertions(+), 6 deletions(-)
 create mode 100644 frontend/workspace/e2e/science/review-report.md

diff --git a/frontend/workspace/e2e/artifact-inspector.spec.ts b/frontend/workspace/e2e/artifact-inspector.spec.ts
index c9a47f0a..d1160c94 100644
--- a/frontend/workspace/e2e/artifact-inspector.spec.ts
+++ b/frontend/workspace/e2e/artifact-inspector.spec.ts
@@ -118,3 +118,47 @@ test("artifact review threads persist and can be resolved", async ({ page, direc
   ).toBeVisible()
   await expect(inspector.getByText("0 open", { exact: true })).toBeVisible()
 })
+
+test("publication review blocks, audits overrides, finalizes, and persists exact manuscript bytes", async ({
+  page,
+  directory,
+  gotoSession,
+}) => {
+  await gotoSession()
+  await openFile(page, directory, "frontend/workspace/e2e/science/review-report.md")
+
+  const inspector = page.locator('[data-component="artifact-inspector"]')
+  await inspector.getByRole("tab", { name: "Review", exact: true }).click()
+  const review = inspector.locator('[data-component="publication-review"]')
+  await expect(review).toHaveAttribute("data-review-state", "not-run")
+  await review.getByRole("button", { name: "Run checks", exact: true }).click()
+  await expect(review).toHaveAttribute("data-review-state", "blocked", { timeout: 30_000 })
+  await expect(review.getByText("Publication is blocked", { exact: true })).toBeVisible()
+  await expect(review.locator('[data-component="publication-finding"]')).not.toHaveCount(0)
+
+  const blockers = () =>
+    review
+      .locator('[data-component="publication-finding"]')
+      .filter({ has: page.getByText("blocking", { exact: true }) })
+      .filter({ has: page.getByRole("button", { name: "Override", exact: true }) })
+  while ((await blockers().count()) > 0) {
+    const before = await blockers().count()
+    const finding = blockers().first()
+    await finding.getByRole("button", { name: "Override", exact: true }).click()
+    await finding.getByLabel(/Override reason for/).fill("Accepted in this preview with an explicit audit record.")
+    await finding.getByRole("button", { name: "Confirm overridden", exact: true }).click()
+    await expect(blockers()).toHaveCount(before - 1)
+  }
+
+  const finalize = review.getByRole("button", { name: "Finalize reviewed bytes", exact: true })
+  await expect(finalize).toBeEnabled()
+  await finalize.click()
+  await expect(review).toHaveAttribute("data-review-state", "finalized")
+  await expect(review.getByText(/Finalized by/)).toBeVisible()
+
+  await openFile(page, directory, "frontend/workspace/e2e/science/water.xyz")
+  await openFile(page, directory, "frontend/workspace/e2e/science/review-report.md")
+  await inspector.getByRole("tab", { name: "Review", exact: true }).click()
+  await expect(review).toHaveAttribute("data-review-state", "finalized")
+  await expect(review.getByText(/sha256 [a-f0-9]{12}/)).toBeVisible()
+})
diff --git a/frontend/workspace/e2e/science/review-report.md b/frontend/workspace/e2e/science/review-report.md
new file mode 100644
index 00000000..7fd7e510
--- /dev/null
+++ b/frontend/workspace/e2e/science/review-report.md
@@ -0,0 +1,11 @@
+---
+bibliography: references.bib
+---
+
+# Candidate publication
+
+The intervention improved the primary endpoint by 42% (p = 0.01).
+
+The proposed mechanism agrees with prior work [@missing-review-source].
+
+![Missing validation panel](figures/missing-validation.svg)
diff --git a/frontend/workspace/script/e2e-local.ts b/frontend/workspace/script/e2e-local.ts
index bf780c7d..49872047 100644
--- a/frontend/workspace/script/e2e-local.ts
+++ b/frontend/workspace/script/e2e-local.ts
@@ -67,7 +67,12 @@ const openscienceDir = path.join(repoDir, "backend", "cli")
 
 const extraArgs = forwardedPlaywrightArgs(process.argv.slice(2))
 
-const [serverPort, webPort, modelPort] = await Promise.all([freePort(), freePort(), freePort()])
+const ports = async (values: number[] = []): Promise<[number, number, number]> => {
+  if (values.length === 3) return values as [number, number, number]
+  const port = await freePort()
+  return ports(values.includes(port) ? values : [...values, port])
+}
+const [serverPort, webPort, modelPort] = await ports()
 const fakeModelServer = startFakeModelServer(modelPort)
 
 const sandbox = await fs.mkdtemp(path.join(os.tmpdir(), "openscience-e2e-"))
diff --git a/frontend/workspace/src/artifacts/ArtifactInspector.tsx b/frontend/workspace/src/artifacts/ArtifactInspector.tsx
index f368d291..4d60d368 100644
--- a/frontend/workspace/src/artifacts/ArtifactInspector.tsx
+++ b/frontend/workspace/src/artifacts/ArtifactInspector.tsx
@@ -21,9 +21,12 @@ import type { ArtifactContext } from "./context"
 import {
   inspectorTabs,
   normalizeInspectorData,
+  normalizePublicationReview,
   type InspectorData,
   type InspectorState,
   type InspectorTab,
+  type PublicationReviewFinding,
+  type PublicationReviewState,
 } from "./inspector"
 
 const labels: Record<InspectorTab, string> = {
@@ -106,13 +109,14 @@ export function ArtifactInspector(props: { context: ArtifactContext; onClose?: (
         if (!response?.ok) return
         return response.json().catch(() => undefined)
       }
-      const [file, provenance, audit, notes] = await Promise.all([
+      const [file, provenance, audit, notes, review] = await Promise.all([
         read("/file/content", current.path),
         read("/file/provenance", current.path),
         read("/file/reproducibility"),
         read("/file/annotations", current.path),
+        read("/file/reviews", current.path),
       ])
-      return { id: current.id, file, provenance, audit, notes }
+      return { id: current.id, file, provenance, audit, notes, review }
     },
   )
   const model = createMemo<InspectorData>(() => {
@@ -120,6 +124,7 @@ export function ArtifactInspector(props: { context: ArtifactContext; onClose?: (
     const input = value?.id === props.context.id ? value : {}
     return normalizeInspectorData(props.context, input)
   })
+  const review = createMemo(() => normalizePublicationReview(props.context.format, records()?.review))
 
   createEffect(() => {
     props.context.id
@@ -176,6 +181,38 @@ export function ArtifactInspector(props: { context: ArtifactContext; onClose?: (
     })
   const updateAnnotation = (id: string, body: Record<string, unknown>) =>
     mutateAnnotation(`/file/annotations/${id}`, "PATCH", body)
+  const mutateReview = async (route: string, method: "POST" | "PATCH", body: Record<string, unknown>) => {
+    const response = await request()(url(route), {
+      method,
+      headers: { "Content-Type": "application/json" },
+      body: JSON.stringify(body),
+    }).catch(() => undefined)
+    if (!response?.ok) {
+      const payload = (await response?.json().catch(() => undefined)) as { error?: unknown } | undefined
+      const detail =
+        typeof payload?.error === "string" ? payload.error : response ? `${response.status}` : "request failed"
+      toast.error("publication review failed", detail)
+      return false
+    }
+    await api.refetch()
+    return true
+  }
+  const actor = () => model().provenance?.commit?.author ?? "Local user"
+  const runReview = () =>
+    mutateReview("/file/reviews", "POST", {
+      path: props.context.path,
+      actor: actor(),
+    })
+  const resolveFinding = (report: string, finding: string, status: "resolved" | "overridden", reason: string) =>
+    mutateReview(`/file/reviews/${report}/findings/${finding}`, "PATCH", {
+      status,
+      actor: actor(),
+      reason,
+    })
+  const finalizeReview = (report: string) =>
+    mutateReview(`/file/reviews/${report}/finalize`, "POST", {
+      actor: actor(),
+    })
 
   const move = (event: KeyboardEvent, current: InspectorTab) => {
     const index = inspectorTabs.indexOf(current)
@@ -341,7 +378,15 @@ export function ArtifactInspector(props: { context: ArtifactContext; onClose?: (
               <Environment data={model()} />
             </Match>
             <Match when={tab() === "review"}>
-              <Review annotations={annotations(records()?.notes)} onAdd={addAnnotation} onUpdate={updateAnnotation} />
+              <Review
+                state={review()}
+                annotations={annotations(records()?.notes)}
+                onRun={runReview}
+                onFinding={resolveFinding}
+                onFinalize={finalizeReview}
+                onAdd={addAnnotation}
+                onUpdate={updateAnnotation}
+              />
             </Match>
             <Match when={tab() === "history"}>
               <History data={model()} />
@@ -354,13 +399,30 @@ export function ArtifactInspector(props: { context: ArtifactContext; onClose?: (
 }
 
 function Review(props: {
+  state: PublicationReviewState
   annotations: Annotation[]
+  onRun(): Promise<boolean>
+  onFinding(report: string, finding: string, status: "resolved" | "overridden", reason: string): Promise<boolean>
+  onFinalize(report: string): Promise<boolean>
   onAdd(body: string): Promise<boolean>
   onUpdate(id: string, body: Record<string, unknown>): Promise<boolean>
 }): JSX.Element {
   const [body, setBody] = createSignal("")
   const [busy, setBusy] = createSignal(false)
   const open = () => props.annotations.filter((item) => item.status === "open").length
+  const run = async () => {
+    if (busy()) return
+    setBusy(true)
+    await props.onRun()
+    setBusy(false)
+  }
+  const finalize = async () => {
+    const report = props.state.report
+    if (!report || busy()) return
+    setBusy(true)
+    await props.onFinalize(report.id)
+    setBusy(false)
+  }
   const add = async () => {
     const value = body().trim()
     if (!value || busy()) return
@@ -371,9 +433,128 @@ function Review(props: {
   }
   return (
     <div style={{ display: "grid", gap: "12px" }}>
+      <section
+        data-component="publication-review"
+        data-review-state={props.state.kind}
+        style={{
+          ...card(),
+          "border-left": `3px solid ${reviewColor(props.state.kind)}`,
+          gap: "10px",
+        }}
+      >
+        <div style={{ display: "flex", "align-items": "flex-start", "justify-content": "space-between", gap: "10px" }}>
+          <div style={{ display: "grid", gap: "3px" }}>
+            <span
+              style={{
+                "font-family": FONT_MONO,
+                "font-size": "9px",
+                "text-transform": "uppercase",
+                "letter-spacing": "0.08em",
+                color: reviewColor(props.state.kind),
+              }}
+            >
+              {props.state.kind.replace("-", " ")}
+            </span>
+            <strong style={{ "font-family": FONT_SANS, "font-size": "13px", color: "var(--color-text)" }}>
+              {props.state.title}
+            </strong>
+            <p style={copyStyle()}>{props.state.detail}</p>
+          </div>
+          <Show when={props.state.kind !== "not-applicable"}>
+            <button
+              type="button"
+              disabled={busy()}
+              style={{ ...actionButton(true), "white-space": "nowrap" }}
+              onClick={() => void run()}
+            >
+              {busy() ? "Checking…" : props.state.report ? "Run again" : "Run checks"}
+            </button>
+          </Show>
+        </div>
+        <Show when={props.state.report}>
+          {(report) => (
+            <>
+              <div
+                style={{
+                  display: "grid",
+                  "grid-template-columns": "repeat(4, minmax(0, 1fr))",
+                  gap: "6px",
+                }}
+              >
+                <ReviewMetric label="blocking" value={report().summary.blocking} tone="blocking" />
+                <ReviewMetric label="major" value={report().summary.major} tone="major" />
+                <ReviewMetric label="minor" value={report().summary.minor} tone="minor" />
+                <ReviewMetric label="closed" value={report().summary.resolved + report().summary.overridden} />
+              </div>
+              <div
+                style={{
+                  display: "flex",
+                  "align-items": "center",
+                  "justify-content": "space-between",
+                  gap: "8px",
+                  "flex-wrap": "wrap",
+                }}
+              >
+                <span style={{ "font-family": FONT_MONO, "font-size": "9px", color: "var(--color-text-faint)" }}>
+                  v{report().version} · sha256 {report().artifactHash.slice(0, 12)}
+                </span>
+                <Show
+                  when={report().finalized}
+                  fallback={
+                    <button
+                      type="button"
+                      disabled={
+                        busy() ||
+                        report().stale ||
+                        report().findings.some(
+                          (finding) => finding.severity === "blocking" && finding.status === "open",
+                        )
+                      }
+                      style={{
+                        ...actionButton(true),
+                        opacity:
+                          busy() ||
+                          report().stale ||
+                          report().findings.some(
+                            (finding) => finding.severity === "blocking" && finding.status === "open",
+                          )
+                            ? 0.45
+                            : 1,
+                      }}
+                      onClick={() => void finalize()}
+                    >
+                      Finalize reviewed bytes
+                    </button>
+                  }
+                >
+                  {(value) => (
+                    <span style={{ "font-family": FONT_MONO, "font-size": "9px", color: "var(--color-success)" }}>
+                      Finalized by {value().actor} · {new Date(value().at).toLocaleString()}
+                    </span>
+                  )}
+                </Show>
+              </div>
+              <Show
+                when={report().findings.length}
+                fallback={
+                  <p style={copyStyle()}>No deterministic findings were recorded for these manuscript bytes.</p>
+                }
+              >
+                <div style={{ display: "grid", gap: "8px" }}>
+                  <For each={report().findings}>
+                    {(finding) => (
+                      <ReviewFindingCard report={report().id} finding={finding} onFinding={props.onFinding} />
+                    )}
+                  </For>
+                </div>
+              </Show>
+            </>
+          )}
+        </Show>
+      </section>
       <section style={card()}>
         <div style={{ display: "flex", "align-items": "center", "justify-content": "space-between", gap: "8px" }}>
-          <Heading icon="review">Review threads</Heading>
+          <Heading icon="review">Manual review threads</Heading>
           <span
             style={{
               "font-family": FONT_MONO,
@@ -431,6 +612,167 @@ function Review(props: {
   )
 }
 
+function ReviewMetric(props: {
+  label: string
+  value: number
+  tone?: PublicationReviewFinding["severity"]
+}): JSX.Element {
+  return (
+    <div
+      style={{
+        padding: "7px 8px",
+        display: "grid",
+        gap: "2px",
+        border: "1px solid var(--color-border)",
+        "border-radius": "5px",
+        background: "var(--color-surface)",
+      }}
+    >
+      <strong
+        style={{
+          "font-family": FONT_MONO,
+          "font-size": "13px",
+          color: props.tone ? findingColor(props.tone) : "var(--color-text)",
+        }}
+      >
+        {props.value}
+      </strong>
+      <span
+        style={{
+          "font-family": FONT_MONO,
+          "font-size": "8px",
+          "text-transform": "uppercase",
+          color: "var(--color-text-faint)",
+        }}
+      >
+        {props.label}
+      </span>
+    </div>
+  )
+}
+
+function ReviewFindingCard(props: {
+  report: string
+  finding: PublicationReviewFinding
+  onFinding(report: string, finding: string, status: "resolved" | "overridden", reason: string): Promise<boolean>
+}): JSX.Element {
+  const [mode, setMode] = createSignal<"resolved" | "overridden">()
+  const [reason, setReason] = createSignal("")
+  const [busy, setBusy] = createSignal(false)
+  const submit = async () => {
+    const status = mode()
+    const note = reason().trim()
+    if (!status || !note || busy()) return
+    setBusy(true)
+    const ok = await props.onFinding(props.report, props.finding.id, status, note)
+    setBusy(false)
+    if (!ok) return
+    setMode()
+    setReason("")
+  }
+  return (
+    <article
+      data-component="publication-finding"
+      data-finding-id={props.finding.id}
+      style={{
+        padding: "10px",
+        display: "grid",
+        gap: "7px",
+        border: "1px solid var(--color-border)",
+        "border-left": `3px solid ${findingColor(props.finding.severity)}`,
+        "border-radius": "5px",
+        background: "var(--color-bg)",
+      }}
+    >
+      <div style={{ display: "flex", "align-items": "center", gap: "6px", "flex-wrap": "wrap" }}>
+        <span style={findingBadge(props.finding.severity)}>{props.finding.severity}</span>
+        <span style={findingBadge()}>{props.finding.check}</span>
+        <span style={{ ...findingBadge(), "margin-left": "auto" }}>{props.finding.status}</span>
+      </div>
+      <strong style={{ "font-family": FONT_SANS, "font-size": "11px", color: "var(--color-text)" }}>
+        {props.finding.title}
+      </strong>
+      <p style={copyStyle()}>{props.finding.detail}</p>
+      <span style={{ "font-family": FONT_MONO, "font-size": "9px", color: "var(--color-text-faint)" }}>
+        {props.finding.location.path}
+        {props.finding.location.line ? `:${props.finding.location.line}` : ""}
+      </span>
+      <Show when={props.finding.evidence.length}>
+        <ul style={{ margin: 0, padding: "0 0 0 16px", display: "grid", gap: "3px" }}>
+          <For each={props.finding.evidence}>
+            {(evidence) => (
+              <li style={{ "font-family": FONT_MONO, "font-size": "9px", color: "var(--color-text-muted)" }}>
+                {evidence}
+              </li>
+            )}
+          </For>
+        </ul>
+      </Show>
+      <Show when={props.finding.resolution}>
+        {(resolution) => (
+          <p style={{ ...copyStyle(), color: "var(--color-text-muted)" }}>
+            {resolution().kind} by {resolution().actor}: {resolution().reason}
+          </p>
+        )}
+      </Show>
+      <Show when={props.finding.status === "open"}>
+        <div style={{ display: "flex", gap: "6px" }}>
+          <button type="button" disabled={busy()} style={quietButton()} onClick={() => setMode("resolved")}>
+            Resolve
+          </button>
+          <button type="button" disabled={busy()} style={quietButton()} onClick={() => setMode("overridden")}>
+            Override
+          </button>
+        </div>
+        <Show when={mode()}>
+          {(status) => (
+            <div style={{ display: "grid", gap: "6px" }}>
+              <textarea
+                aria-label={`${status() === "resolved" ? "Resolution" : "Override"} reason for ${props.finding.title}`}
+                value={reason()}
+                rows={2}
+                placeholder={
+                  status() === "resolved"
+                    ? "What evidence or edit resolves this finding?"
+                    : "Why is it acceptable to publish despite this finding?"
+                }
+                onInput={(event) => setReason(event.currentTarget.value)}
+                style={{
+                  width: "100%",
+                  resize: "vertical",
+                  "box-sizing": "border-box",
+                  padding: "8px",
+                  border: "1px solid var(--color-border)",
+                  "border-radius": "5px",
+                  outline: "none",
+                  background: "var(--color-bg)",
+                  color: "var(--color-text)",
+                  "font-family": FONT_SANS,
+                  "font-size": "10px",
+                  "line-height": 1.5,
+                }}
+              />
+              <div style={{ display: "flex", gap: "6px" }}>
+                <button
+                  type="button"
+                  disabled={!reason().trim() || busy()}
+                  style={{ ...actionButton(true), opacity: !reason().trim() || busy() ? 0.45 : 1 }}
+                  onClick={() => void submit()}
+                >
+                  {busy() ? "Saving…" : `Confirm ${status()}`}
+                </button>
+                <button type="button" disabled={busy()} style={quietButton()} onClick={() => setMode()}>
+                  Cancel
+                </button>
+              </div>
+            </div>
+          )}
+        </Show>
+      </Show>
+    </article>
+  )
+}
+
 function AnnotationThread(props: {
   annotation: Annotation
   onUpdate(id: string, body: Record<string, unknown>): Promise<boolean>
@@ -913,4 +1255,33 @@ function quietButton(): JSX.CSSProperties {
   }
 }
 
+function reviewColor(kind: PublicationReviewState["kind"]): string {
+  if (kind === "blocked" || kind === "stale") return "var(--color-danger, var(--color-error))"
+  if (kind === "warnings") return "var(--color-warning)"
+  if (kind === "ready" || kind === "finalized") return "var(--color-success)"
+  return "var(--color-text-faint)"
+}
+
+function findingColor(severity: PublicationReviewFinding["severity"]): string {
+  if (severity === "blocking") return "var(--color-danger, var(--color-error))"
+  if (severity === "major") return "var(--color-warning)"
+  if (severity === "minor") return "var(--color-text-muted)"
+  return "var(--color-text-faint)"
+}
+
+function findingBadge(severity?: PublicationReviewFinding["severity"]): JSX.CSSProperties {
+  return {
+    padding: "3px 6px",
+    "border-radius": "999px",
+    border: "1px solid var(--color-border)",
+    background: "var(--color-bg-subtle)",
+    color: severity ? findingColor(severity) : "var(--color-text-muted)",
+    "font-family": FONT_MONO,
+    "font-size": "8px",
+    "font-weight": severity ? 650 : 500,
+    "text-transform": "uppercase",
+    "letter-spacing": "0.04em",
+  }
+}
+
 export default ArtifactInspector
diff --git a/frontend/workspace/src/artifacts/inspector.test.ts b/frontend/workspace/src/artifacts/inspector.test.ts
index 1eec2fc1..13cdc66f 100644
--- a/frontend/workspace/src/artifacts/inspector.test.ts
+++ b/frontend/workspace/src/artifacts/inspector.test.ts
@@ -1,6 +1,6 @@
 import { describe, expect, test } from "bun:test"
 import { createArtifactContext } from "./context"
-import { inspectorTabs, normalizeInspectorData } from "./inspector"
+import { inspectorTabs, normalizeInspectorData, normalizePublicationReview } from "./inspector"
 
 const context = createArtifactContext({
   directory: "/work/project",
@@ -71,4 +71,67 @@ describe("artifact inspector model", () => {
   test("publishes the complete stable inspector tab order", () => {
     expect(inspectorTabs).toEqual(["details", "code", "run", "messages", "environment", "review", "history"])
   })
+
+  test("normalizes publication readiness without inventing a review", () => {
+    const skipped = normalizePublicationReview("pdb", undefined)
+    expect(skipped.kind).toBe("not-applicable")
+    expect(skipped.report).toBeUndefined()
+    const missing = normalizePublicationReview("md", { status: "ready" })
+    expect(missing.kind).toBe("not-run")
+    expect(missing.report).toBeUndefined()
+  })
+
+  test("distinguishes blocked, stale, and finalized manuscript states", () => {
+    const report = {
+      format: "openscience.publication-review.v1",
+      id: "review_01",
+      path: "report.md",
+      artifactHash: "a".repeat(64),
+      version: 2,
+      status: "blocked",
+      stale: false,
+      summary: {
+        total: 2,
+        open: 1,
+        blocking: 1,
+        major: 1,
+        minor: 0,
+        info: 0,
+        resolved: 1,
+        overridden: 0,
+      },
+      findings: [
+        {
+          id: "finding_01",
+          check: "citation",
+          severity: "blocking",
+          status: "open",
+          title: "Citation is unresolved",
+          detail: "Add a bibliography entry.",
+          evidence: ["report.md:4"],
+          location: { path: "report.md", line: 4 },
+        },
+      ],
+      events: [{ version: 1, type: "generated", actor: "Reviewer", at: 1 }],
+      createdAt: 1,
+      updatedAt: 2,
+    }
+    expect(normalizePublicationReview("md", report)).toMatchObject({
+      kind: "blocked",
+      report: { id: "review_01" },
+    })
+    expect(normalizePublicationReview("md", { ...report, stale: true })).toMatchObject({
+      kind: "stale",
+    })
+    expect(
+      normalizePublicationReview("md", {
+        ...report,
+        status: "warnings",
+        finalized: { actor: "Aayam Bansal", at: 3, artifactHash: "a".repeat(64) },
+      }),
+    ).toMatchObject({
+      kind: "finalized",
+      report: { finalized: { actor: "Aayam Bansal" } },
+    })
+  })
 })
diff --git a/frontend/workspace/src/artifacts/inspector.ts b/frontend/workspace/src/artifacts/inspector.ts
index 46b092b8..233a2f7f 100644
--- a/frontend/workspace/src/artifacts/inspector.ts
+++ b/frontend/workspace/src/artifacts/inspector.ts
@@ -35,6 +35,78 @@ export interface InspectorData {
   tabs: Record<InspectorTab, InspectorState>
 }
 
+export type PublicationReviewKind =
+  | "not-applicable"
+  | "not-run"
+  | "blocked"
+  | "warnings"
+  | "ready"
+  | "finalized"
+  | "stale"
+export type PublicationReviewCheck = "citation" | "numeric" | "figure" | "provenance"
+export type PublicationReviewSeverity = "blocking" | "major" | "minor" | "info"
+export type PublicationReviewFindingStatus = "open" | "resolved" | "overridden"
+
+export interface PublicationReviewFinding {
+  id: string
+  check: PublicationReviewCheck
+  severity: PublicationReviewSeverity
+  status: PublicationReviewFindingStatus
+  title: string
+  detail: string
+  evidence: string[]
+  location: { path: string; line?: number }
+  resolution?: {
+    kind: "resolved" | "overridden"
+    actor: string
+    reason: string
+    at: number
+  }
+}
+
+export interface PublicationReviewReport {
+  format: "openscience.publication-review.v1"
+  id: string
+  path: string
+  artifactHash: string
+  version: number
+  status: "blocked" | "warnings" | "ready"
+  stale: boolean
+  summary: {
+    total: number
+    open: number
+    blocking: number
+    major: number
+    minor: number
+    info: number
+    resolved: number
+    overridden: number
+  }
+  findings: PublicationReviewFinding[]
+  events: Array<{
+    version: number
+    type: "generated" | "resolved" | "overridden" | "finalized"
+    actor: string
+    at: number
+    findingID?: string
+    reason?: string
+  }>
+  finalized?: {
+    actor: string
+    at: number
+    artifactHash: string
+  }
+  createdAt: number
+  updatedAt: number
+}
+
+export interface PublicationReviewState {
+  kind: PublicationReviewKind
+  title: string
+  detail: string
+  report?: PublicationReviewReport
+}
+
 interface InspectorInput {
   file?: unknown
   provenance?: unknown
@@ -105,6 +177,62 @@ function state(available: boolean, title: string, detail: string): InspectorStat
   return { available, title, detail }
 }
 
+export function normalizePublicationReview(format: string, value: unknown): PublicationReviewState {
+  if (!["md", "markdown"].includes(format.toLowerCase())) {
+    return {
+      kind: "not-applicable",
+      title: "Publication checks do not apply",
+      detail: "Deterministic publication readiness currently applies to Markdown manuscripts.",
+    }
+  }
+  const report = review(value)
+  if (!report) {
+    return {
+      kind: "not-run",
+      title: "No publication review yet",
+      detail: "Run deterministic citation, numeric, figure, and provenance checks against this manuscript.",
+    }
+  }
+  if (report.stale) {
+    return {
+      kind: "stale",
+      title: "Review is stale",
+      detail: "The manuscript changed after this report was generated. Run the checks again.",
+      report,
+    }
+  }
+  if (report.finalized) {
+    return {
+      kind: "finalized",
+      title: report.status === "ready" ? "Publication review finalized" : "Finalized with recorded warnings",
+      detail: `Bound to ${report.artifactHash.slice(0, 12)} by ${report.finalized.actor}.`,
+      report,
+    }
+  }
+  if (report.status === "blocked") {
+    return {
+      kind: "blocked",
+      title: "Publication is blocked",
+      detail: `${report.summary.blocking} blocking finding${report.summary.blocking === 1 ? "" : "s"} must be resolved or explicitly overridden.`,
+      report,
+    }
+  }
+  if (report.status === "warnings") {
+    return {
+      kind: "warnings",
+      title: "Review has open warnings",
+      detail: `${report.summary.open} non-blocking finding${report.summary.open === 1 ? "" : "s"} remain.`,
+      report,
+    }
+  }
+  return {
+    kind: "ready",
+    title: "Ready to finalize",
+    detail: "No open deterministic findings remain for these manuscript bytes.",
+    report,
+  }
+}
+
 export function normalizeInspectorData(context: ArtifactContext, input: InspectorInput): InspectorData {
   const text = source(input.file)
   const version = provenance(input.provenance)
@@ -140,3 +268,147 @@ export function normalizeInspectorData(context: ArtifactContext, input: Inspecto
     },
   }
 }
+
+function review(value: unknown): PublicationReviewReport | undefined {
+  const row = record(value)
+  if (!row) return
+  const statuses = new Set(["blocked", "warnings", "ready"])
+  if (
+    row.format !== "openscience.publication-review.v1" ||
+    typeof row.id !== "string" ||
+    typeof row.path !== "string" ||
+    typeof row.artifactHash !== "string" ||
+    !/^[a-f0-9]{64}$/.test(row.artifactHash) ||
+    typeof row.version !== "number" ||
+    typeof row.status !== "string" ||
+    !statuses.has(row.status) ||
+    typeof row.stale !== "boolean" ||
+    typeof row.createdAt !== "number" ||
+    typeof row.updatedAt !== "number" ||
+    !Array.isArray(row.findings) ||
+    !Array.isArray(row.events)
+  )
+    return
+  const summary = record(row.summary)
+  if (
+    !summary ||
+    !["total", "open", "blocking", "major", "minor", "info", "resolved", "overridden"].every(
+      (key) => typeof summary[key] === "number",
+    )
+  )
+    return
+  const findings = row.findings.map(reviewFinding)
+  if (findings.some((finding) => !finding)) return
+  const events = row.events.flatMap((item) => {
+    const event = record(item)
+    const types = new Set(["generated", "resolved", "overridden", "finalized"])
+    if (
+      !event ||
+      typeof event.version !== "number" ||
+      typeof event.type !== "string" ||
+      !types.has(event.type) ||
+      typeof event.actor !== "string" ||
+      typeof event.at !== "number"
+    )
+      return []
+    return [
+      {
+        version: event.version,
+        type: event.type as PublicationReviewReport["events"][number]["type"],
+        actor: event.actor,
+        at: event.at,
+        ...(typeof event.findingID === "string" ? { findingID: event.findingID } : {}),
+        ...(typeof event.reason === "string" ? { reason: event.reason } : {}),
+      },
+    ]
+  })
+  if (events.length !== row.events.length) return
+  const final = record(row.finalized)
+  const finalized =
+    final &&
+    typeof final.actor === "string" &&
+    typeof final.at === "number" &&
+    typeof final.artifactHash === "string" &&
+    /^[a-f0-9]{64}$/.test(final.artifactHash)
+      ? { actor: final.actor, at: final.at, artifactHash: final.artifactHash }
+      : undefined
+  if (row.finalized !== undefined && !finalized) return
+  return {
+    format: "openscience.publication-review.v1",
+    id: row.id,
+    path: row.path,
+    artifactHash: row.artifactHash,
+    version: row.version,
+    status: row.status as PublicationReviewReport["status"],
+    stale: row.stale,
+    summary: {
+      total: summary.total as number,
+      open: summary.open as number,
+      blocking: summary.blocking as number,
+      major: summary.major as number,
+      minor: summary.minor as number,
+      info: summary.info as number,
+      resolved: summary.resolved as number,
+      overridden: summary.overridden as number,
+    },
+    findings: findings as PublicationReviewFinding[],
+    events,
+    ...(finalized ? { finalized } : {}),
+    createdAt: row.createdAt,
+    updatedAt: row.updatedAt,
+  }
+}
+
+function reviewFinding(value: unknown): PublicationReviewFinding | undefined {
+  const row = record(value)
+  const location = record(row?.location)
+  const resolution = record(row?.resolution)
+  const checks = new Set(["citation", "numeric", "figure", "provenance"])
+  const severities = new Set(["blocking", "major", "minor", "info"])
+  const statuses = new Set(["open", "resolved", "overridden"])
+  if (
+    !row ||
+    typeof row.id !== "string" ||
+    typeof row.check !== "string" ||
+    !checks.has(row.check) ||
+    typeof row.severity !== "string" ||
+    !severities.has(row.severity) ||
+    typeof row.status !== "string" ||
+    !statuses.has(row.status) ||
+    typeof row.title !== "string" ||
+    typeof row.detail !== "string" ||
+    !Array.isArray(row.evidence) ||
+    !row.evidence.every((item) => typeof item === "string") ||
+    !location ||
+    typeof location.path !== "string"
+  )
+    return
+  const parsed =
+    resolution &&
+    (resolution.kind === "resolved" || resolution.kind === "overridden") &&
+    typeof resolution.actor === "string" &&
+    typeof resolution.reason === "string" &&
+    typeof resolution.at === "number"
+      ? {
+          kind: resolution.kind as "resolved" | "overridden",
+          actor: resolution.actor,
+          reason: resolution.reason,
+          at: resolution.at,
+        }
+      : undefined
+  if (row.resolution !== undefined && !parsed) return
+  return {
+    id: row.id,
+    check: row.check as PublicationReviewCheck,
+    severity: row.severity as PublicationReviewSeverity,
+    status: row.status as PublicationReviewFindingStatus,
+    title: row.title,
+    detail: row.detail,
+    evidence: row.evidence as string[],
+    location: {
+      path: location.path,
+      ...(typeof location.line === "number" ? { line: location.line } : {}),
+    },
+    ...(parsed ? { resolution: parsed } : {}),
+  }
+}

From 4e6ac0fa8cef84964ea3044a64fb41f42b79a109 Mon Sep 17 00:00:00 2001
From: Aayam Bansal <aayambansal@gmail.com>
Date: Wed, 29 Jul 2026 15:18:53 +0800
Subject: [PATCH 35/40] fix: explain Muse regional availability

---
 backend/cli/src/provider/transform.ts  |  9 +++++++++
 backend/cli/test/session/retry.test.ts | 27 ++++++++++++++++++++++++++
 2 files changed, 36 insertions(+)

diff --git a/backend/cli/src/provider/transform.ts b/backend/cli/src/provider/transform.ts
index fcdc3abc..b1b8e083 100644
--- a/backend/cli/src/provider/transform.ts
+++ b/backend/cli/src/provider/transform.ts
@@ -1147,6 +1147,15 @@ export namespace ProviderTransform {
 
   export function error(providerID: string, error: APICallError) {
     let message = error.message
+    const body = error.responseBody?.toLowerCase() ?? ""
+    if (
+      providerID === "openrouter" &&
+      error.statusCode === 403 &&
+      body.includes("this model is only available in the united states") &&
+      body.includes('"provider_name":"meta"')
+    ) {
+      return "Muse Spark 1.1 is currently restricted by Meta to requests routed from the United States. Choose another model, or retry from a supported U.S. region."
+    }
     if (providerID.includes("github-copilot") && error.statusCode === 403) {
       return "Please reauthenticate with the copilot provider to ensure your credentials work properly with OpenScience."
     }
diff --git a/backend/cli/test/session/retry.test.ts b/backend/cli/test/session/retry.test.ts
index c0cdaba4..9d2fe03b 100644
--- a/backend/cli/test/session/retry.test.ts
+++ b/backend/cli/test/session/retry.test.ts
@@ -176,6 +176,33 @@ describe("session.message-v2.fromError", () => {
     const result = MessageV2.fromError(error, { providerID: "openai" }) as MessageV2.APIError
     expect(result.data.isRetryable).toBe(true)
   })
+
+  test("explains Muse Spark's United States availability restriction", () => {
+    const error = new APICallError({
+      message: "Provider returned error",
+      url: "https://openrouter.ai/api/v1/chat/completions",
+      requestBodyValues: {},
+      statusCode: 403,
+      responseHeaders: { "content-type": "application/json" },
+      responseBody: JSON.stringify({
+        error: {
+          message: "Provider returned error",
+          code: 403,
+          metadata: {
+            raw: "This model is only available in the United States.",
+            provider_name: "Meta",
+          },
+        },
+      }),
+      isRetryable: false,
+    })
+
+    const result = MessageV2.fromError(error, { providerID: "openrouter" }) as MessageV2.APIError
+    expect(result.data.message).toBe(
+      "Muse Spark 1.1 is currently restricted by Meta to requests routed from the United States. Choose another model, or retry from a supported U.S. region.",
+    )
+    expect(result.data.isRetryable).toBe(false)
+  })
 })
 
 describe("SessionRetry.isContextOverflow", () => {

From 3c46f5d64887d8afb549d199d244e46e5deec1d4 Mon Sep 17 00:00:00 2001
From: Aayam Bansal <aayambansal@gmail.com>
Date: Wed, 29 Jul 2026 15:21:06 +0800
Subject: [PATCH 36/40] test: harden packaged panel selectors

---
 frontend/workspace/e2e/atlas-bridge.spec.ts  |  4 ++--
 frontend/workspace/e2e/terminal-init.spec.ts | 10 +++++-----
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/frontend/workspace/e2e/atlas-bridge.spec.ts b/frontend/workspace/e2e/atlas-bridge.spec.ts
index 2dd5f2b7..d2aa37ee 100644
--- a/frontend/workspace/e2e/atlas-bridge.spec.ts
+++ b/frontend/workspace/e2e/atlas-bridge.spec.ts
@@ -63,8 +63,8 @@ test("Atlas canvas distinguishes a connected graph from an unavailable bridge",
 
   await gotoSession()
 
-  await page.getByRole("button", { name: "atlas", exact: true }).click()
-  const atlasTab = page.getByRole("tab", { name: "atlas", exact: true })
+  await page.getByRole("button", { name: /^atlas$/i }).click()
+  const atlasTab = page.getByRole("tab", { name: /^atlas$/i })
   await expect(atlasTab).toHaveAttribute("aria-selected", "true")
 
   if (response.ok()) {
diff --git a/frontend/workspace/e2e/terminal-init.spec.ts b/frontend/workspace/e2e/terminal-init.spec.ts
index 6a567c3c..5a8cf373 100644
--- a/frontend/workspace/e2e/terminal-init.spec.ts
+++ b/frontend/workspace/e2e/terminal-init.spec.ts
@@ -18,8 +18,8 @@ test("terminal executes output and can switch and close another tab", async ({ p
   try {
     await gotoSession()
 
-    await page.getByRole("button", { name: "terminal", exact: true }).click()
-    const terminalTab = page.getByRole("tab", { name: "terminal", exact: true })
+    await page.getByRole("button", { name: /^terminal$/i }).click()
+    const terminalTab = page.getByRole("tab", { name: /^terminal$/i })
     await expect(terminalTab).toHaveAttribute("aria-selected", "true")
 
     const terminals = page.locator(terminalSelector)
@@ -88,15 +88,15 @@ test("terminal executes output and can switch and close another tab", async ({ p
 test("terminal panel can be collapsed and reopened", async ({ page, gotoSession }) => {
   await gotoSession()
 
-  await page.getByRole("button", { name: "terminal", exact: true }).click()
-  const terminalTab = page.getByRole("tab", { name: "terminal", exact: true })
+  await page.getByRole("button", { name: /^terminal$/i }).click()
+  const terminalTab = page.getByRole("tab", { name: /^terminal$/i })
   await expect(terminalTab).toBeVisible()
   await expect(terminalTab).toHaveAttribute("aria-selected", "true")
 
   await page.getByTitle("hide panel", { exact: true }).click()
   await expect(terminalTab).toHaveCount(0)
 
-  await page.getByRole("button", { name: "terminal", exact: true }).click()
+  await page.getByRole("button", { name: /^terminal$/i }).click()
   await expect(terminalTab).toBeVisible()
   await expect(terminalTab).toHaveAttribute("aria-selected", "true")
 })

From 1c0a49a36348881922666ae5609abbe65a544d34 Mon Sep 17 00:00:00 2001
From: Aayam Bansal <aayambansal@gmail.com>
Date: Wed, 29 Jul 2026 15:38:26 +0800
Subject: [PATCH 37/40] feat: add manuscript authoring workbench

---
 .../plans/2026-07-29-manuscript-workbench.md  |  66 ++
 .../e2e/manuscript-workbench.spec.ts          |  99 +++
 .../e2e/science/manuscript-figure.svg         |   9 +
 frontend/workspace/e2e/science/manuscript.md  |   8 +
 frontend/workspace/e2e/science/references.bib |  12 +
 frontend/workspace/src/atlas/FilePreview.tsx  |  12 +-
 .../src/manuscript/ManuscriptWorkbench.tsx    | 796 ++++++++++++++++++
 .../workspace/src/manuscript/model.test.ts    | 114 +++
 frontend/workspace/src/manuscript/model.ts    | 178 ++++
 9 files changed, 1291 insertions(+), 3 deletions(-)
 create mode 100644 docs/superpowers/plans/2026-07-29-manuscript-workbench.md
 create mode 100644 frontend/workspace/e2e/manuscript-workbench.spec.ts
 create mode 100644 frontend/workspace/e2e/science/manuscript-figure.svg
 create mode 100644 frontend/workspace/e2e/science/manuscript.md
 create mode 100644 frontend/workspace/e2e/science/references.bib
 create mode 100644 frontend/workspace/src/manuscript/ManuscriptWorkbench.tsx
 create mode 100644 frontend/workspace/src/manuscript/model.test.ts
 create mode 100644 frontend/workspace/src/manuscript/model.ts

diff --git a/docs/superpowers/plans/2026-07-29-manuscript-workbench.md b/docs/superpowers/plans/2026-07-29-manuscript-workbench.md
new file mode 100644
index 00000000..364f8206
--- /dev/null
+++ b/docs/superpowers/plans/2026-07-29-manuscript-workbench.md
@@ -0,0 +1,66 @@
+# Manuscript Workbench Implementation Plan
+
+> **Execution note:** Follow the test-driven-development and verification-before-completion skills for each task.
+
+**Goal:** Turn Markdown reports into a practical scientific authoring surface with live preview, local citations and figures, and trustworthy publication exports.
+
+**Architecture:** Keep file persistence in `FileView`. Add a focused `ManuscriptWorkbench` for Markdown authoring, backed by pure parsing/insertion helpers. Reuse the existing artifact discovery, publication capability, review, and export endpoints; no Atlas changes are required.
+
+**Tech stack:** SolidJS, TypeScript, Bun tests, Playwright.
+
+---
+
+### Task 1: Manuscript parsing and insertion model
+
+**Files:**
+- Create: `frontend/workspace/src/manuscript/model.ts`
+- Test: `frontend/workspace/src/manuscript/model.test.ts`
+
+1. Add failing tests for stripping YAML frontmatter, resolving bibliography declarations, parsing BibTeX entries, computing relative figure paths, and replacing an editor selection.
+2. Implement the smallest pure helpers that pass those tests.
+3. Run the focused Bun test.
+
+### Task 2: Live Markdown authoring workbench
+
+**Files:**
+- Create: `frontend/workspace/src/manuscript/ManuscriptWorkbench.tsx`
+- Modify: `frontend/workspace/src/atlas/FilePreview.tsx`
+
+1. Mount a side-by-side source editor and rendered preview for Markdown.
+2. Preserve dirty/reset/save behavior owned by `FileView`.
+3. Render only the Markdown body while preserving frontmatter in the saved source.
+4. Keep the existing raw-source control as a compact fallback mode.
+
+### Task 3: Citation and figure browsers
+
+**Files:**
+- Modify: `frontend/workspace/src/manuscript/ManuscriptWorkbench.tsx`
+- Test: `frontend/workspace/e2e/manuscript-workbench.spec.ts`
+- Create: `frontend/workspace/e2e/science/manuscript.md`
+- Create: `frontend/workspace/e2e/science/references.bib`
+- Create: `frontend/workspace/e2e/science/figure.svg`
+
+1. Load frontmatter-declared local `.bib` files and expose searchable citation cards.
+2. Insert `[@key]` at the current editor selection and restore focus/cursor.
+3. Discover local figure artifacts and insert relative Markdown image syntax.
+4. Prove both flows through the real local file APIs in Playwright.
+
+### Task 4: Review-aware publication exports
+
+**Files:**
+- Modify: `frontend/workspace/src/manuscript/ManuscriptWorkbench.tsx`
+- Modify: `frontend/workspace/e2e/manuscript-workbench.spec.ts`
+
+1. Load local publication capabilities and the current exact-byte review state.
+2. Offer draft export for every locally supported format.
+3. Offer reviewed export only for a finalized, non-stale review and include its `review_id`.
+4. Open generated browser-readable artifacts and download Word/PowerPoint outputs.
+5. Show actionable local-tool and review-gate explanations instead of dead controls.
+
+### Task 5: Verification and branch delivery
+
+1. Run focused model and Playwright tests.
+2. Run workspace typecheck, formatting, production build, backend tests, and the full browser suite.
+3. Commit each coherent feature with Aayam Bansal’s configured identity and push only `openscience/aayam-new`.
+4. Validate branch CI.
+5. Include this batch in the next npm `test` dist-tag release; never publish `latest`.
diff --git a/frontend/workspace/e2e/manuscript-workbench.spec.ts b/frontend/workspace/e2e/manuscript-workbench.spec.ts
new file mode 100644
index 00000000..e2ed5709
--- /dev/null
+++ b/frontend/workspace/e2e/manuscript-workbench.spec.ts
@@ -0,0 +1,99 @@
+import path from "node:path"
+import type { Page } from "@playwright/test"
+import { test, expect } from "./fixtures"
+
+const escapeRegex = (value: string) => value.replace(/[.*+?^${}()|[\]\\]/g, "\\$&")
+
+async function openFile(page: Page, directory: string, relativePath: string) {
+  await page.getByRole("tab", { name: "Files", exact: true }).click()
+  const folder = path.join(directory, path.dirname(relativePath))
+  const filename = path.basename(relativePath)
+  const location = page.getByPlaceholder("/absolute/path")
+  await location.fill(folder)
+  await location.press("Enter")
+  await page.getByPlaceholder("filter this folder…").fill(filename)
+  const file = page.getByRole("button", { name: new RegExp(`^${escapeRegex(filename)}\\b`) }).first()
+  await expect(file).toBeVisible()
+  await file.click()
+}
+
+test("authors Markdown with live preview, local citations, and local figures", async ({
+  page,
+  directory,
+  gotoSession,
+}) => {
+  await gotoSession()
+  await openFile(page, directory, "frontend/workspace/e2e/science/manuscript.md")
+
+  const workbench = page.locator('[data-component="manuscript-workbench"]')
+  const editor = workbench.getByLabel("Manuscript source")
+  const preview = workbench.locator('[data-slot="manuscript-preview"]')
+  await expect(workbench).toBeVisible()
+  await expect(editor).toBeVisible()
+  await expect(preview.getByRole("heading", { name: "Manuscript workbench", exact: true })).toBeVisible()
+  await expect(preview).not.toContainText("bibliography: references.bib")
+
+  await editor.evaluate((node: HTMLTextAreaElement) => node.setSelectionRange(node.value.length, node.value.length))
+  await workbench.getByRole("button", { name: "Citations", exact: true }).click()
+  const citations = workbench.locator('[data-component="citation-browser"]')
+  await expect(citations.getByText("Reliable Scientific Interfaces", { exact: true })).toBeVisible()
+  await citations.getByPlaceholder("Find by author, title, or key…").fill("smith")
+  await citations.getByRole("button", { name: "Insert @smith2026", exact: true }).click()
+  await expect(editor).toHaveValue(/\[@smith2026\]$/)
+
+  await workbench.getByRole("button", { name: "Figures", exact: true }).click()
+  const figures = workbench.locator('[data-component="figure-browser"]')
+  await figures.getByPlaceholder("Find a local figure…").fill("manuscript-figure")
+  await figures.getByLabel("Figure alt text").fill("Primary endpoint")
+  await figures.getByRole("button", { name: "Insert manuscript-figure.svg", exact: true }).click()
+  await expect(editor).toHaveValue(/!\[Primary endpoint\]\(manuscript-figure\.svg\)$/)
+  await expect(preview.getByRole("img", { name: "Primary endpoint", exact: true })).toBeVisible()
+
+  await page.getByRole("button", { name: "reset", exact: true }).click()
+  await expect(editor).not.toHaveValue(/\[@smith2026\]/)
+})
+
+test("exposes exact-byte review and publication export controls", async ({ page, directory, gotoSession }) => {
+  const exports: Array<Record<string, unknown>> = []
+  await page.route("**/file/publication?**", async (route) => {
+    if (route.request().method() !== "POST") {
+      await route.continue()
+      return
+    }
+    exports.push(route.request().postDataJSON() as Record<string, unknown>)
+    await route.fulfill({
+      status: 200,
+      contentType: "application/json",
+      body: JSON.stringify({
+        path: "exports/manuscript-preview.html",
+        format: "html",
+        size: 512,
+        created_at: new Date().toISOString(),
+        engine: "OpenScience Markdown",
+        readiness: "draft",
+      }),
+    })
+  })
+
+  await gotoSession()
+  await openFile(page, directory, "frontend/workspace/e2e/science/manuscript.md")
+  const workbench = page.locator('[data-component="manuscript-workbench"]')
+
+  await workbench.getByRole("button", { name: "Review", exact: true }).click()
+  const inspector = page.locator('[data-component="artifact-inspector"]')
+  await expect(inspector.getByRole("tab", { name: "Review", exact: true })).toHaveAttribute("aria-selected", "true")
+
+  await workbench.getByRole("button", { name: "Publish", exact: true }).click()
+  const publish = workbench.locator('[data-component="publication-controls"]')
+  await expect(publish.getByText("Reviewed export locked", { exact: true })).toBeVisible()
+  await publish.getByRole("button", { name: "Export draft HTML", exact: true }).click()
+  await expect
+    .poll(() => exports)
+    .toEqual([
+      {
+        path: "manuscript.md",
+        format: "html",
+        readiness: "draft",
+      },
+    ])
+})
diff --git a/frontend/workspace/e2e/science/manuscript-figure.svg b/frontend/workspace/e2e/science/manuscript-figure.svg
new file mode 100644
index 00000000..1e83ff8d
--- /dev/null
+++ b/frontend/workspace/e2e/science/manuscript-figure.svg
@@ -0,0 +1,9 @@
+<svg xmlns="http://www.w3.org/2000/svg" width="480" height="280" viewBox="0 0 480 280">
+  <rect width="480" height="280" fill="#f4f1e8"/>
+  <path d="M60 220 L160 138 L260 172 L420 55" fill="none" stroke="#326a65" stroke-width="8"/>
+  <circle cx="60" cy="220" r="10" fill="#326a65"/>
+  <circle cx="160" cy="138" r="10" fill="#326a65"/>
+  <circle cx="260" cy="172" r="10" fill="#326a65"/>
+  <circle cx="420" cy="55" r="10" fill="#326a65"/>
+  <text x="28" y="36" fill="#252821" font-family="system-ui" font-size="18">Primary endpoint</text>
+</svg>
diff --git a/frontend/workspace/e2e/science/manuscript.md b/frontend/workspace/e2e/science/manuscript.md
new file mode 100644
index 00000000..5034f0ef
--- /dev/null
+++ b/frontend/workspace/e2e/science/manuscript.md
@@ -0,0 +1,8 @@
+---
+title: Manuscript workbench
+bibliography: references.bib
+---
+
+# Manuscript workbench
+
+The live preview starts with the manuscript body.
diff --git a/frontend/workspace/e2e/science/references.bib b/frontend/workspace/e2e/science/references.bib
new file mode 100644
index 00000000..40dceb6f
--- /dev/null
+++ b/frontend/workspace/e2e/science/references.bib
@@ -0,0 +1,12 @@
+@article{smith2026,
+  title = {Reliable Scientific Interfaces},
+  author = {Smith, Ada and Chen, Lin},
+  year = {2026},
+  journal = {Journal of Open Research}
+}
+
+@misc{dataset2025,
+  title = {Workbench validation dataset},
+  author = {Open Science Team},
+  year = {2025}
+}
diff --git a/frontend/workspace/src/atlas/FilePreview.tsx b/frontend/workspace/src/atlas/FilePreview.tsx
index 1de280e7..458af0f5 100644
--- a/frontend/workspace/src/atlas/FilePreview.tsx
+++ b/frontend/workspace/src/atlas/FilePreview.tsx
@@ -26,6 +26,7 @@ import { detectBinaryScienceFormat } from "@/science/formats/binary"
 import { NotebookView } from "@/notebook/NotebookView"
 import { DataTableView } from "@/data/DataTableView"
 import type { TableFormat } from "@/data/table"
+import { ManuscriptWorkbench } from "@/manuscript/ManuscriptWorkbench"
 import { artifactContext, createArtifactContext } from "@/artifacts/context"
 import type { ArtifactInspection } from "@/science/renderers"
 import { toast } from "@/atlas/Toast"
@@ -501,9 +502,14 @@ export function FileView(props: {
             <Switch>
               {/* markdown */}
               <Match when={kind() === "markdown" && !showSource()}>
-                <div style={{ padding: "22px 26px", "max-width": "820px", margin: "0 auto" }}>
-                  <Markdown class="atlas-md" text={draft()} />
-                </div>
+                <ManuscriptWorkbench
+                  directory={directory()}
+                  path={props.path}
+                  text={draft()}
+                  dirty={dirty()}
+                  saving={saving()}
+                  onChange={setDraft}
+                />
               </Match>
 
               {/* notebook */}
diff --git a/frontend/workspace/src/manuscript/ManuscriptWorkbench.tsx b/frontend/workspace/src/manuscript/ManuscriptWorkbench.tsx
new file mode 100644
index 00000000..0abd9a8b
--- /dev/null
+++ b/frontend/workspace/src/manuscript/ManuscriptWorkbench.tsx
@@ -0,0 +1,796 @@
+import { For, Show, createMemo, createResource, createSignal, type JSX } from "solid-js"
+import { Markdown } from "@synsci/ui/markdown"
+import { usePlatform } from "@/context/platform"
+import { useSDK } from "@/context/sdk"
+import { centerTabs } from "@/atlas/store/centerTabs"
+import { uiStore } from "@/atlas/store/ui"
+import { toast } from "@/atlas/Toast"
+import { IconBookOpen, IconCheckCircle, IconDownload, IconFile, IconSearch, IconSparkles } from "@/atlas/shared/Icon"
+import { FONT_CODE, FONT_MONO, FONT_SANS } from "@/styles/tokens"
+import type { ArtifactInfo } from "@/artifacts/model"
+import {
+  figureMarkdown,
+  insertSelection,
+  parseBibtex,
+  parseManuscript,
+  resolveReferencePath,
+  rewritePreviewImages,
+  type Citation,
+} from "./model"
+
+type Panel = "citations" | "figures" | "publish"
+type PublicationFormat = "html" | "pdf" | "docx" | "latex" | "pptx"
+
+interface PublicationCapabilities {
+  pandoc: boolean
+  pdf_engine?: string
+  formats: Record<PublicationFormat, boolean>
+}
+
+interface PublicationReview {
+  id: string
+  stale: boolean
+  finalized?: {
+    actor: string
+    at: number
+    artifactHash: string
+  }
+}
+
+interface PublicationResult {
+  path: string
+  format: PublicationFormat
+  readiness: "draft" | "reviewed"
+}
+
+interface CitationItem extends Citation {
+  source: string
+}
+
+export function ManuscriptWorkbench(props: {
+  directory: string
+  path: string
+  text: string
+  dirty: boolean
+  saving: boolean
+  onChange: (text: string) => void
+}): JSX.Element {
+  const sdk = useSDK()
+  const platform = usePlatform()
+  const [panel, setPanel] = createSignal<Panel>()
+  const [citationQuery, setCitationQuery] = createSignal("")
+  const [figureQuery, setFigureQuery] = createSignal("")
+  const [alt, setAlt] = createSignal("")
+  const [posting, setPosting] = createSignal<string>()
+  const [editor, setEditor] = createSignal<HTMLTextAreaElement>()
+  const [reviewKey, setReviewKey] = createSignal(0)
+  const manuscript = createMemo(() => parseManuscript(props.text))
+  const request = () => platform.fetch ?? fetch
+  const url = (route: string, path?: string) =>
+    `${sdk.url.replace(/\/$/, "")}${route}?directory=${encodeURIComponent(props.directory)}${path ? `&path=${encodeURIComponent(path)}` : ""}`
+
+  const [artifacts] = createResource(
+    () => props.directory,
+    async () => {
+      const response = await request()(url("/file/artifacts"))
+      if (!response.ok) throw new Error(`Artifact discovery failed (${response.status})`)
+      const value: unknown = await response.json()
+      if (!Array.isArray(value)) return []
+      return value.filter(isArtifact)
+    },
+  )
+
+  const [citations] = createResource(
+    () => `${props.directory}:${props.path}:${manuscript().bibliographies.join("|")}`,
+    async () => {
+      const rows = await Promise.all(
+        manuscript().bibliographies.map(async (reference) => {
+          const path = resolveReferencePath(props.path, reference)
+          const response = await request()(url("/file/content", path))
+          if (!response.ok) return []
+          const value: unknown = await response.json()
+          const content = record(value)?.content
+          if (typeof content !== "string") return []
+          return parseBibtex(content).map((citation) => ({ ...citation, source: path }))
+        }),
+      )
+      const unique = new Map<string, CitationItem>()
+      for (const citation of rows.flat()) unique.set(citation.key, citation)
+      return Array.from(unique.values()).toSorted((a, b) => a.key.localeCompare(b.key))
+    },
+  )
+
+  const [capabilities] = createResource(
+    () => props.directory,
+    async () => {
+      const response = await request()(url("/file/publication/capabilities"))
+      if (!response.ok) throw new Error(`Publication tools unavailable (${response.status})`)
+      return (await response.json()) as PublicationCapabilities
+    },
+  )
+
+  const [review, reviewApi] = createResource(
+    () => `${props.directory}:${props.path}:${reviewKey()}`,
+    async () => {
+      const response = await request()(url("/file/reviews", props.path))
+      if (response.status === 404) return
+      if (!response.ok) throw new Error(`Publication review unavailable (${response.status})`)
+      return (await response.json()) as PublicationReview
+    },
+  )
+
+  const figures = createMemo(() => {
+    const query = figureQuery().trim().toLowerCase()
+    return (artifacts.latest ?? [])
+      .filter((item) => item.kind === "figure")
+      .filter((item) => !query || `${item.name} ${item.path}`.toLowerCase().includes(query))
+  })
+  const filteredCitations = createMemo(() => {
+    const query = citationQuery().trim().toLowerCase()
+    if (!query) return citations.latest ?? []
+    return (citations.latest ?? []).filter((citation) =>
+      [citation.key, citation.title, citation.author, citation.year, citation.venue]
+        .filter(Boolean)
+        .join(" ")
+        .toLowerCase()
+        .includes(query),
+    )
+  })
+  const formats = createMemo(() =>
+    (["html", "pdf", "docx", "latex", "pptx"] as PublicationFormat[]).filter(
+      (format) => capabilities.latest?.formats[format],
+    ),
+  )
+  const reviewed = createMemo(() => Boolean(review.latest?.finalized && !review.latest.stale && !props.dirty))
+  const preview = createMemo(() =>
+    rewritePreviewImages(manuscript().body, props.path, (path) => url("/file/raw", path)),
+  )
+
+  const toggle = (next: Panel) => setPanel((current) => (current === next ? undefined : next))
+  const openPublish = () => {
+    const opening = panel() !== "publish"
+    toggle("publish")
+    if (!opening) return
+    setReviewKey((value) => value + 1)
+    void reviewApi.refetch()
+  }
+  const insert = (value: string) => {
+    const target = editor()
+    const result = insertSelection(
+      props.text,
+      value,
+      target?.selectionStart ?? props.text.length,
+      target?.selectionEnd ?? props.text.length,
+    )
+    props.onChange(result.text)
+    queueMicrotask(() => {
+      const next = editor()
+      next?.focus()
+      next?.setSelectionRange(result.start, result.end)
+    })
+  }
+  const addCitation = (citation: CitationItem) => {
+    insert(`[@${citation.key}]`)
+    setPanel(undefined)
+    toast.success("citation inserted", `@${citation.key}`)
+  }
+  const addFigure = (figure: ArtifactInfo) => {
+    const markdown = figureMarkdown(alt(), props.path, figure.path)
+    const prefix = props.text.endsWith("\n\n") ? "" : props.text.endsWith("\n") ? "\n" : "\n\n"
+    insert(`${prefix}${markdown}`)
+    setPanel(undefined)
+    setAlt("")
+    toast.success("figure inserted", figure.path)
+  }
+  const openReview = () => {
+    uiStore.setRightPaneMode("artifact")
+    uiStore.setRightPaneOpen(true)
+    requestAnimationFrame(() => document.getElementById("artifact-inspector-tab-review")?.click())
+    setReviewKey((value) => value + 1)
+    void reviewApi.refetch()
+  }
+  const publish = async (format: PublicationFormat, readiness: "draft" | "reviewed") => {
+    if (props.dirty || props.saving) {
+      toast.error("save before export", "Publication exports are generated from exact saved bytes.")
+      return
+    }
+    const report = review.latest
+    if (readiness === "reviewed" && (!report?.finalized || report.stale)) {
+      toast.error("reviewed export locked", "Finalize a current publication review first.")
+      return
+    }
+    const key = `${readiness}:${format}`
+    setPosting(key)
+    const response = await request()(url("/file/publication"), {
+      method: "POST",
+      headers: { "Content-Type": "application/json" },
+      body: JSON.stringify({
+        path: props.path,
+        format,
+        readiness,
+        ...(readiness === "reviewed" && report ? { review_id: report.id } : {}),
+      }),
+    }).catch(() => undefined)
+    setPosting(undefined)
+    if (!response?.ok) {
+      const detail = await response?.text().catch(() => "")
+      toast.error("publication export failed", detail || (response ? `${response.status}` : "request failed"))
+      return
+    }
+    const result = (await response.json()) as PublicationResult
+    toast.success(`${format.toUpperCase()} ready`, result.path)
+    if (!["docx", "pptx"].includes(result.format)) {
+      centerTabs.openFile(props.directory, result.path)
+      return
+    }
+    const raw = await request()(url("/file/raw", result.path))
+    if (!raw.ok) return
+    const object = URL.createObjectURL(await raw.blob())
+    const anchor = document.createElement("a")
+    anchor.href = object
+    anchor.download = result.path.split("/").pop() || `manuscript.${result.format}`
+    anchor.click()
+    URL.revokeObjectURL(object)
+  }
+
+  return (
+    <div
+      data-component="manuscript-workbench"
+      style={{
+        height: "100%",
+        "min-height": 0,
+        display: "flex",
+        "flex-direction": "column",
+        background: "var(--color-bg-subtle)",
+      }}
+    >
+      <div
+        style={{
+          display: "flex",
+          "align-items": "center",
+          gap: "6px",
+          padding: "8px 10px",
+          border: "0",
+          "border-bottom": "1px solid var(--color-border)",
+          background: "var(--color-bg)",
+          "flex-shrink": 0,
+        }}
+      >
+        <span style={eyebrow()}>MANUSCRIPT</span>
+        <span style={{ flex: 1, "font-family": FONT_MONO, "font-size": "9px", color: "var(--color-text-faint)" }}>
+          live source + preview
+        </span>
+        <button type="button" style={toolButton(panel() === "citations")} onClick={() => toggle("citations")}>
+          <IconBookOpen size={11} /> Citations
+        </button>
+        <button type="button" style={toolButton(panel() === "figures")} onClick={() => toggle("figures")}>
+          <IconFile size={11} /> Figures
+        </button>
+        <button type="button" style={toolButton()} onClick={openReview}>
+          <IconCheckCircle size={11} /> Review
+        </button>
+        <button type="button" style={toolButton(panel() === "publish")} onClick={openPublish}>
+          <IconDownload size={11} /> Publish
+        </button>
+      </div>
+
+      <Show when={panel() === "citations"}>
+        <BrowserShell
+          component="citation-browser"
+          title="Citation library"
+          detail={citationDetail(manuscript().bibliographies)}
+        >
+          <Search value={citationQuery()} placeholder="Find by author, title, or key…" onInput={setCitationQuery} />
+          <div class="atlas-scroll" style={browserList()}>
+            <Show when={!citations.loading} fallback={<Empty>Reading local bibliographies…</Empty>}>
+              <Show
+                when={filteredCitations().length}
+                fallback={
+                  <Empty>
+                    {manuscript().bibliographies.length
+                      ? "No matching BibTeX entries."
+                      : "Add bibliography: references.bib to the manuscript frontmatter."}
+                  </Empty>
+                }
+              >
+                <For each={filteredCitations()}>
+                  {(citation) => (
+                    <button
+                      type="button"
+                      aria-label={`Insert @${citation.key}`}
+                      style={browserRow()}
+                      onClick={() => addCitation(citation)}
+                    >
+                      <span style={rowText()}>
+                        <strong>{citation.title || citation.key}</strong>
+                        <small>
+                          {[citation.author, citation.venue, citation.year].filter(Boolean).join(" · ") ||
+                            citation.source}
+                        </small>
+                      </span>
+                      <span style={keyBadge()}>@{citation.key}</span>
+                    </button>
+                  )}
+                </For>
+              </Show>
+            </Show>
+          </div>
+        </BrowserShell>
+      </Show>
+
+      <Show when={panel() === "figures"}>
+        <BrowserShell
+          component="figure-browser"
+          title="Local figures"
+          detail={`${(artifacts.latest ?? []).filter((item) => item.kind === "figure").length} discovered`}
+        >
+          <div style={{ display: "grid", gap: "5px" }}>
+            <Search value={figureQuery()} placeholder="Find a local figure…" onInput={setFigureQuery} />
+            <input
+              aria-label="Figure alt text"
+              value={alt()}
+              onInput={(event) => setAlt(event.currentTarget.value)}
+              placeholder="Describe the figure for readers…"
+              style={input()}
+            />
+          </div>
+          <div class="atlas-scroll" style={browserList()}>
+            <Show when={!artifacts.loading} fallback={<Empty>Discovering local figures…</Empty>}>
+              <Show when={figures().length} fallback={<Empty>No matching local figures.</Empty>}>
+                <For each={figures()}>
+                  {(figure) => (
+                    <button
+                      type="button"
+                      aria-label={`Insert ${figure.name}`}
+                      style={browserRow()}
+                      onClick={() => addFigure(figure)}
+                    >
+                      <img
+                        src={url("/file/raw", figure.path)}
+                        alt=""
+                        style={{ width: "50px", height: "34px", "object-fit": "cover", "border-radius": "3px" }}
+                      />
+                      <span style={rowText()}>
+                        <strong>{figure.name}</strong>
+                        <small>{figure.path}</small>
+                      </span>
+                      <span style={keyBadge()}>{figure.format.toUpperCase()}</span>
+                    </button>
+                  )}
+                </For>
+              </Show>
+            </Show>
+          </div>
+        </BrowserShell>
+      </Show>
+
+      <Show when={panel() === "publish"}>
+        <BrowserShell
+          component="publication-controls"
+          title="Publication exports"
+          detail="Generated locally from exact saved bytes"
+        >
+          <div style={{ "grid-column": "2 / -1", "min-width": 0 }}>
+            <Show when={!capabilities.loading} fallback={<Empty>Checking local publication tools…</Empty>}>
+              <div style={{ display: "grid", "grid-template-columns": "repeat(2, minmax(0, 1fr))", gap: "10px" }}>
+                <ExportGroup
+                  title="Draft"
+                  detail={props.dirty ? "Save changes before exporting." : "Watermarked as draft."}
+                >
+                  <For each={formats()}>
+                    {(format) => (
+                      <ExportButton
+                        format={format}
+                        readiness="draft"
+                        busy={posting() === `draft:${format}`}
+                        disabled={props.dirty || Boolean(posting())}
+                        onClick={() => void publish(format, "draft")}
+                      />
+                    )}
+                  </For>
+                </ExportGroup>
+                <ExportGroup
+                  title={reviewed() ? "Reviewed bytes" : "Reviewed export locked"}
+                  detail={
+                    reviewed()
+                      ? `Bound to ${review.latest!.finalized!.artifactHash.slice(0, 12)}.`
+                      : props.dirty
+                        ? "Save the manuscript, then refresh its review."
+                        : review.latest?.stale
+                          ? "The last review is stale. Run and finalize it again."
+                          : "Run and finalize the publication review first."
+                  }
+                >
+                  <Show
+                    when={reviewed()}
+                    fallback={
+                      <button type="button" style={reviewButton()} onClick={openReview}>
+                        open review
+                      </button>
+                    }
+                  >
+                    <For each={formats()}>
+                      {(format) => (
+                        <ExportButton
+                          format={format}
+                          readiness="reviewed"
+                          busy={posting() === `reviewed:${format}`}
+                          disabled={Boolean(posting())}
+                          onClick={() => void publish(format, "reviewed")}
+                        />
+                      )}
+                    </For>
+                  </Show>
+                </ExportGroup>
+              </div>
+              <Show when={!capabilities.latest?.pandoc}>
+                <span style={notice()}>HTML is ready. Install Pandoc to add Word, LaTeX, and PowerPoint.</span>
+              </Show>
+              <Show when={capabilities.latest?.pandoc && !capabilities.latest.formats.pdf}>
+                <span style={notice()}>Install a local TeX or Typst engine to add PDF export.</span>
+              </Show>
+            </Show>
+          </div>
+        </BrowserShell>
+      </Show>
+
+      <div style={{ flex: 1, "min-height": 0, display: "flex", overflow: "hidden" }}>
+        <section
+          data-slot="manuscript-source"
+          style={{
+            flex: "1 1 50%",
+            "min-width": "280px",
+            "min-height": 0,
+            display: "flex",
+            "flex-direction": "column",
+            border: "0",
+            "border-right": "1px solid var(--color-border)",
+            background: "var(--color-bg)",
+          }}
+        >
+          <PaneLabel label="SOURCE" detail={props.dirty ? "unsaved changes" : "saved"} active={props.dirty} />
+          <textarea
+            ref={setEditor}
+            aria-label="Manuscript source"
+            value={props.text}
+            spellcheck
+            onInput={(event) => props.onChange(event.currentTarget.value)}
+            class="atlas-scroll"
+            style={{
+              all: "unset",
+              "box-sizing": "border-box",
+              flex: 1,
+              "min-height": 0,
+              overflow: "auto",
+              padding: "18px 20px 42px",
+              "font-family": FONT_CODE,
+              "font-size": "12px",
+              "line-height": 1.72,
+              color: "var(--color-text)",
+              "white-space": "pre-wrap",
+              "tab-size": 2,
+            }}
+          />
+        </section>
+        <section
+          data-slot="manuscript-preview-pane"
+          style={{
+            flex: "1.08 1 50%",
+            "min-width": "300px",
+            "min-height": 0,
+            display: "flex",
+            "flex-direction": "column",
+            background: "var(--color-bg-subtle)",
+          }}
+        >
+          <PaneLabel label="LIVE PREVIEW" detail={`${wordCount(manuscript().body)} words`} />
+          <div
+            data-slot="manuscript-preview"
+            class="atlas-scroll"
+            style={{ flex: 1, "min-height": 0, overflow: "auto", padding: "24px 28px 64px" }}
+          >
+            <div style={{ "max-width": "780px", margin: "0 auto" }}>
+              <Markdown class="atlas-md" text={preview()} />
+            </div>
+          </div>
+        </section>
+      </div>
+    </div>
+  )
+}
+
+function BrowserShell(props: { component: string; title: string; detail: string; children: JSX.Element }): JSX.Element {
+  return (
+    <section
+      data-component={props.component}
+      style={{
+        display: "grid",
+        "grid-template-columns": "minmax(150px, .55fr) minmax(190px, .7fr) minmax(280px, 1.75fr)",
+        gap: "8px",
+        "align-items": "center",
+        padding: "10px",
+        "max-height": "190px",
+        border: "0",
+        "border-bottom": "1px solid var(--color-border)",
+        background: "var(--color-bg-subtle)",
+        "flex-shrink": 0,
+        overflow: "hidden",
+      }}
+    >
+      <div style={{ display: "grid", gap: "3px", "align-self": "start", padding: "5px 6px" }}>
+        <strong style={{ "font-family": FONT_SANS, "font-size": "11px", color: "var(--color-text)" }}>
+          {props.title}
+        </strong>
+        <span style={{ "font-family": FONT_MONO, "font-size": "9px", color: "var(--color-text-faint)" }}>
+          {props.detail}
+        </span>
+      </div>
+      {props.children}
+    </section>
+  )
+}
+
+function Search(props: { value: string; placeholder: string; onInput: (value: string) => void }): JSX.Element {
+  return (
+    <label style={{ ...input(), display: "flex", "align-items": "center", gap: "6px" }}>
+      <IconSearch size={11} />
+      <input
+        value={props.value}
+        onInput={(event) => props.onInput(event.currentTarget.value)}
+        placeholder={props.placeholder}
+        style={{ all: "unset", width: "100%", "min-width": 0 }}
+      />
+    </label>
+  )
+}
+
+function Empty(props: { children: JSX.Element }): JSX.Element {
+  return (
+    <span
+      style={{
+        display: "grid",
+        "place-items": "center",
+        "min-height": "42px",
+        padding: "8px",
+        "font-family": FONT_SANS,
+        "font-size": "10px",
+        color: "var(--color-text-faint)",
+        "text-align": "center",
+      }}
+    >
+      {props.children}
+    </span>
+  )
+}
+
+function ExportGroup(props: { title: string; detail: string; children: JSX.Element }): JSX.Element {
+  return (
+    <div style={{ display: "grid", gap: "6px", "align-content": "start" }}>
+      <div style={{ display: "grid", gap: "2px" }}>
+        <strong style={{ "font-family": FONT_SANS, "font-size": "10px", color: "var(--color-text)" }}>
+          {props.title}
+        </strong>
+        <span style={{ "font-family": FONT_SANS, "font-size": "9px", color: "var(--color-text-faint)" }}>
+          {props.detail}
+        </span>
+      </div>
+      <div style={{ display: "flex", gap: "4px", "flex-wrap": "wrap" }}>{props.children}</div>
+    </div>
+  )
+}
+
+function ExportButton(props: {
+  format: PublicationFormat
+  readiness: "draft" | "reviewed"
+  busy: boolean
+  disabled: boolean
+  onClick: () => void
+}): JSX.Element {
+  const label = () =>
+    props.format === "docx" ? "Word" : props.format === "pptx" ? "PowerPoint" : props.format.toUpperCase()
+  return (
+    <button
+      type="button"
+      aria-label={`Export ${props.readiness} ${label()}`}
+      disabled={props.disabled}
+      onClick={props.onClick}
+      style={exportButton(props.disabled)}
+    >
+      <IconDownload size={9} />
+      {props.busy ? "working…" : label()}
+    </button>
+  )
+}
+
+function PaneLabel(props: { label: string; detail: string; active?: boolean }): JSX.Element {
+  return (
+    <div
+      style={{
+        display: "flex",
+        "align-items": "center",
+        gap: "8px",
+        height: "30px",
+        padding: "0 12px",
+        border: "0",
+        "border-bottom": "1px solid var(--color-border)",
+        background: "var(--color-bg-subtle)",
+        "flex-shrink": 0,
+      }}
+    >
+      <span style={{ ...eyebrow(), color: props.active ? "var(--color-warning)" : "var(--color-text-faint)" }}>
+        {props.label}
+      </span>
+      <span style={{ flex: 1, "font-family": FONT_MONO, "font-size": "9px", color: "var(--color-text-faint)" }}>
+        {props.detail}
+      </span>
+      <Show when={props.label === "LIVE PREVIEW"}>
+        <IconSparkles size={10} style={{ color: "var(--color-text-faint)" }} />
+      </Show>
+    </div>
+  )
+}
+
+function isArtifact(value: unknown): value is ArtifactInfo {
+  const item = record(value)
+  return (
+    typeof item?.name === "string" &&
+    typeof item.path === "string" &&
+    typeof item.kind === "string" &&
+    typeof item.format === "string" &&
+    typeof item.size === "number" &&
+    typeof item.modified === "number"
+  )
+}
+
+function record(value: unknown): Record<string, unknown> | undefined {
+  if (!value || typeof value !== "object" || Array.isArray(value)) return
+  return value as Record<string, unknown>
+}
+
+function wordCount(value: string): number {
+  return value.trim() ? value.trim().split(/\s+/).length : 0
+}
+
+function citationDetail(paths: string[]): string {
+  if (!paths.length) return "No bibliography declared"
+  return paths.length === 1 ? paths[0]! : `${paths.length} bibliography files`
+}
+
+function eyebrow(): JSX.CSSProperties {
+  return {
+    "font-family": FONT_MONO,
+    "font-size": "9px",
+    "font-weight": 650,
+    "letter-spacing": "0.08em",
+    color: "var(--color-text-faint)",
+  }
+}
+
+function toolButton(active = false): JSX.CSSProperties {
+  return {
+    all: "unset",
+    cursor: "pointer",
+    display: "inline-flex",
+    "align-items": "center",
+    gap: "5px",
+    height: "25px",
+    padding: "0 8px",
+    "border-radius": "5px",
+    border: `1px solid ${active ? "var(--color-border-strong)" : "var(--color-border)"}`,
+    background: active ? "var(--color-accent-subtle)" : "var(--color-bg-subtle)",
+    color: active ? "var(--color-text)" : "var(--color-text-muted)",
+    "font-family": FONT_SANS,
+    "font-size": "10px",
+    "font-weight": 550,
+  }
+}
+
+function input(): JSX.CSSProperties {
+  return {
+    "box-sizing": "border-box",
+    width: "100%",
+    height: "29px",
+    padding: "0 9px",
+    border: "1px solid var(--color-border)",
+    "border-radius": "5px",
+    outline: "none",
+    background: "var(--color-bg)",
+    color: "var(--color-text)",
+    "font-family": FONT_SANS,
+    "font-size": "10px",
+  }
+}
+
+function browserList(): JSX.CSSProperties {
+  return {
+    display: "grid",
+    gap: "4px",
+    "max-height": "126px",
+    overflow: "auto",
+    "align-content": "start",
+  }
+}
+
+function browserRow(): JSX.CSSProperties {
+  return {
+    all: "unset",
+    cursor: "pointer",
+    display: "flex",
+    "align-items": "center",
+    gap: "8px",
+    padding: "7px 8px",
+    "border-radius": "5px",
+    border: "1px solid var(--color-border)",
+    background: "var(--color-bg)",
+  }
+}
+
+function rowText(): JSX.CSSProperties {
+  return {
+    flex: 1,
+    "min-width": 0,
+    display: "grid",
+    gap: "2px",
+    "text-align": "left",
+    "font-family": FONT_SANS,
+    color: "var(--color-text)",
+    overflow: "hidden",
+    "text-overflow": "ellipsis",
+    "white-space": "nowrap",
+  }
+}
+
+function keyBadge(): JSX.CSSProperties {
+  return {
+    padding: "2px 5px",
+    "border-radius": "3px",
+    background: "var(--color-accent-subtle)",
+    "font-family": FONT_MONO,
+    "font-size": "8px",
+    color: "var(--color-text-muted)",
+    "flex-shrink": 0,
+  }
+}
+
+function exportButton(disabled: boolean): JSX.CSSProperties {
+  return {
+    all: "unset",
+    cursor: disabled ? "not-allowed" : "pointer",
+    display: "inline-flex",
+    "align-items": "center",
+    gap: "4px",
+    padding: "4px 7px",
+    "border-radius": "4px",
+    border: "1px solid var(--color-border)",
+    background: "var(--color-bg)",
+    color: "var(--color-text-muted)",
+    opacity: disabled ? 0.48 : 1,
+    "font-family": FONT_MONO,
+    "font-size": "9px",
+  }
+}
+
+function reviewButton(): JSX.CSSProperties {
+  return {
+    all: "unset",
+    cursor: "pointer",
+    width: "fit-content",
+    padding: "4px 8px",
+    "border-radius": "4px",
+    border: "1px solid var(--color-border)",
+    "font-family": FONT_MONO,
+    "font-size": "9px",
+    color: "var(--color-text-muted)",
+  }
+}
+
+function notice(): JSX.CSSProperties {
+  return {
+    "grid-column": "1 / -1",
+    "font-family": FONT_SANS,
+    "font-size": "9px",
+    color: "var(--color-warning)",
+  }
+}
+
+export default ManuscriptWorkbench
diff --git a/frontend/workspace/src/manuscript/model.test.ts b/frontend/workspace/src/manuscript/model.test.ts
new file mode 100644
index 00000000..40b1d7aa
--- /dev/null
+++ b/frontend/workspace/src/manuscript/model.test.ts
@@ -0,0 +1,114 @@
+import { describe, expect, test } from "bun:test"
+import {
+  figureMarkdown,
+  insertSelection,
+  parseBibtex,
+  parseManuscript,
+  relativeArtifactPath,
+  resolveReferencePath,
+  rewritePreviewImages,
+} from "./model"
+
+describe("manuscript model", () => {
+  test("keeps YAML frontmatter in source but removes it from the rendered body", () => {
+    const source = `---
+title: Result
+bibliography: references.bib
+---
+
+# Result
+
+Evidence [@doe2025].
+`
+    const manuscript = parseManuscript(source)
+
+    expect(manuscript.frontmatter).toContain("title: Result")
+    expect(manuscript.bibliographies).toEqual(["references.bib"])
+    expect(manuscript.body).toBe("# Result\n\nEvidence [@doe2025].\n")
+  })
+
+  test("reads inline and block bibliography declarations without duplicates", () => {
+    expect(
+      parseManuscript(`---
+bibliography: [refs/core.bib, "refs/more.bib", refs/core.bib]
+---
+Body`).bibliographies,
+    ).toEqual(["refs/core.bib", "refs/more.bib"])
+
+    expect(
+      parseManuscript(`---
+bibliography:
+  - refs/biology.bib
+  - 'refs/chemistry.bib'
+---
+Body`).bibliographies,
+    ).toEqual(["refs/biology.bib", "refs/chemistry.bib"])
+  })
+
+  test("parses BibTeX keys and useful citation metadata", () => {
+    const citations = parseBibtex(`
+@article{doe2025,
+  title = {A {Nested} Scientific Result},
+  author = {Doe, Jane and Roe, Richard},
+  year = "2025",
+  journal = {Open Research}
+}
+@misc{dataset,
+  title={Reference dataset},
+  year={2024}
+}`)
+
+    expect(citations).toEqual([
+      {
+        key: "doe2025",
+        title: "A Nested Scientific Result",
+        author: "Doe, Jane and Roe, Richard",
+        year: "2025",
+        venue: "Open Research",
+      },
+      {
+        key: "dataset",
+        title: "Reference dataset",
+        year: "2024",
+      },
+    ])
+  })
+
+  test("computes portable paths and figure Markdown relative to the manuscript", () => {
+    expect(relativeArtifactPath("reports/paper.md", "figures/result plot.svg")).toBe("../figures/result plot.svg")
+    expect(relativeArtifactPath("paper.md", "figures/result.svg")).toBe("figures/result.svg")
+    expect(resolveReferencePath("reports/paper.md", "../references/core.bib")).toBe("references/core.bib")
+    expect(figureMarkdown("Primary endpoint", "reports/paper.md", "figures/result plot.svg")).toBe(
+      "![Primary endpoint](../figures/result%20plot.svg)",
+    )
+  })
+
+  test("rewrites local preview images through the file server without touching remote assets", () => {
+    const markdown = [
+      "![Local](../figures/result%20plot.svg)",
+      "![Remote](https://example.com/result.svg)",
+      "![Inline](data:image/png;base64,abc)",
+    ].join("\n")
+
+    expect(rewritePreviewImages(markdown, "reports/paper.md", (path) => `/raw?path=${encodeURIComponent(path)}`)).toBe(
+      [
+        "![Local](/raw?path=figures%2Fresult%20plot.svg)",
+        "![Remote](https://example.com/result.svg)",
+        "![Inline](data:image/png;base64,abc)",
+      ].join("\n"),
+    )
+  })
+
+  test("replaces the current editor selection and returns the next caret", () => {
+    expect(insertSelection("Alpha placeholder omega", "[@doe2025]", 6, 17)).toEqual({
+      text: "Alpha [@doe2025] omega",
+      start: 16,
+      end: 16,
+    })
+    expect(insertSelection("Alpha", " figure", 99, 99)).toEqual({
+      text: "Alpha figure",
+      start: 12,
+      end: 12,
+    })
+  })
+})
diff --git a/frontend/workspace/src/manuscript/model.ts b/frontend/workspace/src/manuscript/model.ts
new file mode 100644
index 00000000..24e4b062
--- /dev/null
+++ b/frontend/workspace/src/manuscript/model.ts
@@ -0,0 +1,178 @@
+export interface Manuscript {
+  frontmatter: string
+  body: string
+  bibliographies: string[]
+}
+
+export interface Citation {
+  key: string
+  title?: string
+  author?: string
+  year?: string
+  venue?: string
+}
+
+export interface Insertion {
+  text: string
+  start: number
+  end: number
+}
+
+export function parseManuscript(source: string): Manuscript {
+  const normalized = source.replaceAll("\r\n", "\n")
+  const match = /^---[ \t]*\n([\s\S]*?)\n---[ \t]*(?:\n|$)/.exec(normalized)
+  if (!match) return { frontmatter: "", body: normalized, bibliographies: [] }
+  const frontmatter = match[1] ?? ""
+  const body = normalized.slice(match[0].length).replace(/^\n/, "")
+  return {
+    frontmatter,
+    body,
+    bibliographies: bibliographyPaths(frontmatter),
+  }
+}
+
+export function parseBibtex(source: string): Citation[] {
+  const headers = Array.from(source.matchAll(/@[a-z]+\s*\{\s*([^,\s]+)\s*,/gi))
+  return headers.flatMap((header) => {
+    const index = header.index ?? 0
+    const open = source.indexOf("{", index)
+    const close = closingBrace(source, open)
+    if (open < 0 || close < 0) return []
+    const body = source.slice(index + header[0].length, close)
+    const fields = bibFields(body)
+    const title = cleanBib(fields.title)
+    const author = cleanBib(fields.author)
+    const year = cleanBib(fields.year)
+    const venue = cleanBib(fields.journal ?? fields.booktitle ?? fields.publisher)
+    return [
+      {
+        key: header[1]!,
+        ...(title ? { title } : {}),
+        ...(author ? { author } : {}),
+        ...(year ? { year } : {}),
+        ...(venue ? { venue } : {}),
+      },
+    ]
+  })
+}
+
+export function relativeArtifactPath(manuscript: string, artifact: string): string {
+  const from = cleanPath(manuscript).split("/").slice(0, -1)
+  const target = cleanPath(artifact).split("/")
+  const shared = from.findIndex((part, index) => part !== target[index])
+  const common = shared < 0 ? Math.min(from.length, target.length) : shared
+  const parents = Array.from({ length: from.length - common }, () => "..")
+  const relative = [...parents, ...target.slice(common)].join("/")
+  return relative || target.at(-1) || artifact
+}
+
+export function resolveReferencePath(manuscript: string, reference: string): string {
+  const base = cleanPath(manuscript).split("/").slice(0, -1)
+  const parts = [...base, ...cleanPath(reference).split("/")]
+  return parts
+    .reduce<string[]>((result, part) => {
+      if (!part || part === ".") return result
+      if (part === "..") {
+        result.pop()
+        return result
+      }
+      result.push(part)
+      return result
+    }, [])
+    .join("/")
+}
+
+export function rewritePreviewImages(markdown: string, manuscript: string, asset: (path: string) => string): string {
+  return markdown.replace(/!\[([^\]]*)\]\(([^)\s]+)\)/g, (match, alt: string, target: string) => {
+    if (/^(?:[a-z][a-z0-9+.-]*:|#|\/)/i.test(target)) return match
+    const decoded = decodeURIComponent(target.replace(/^<|>$/g, ""))
+    return `![${alt}](${asset(resolveReferencePath(manuscript, decoded))})`
+  })
+}
+
+export function figureMarkdown(label: string, manuscript: string, artifact: string): string {
+  const alt =
+    label.trim() ||
+    artifact
+      .split("/")
+      .pop()
+      ?.replace(/\.[^.]+$/, "") ||
+    "Figure"
+  const target = relativeArtifactPath(manuscript, artifact)
+    .split("/")
+    .map((part) => encodeURIComponent(part))
+    .join("/")
+  return `![${alt.replaceAll("]", "\\]")}](${target})`
+}
+
+export function insertSelection(source: string, insertion: string, start: number, end: number): Insertion {
+  const lower = Math.max(0, Math.min(start, source.length))
+  const upper = Math.max(lower, Math.min(end, source.length))
+  const text = `${source.slice(0, lower)}${insertion}${source.slice(upper)}`
+  const caret = lower + insertion.length
+  return { text, start: caret, end: caret }
+}
+
+function bibliographyPaths(frontmatter: string): string[] {
+  const lines = frontmatter.split("\n")
+  const row = lines.findIndex((line) => /^\s*bibliography\s*:/.test(line))
+  if (row < 0) return []
+  const value = lines[row]!.replace(/^\s*bibliography\s*:\s*/, "").trim()
+  const inline = value.startsWith("[") && value.endsWith("]") ? value.slice(1, -1).split(",") : value ? [value] : []
+  const tail = lines.slice(row + 1)
+  const stop = tail.findIndex((line) => !/^\s+-\s+/.test(line))
+  const block = value ? [] : tail.slice(0, stop < 0 ? tail.length : stop).map((line) => line.replace(/^\s+-\s+/, ""))
+  return Array.from(new Set([...inline, ...block].map(unquote).filter(Boolean)))
+}
+
+function bibFields(source: string): Record<string, string> {
+  const fields: Record<string, string> = {}
+  const headers = Array.from(source.matchAll(/\b([a-z][a-z0-9_-]*)\s*=\s*/gi))
+  for (const [index, header] of headers.entries()) {
+    const start = (header.index ?? 0) + header[0].length
+    const end = headers[index + 1]?.index ?? source.length
+    const raw = source.slice(start, end).replace(/,\s*$/, "").trim()
+    fields[header[1]!.toLowerCase()] = raw
+  }
+  return fields
+}
+
+function closingBrace(source: string, start: number): number {
+  const state = { depth: 0, end: -1, quote: false, escaped: false }
+  for (const [offset, char] of Array.from(source.slice(start)).entries()) {
+    if (state.end >= 0) continue
+    if (char === "\\" && !state.escaped) {
+      state.escaped = true
+      continue
+    }
+    if (char === '"' && !state.escaped) state.quote = !state.quote
+    if (!state.quote && char === "{") state.depth += 1
+    if (!state.quote && char === "}") state.depth -= 1
+    if (state.depth === 0) state.end = start + offset
+    state.escaped = false
+  }
+  return state.end
+}
+
+function cleanBib(value: string | undefined): string | undefined {
+  if (!value) return
+  const clean = value
+    .trim()
+    .replace(/^["{]+|["}]+$/g, "")
+    .replaceAll("{", "")
+    .replaceAll("}", "")
+    .replace(/\s+/g, " ")
+    .trim()
+  return clean || undefined
+}
+
+function cleanPath(value: string): string {
+  return value
+    .replaceAll("\\", "/")
+    .replace(/^(?:\.\/)+/, "")
+    .replace(/\/+/g, "/")
+}
+
+function unquote(value: string): string {
+  return value.trim().replace(/^(['"])(.*)\1$/, "$2")
+}

From 0854d7214c9497cc2a98a39283baa22d6b0f3500 Mon Sep 17 00:00:00 2001
From: Aayam Bansal <aayambansal@gmail.com>
Date: Wed, 29 Jul 2026 16:07:05 +0800
Subject: [PATCH 38/40] fix: harden research release boundaries

---
 backend/cli/src/compute/jobs.ts               | 15 ++--
 backend/cli/src/file/index.ts                 | 17 +++-
 backend/cli/src/file/publication.ts           | 23 ++++-
 backend/cli/src/file/review.ts                |  8 +-
 backend/cli/test/compute/jobs.test.ts         | 37 ++++++++
 backend/cli/test/file/publication.test.ts     | 89 +++++++++++++++++++
 backend/cli/test/file/science-inspect.test.ts | 23 +++++
 frontend/workspace/e2e/compute-jobs.spec.ts   | 47 ++++++++++
 frontend/workspace/src/atlas/ComputeJobs.tsx  |  6 +-
 frontend/workspace/src/atlas/FilePreview.tsx  | 41 ++++++++-
 10 files changed, 282 insertions(+), 24 deletions(-)

diff --git a/backend/cli/src/compute/jobs.ts b/backend/cli/src/compute/jobs.ts
index e6e4b717..f0a49ffa 100644
--- a/backend/cli/src/compute/jobs.ts
+++ b/backend/cli/src/compute/jobs.ts
@@ -572,6 +572,10 @@ export namespace ComputeJobs {
       windowsHide: true,
       stdio: ["ignore", output.fd, output.fd],
     })
+    const result = new Promise<{ code: number | null; error?: string }>((resolve) => {
+      proc.once("error", (error) => resolve({ code: null, error: error.message }))
+      proc.once("exit", (code) => resolve({ code }))
+    })
     await output.close()
     const current = await get(job.id, { root })
     if (current?.status === "cancelled") {
@@ -587,10 +591,7 @@ export namespace ComputeJobs {
       started_at: new Date().toISOString(),
       pid: proc.pid,
     })
-    const result = await new Promise<{ code: number | null; error?: string }>((resolve) => {
-      proc.once("error", (error) => resolve({ code: null, error: error.message }))
-      proc.once("exit", (code) => resolve({ code }))
-    })
+    const completed = await result
     const final = await get(job.id, { root })
     if (final?.status === "cancelled") {
       active.delete(keyOf(root, job.id))
@@ -604,10 +605,10 @@ export namespace ComputeJobs {
             capture_error: error instanceof Error ? error.message : String(error),
           }))
     await patch(root, job.id, {
-      status: result.code === 0 ? "succeeded" : "failed",
+      status: completed.code === 0 ? "succeeded" : "failed",
       completed_at: new Date().toISOString(),
-      exit_code: result.code,
-      error: result.error,
+      exit_code: completed.code,
+      error: completed.error,
       ...captureResult,
     }).finally(() => active.delete(keyOf(root, job.id)))
   }
diff --git a/backend/cli/src/file/index.ts b/backend/cli/src/file/index.ts
index eb6a7928..923a22b0 100644
--- a/backend/cli/src/file/index.ts
+++ b/backend/cli/src/file/index.ts
@@ -23,6 +23,7 @@ import { PublicationReview } from "./review"
 
 export namespace File {
   const log = Log.create({ service: "file" })
+  const preview = 8 * 1024 * 1024
 
   export const Info = z
     .object({
@@ -329,10 +330,18 @@ export namespace File {
       return { type: "text", content, mimeType, encoding: "base64", size: bunFile.size }
     }
 
-    // Return the file content verbatim — callers like the web editor write
-    // it back, so trimming here would silently strip leading/trailing
-    // whitespace and the trailing newline on the first save.
-    const content = await bunFile.text().catch(() => "")
+    const truncated = bunFile.size > preview
+    // Keep scientific/text previews bounded. The UI treats this response as
+    // read-only, so a partial preview can never overwrite the source file.
+    const content = await (truncated ? bunFile.slice(0, preview) : bunFile).text().catch(() => "")
+    if (truncated) {
+      return {
+        type: "text",
+        content,
+        size: bunFile.size,
+        truncated: true,
+      }
+    }
 
     if (project.vcs === "git") {
       let diff = await $`git diff ${file}`.cwd(Instance.directory).quiet().nothrow().text()
diff --git a/backend/cli/src/file/publication.ts b/backend/cli/src/file/publication.ts
index 3c98b629..f13df71e 100644
--- a/backend/cli/src/file/publication.ts
+++ b/backend/cli/src/file/publication.ts
@@ -3,6 +3,7 @@ import path from "node:path"
 import { marked, Renderer } from "marked"
 import z from "zod"
 import { OpenScience } from "../openscience"
+import { Filesystem } from "../util/filesystem"
 import { escapeHtml } from "../util/html"
 import { PublicationReview } from "./review"
 
@@ -75,9 +76,17 @@ export namespace PublicationFile {
     if (![".md", ".markdown"].includes(path.extname(source).toLowerCase())) {
       throw new Error("Publication export currently requires a Markdown report")
     }
+    if (!(await Filesystem.containsCanonical(root, source))) {
+      throw new Error("Publication path escapes the project directory")
+    }
     if (!(await Bun.file(source).exists())) throw new Error(`Report not found: ${parsed.path}`)
+    const snapshot = await Bun.file(source).arrayBuffer()
+    const markdown = new TextDecoder().decode(snapshot)
+    const artifactHash = await hash(snapshot)
     const review =
-      parsed.readiness === "reviewed" ? await PublicationReview.assertReady(parsed.path, parsed.review_id!) : undefined
+      parsed.readiness === "reviewed"
+        ? await PublicationReview.assertReady(parsed.path, parsed.review_id!, artifactHash)
+        : undefined
     const support = await capabilities()
     if (!support.formats[parsed.format]) {
       throw new Error(
@@ -117,7 +126,6 @@ export namespace PublicationFile {
         const hint = title ? ` title="${escapeHtml(title)}"` : ""
         return `<img src="${escapeHtml(target)}" alt="${escapeHtml(text)}"${hint}>`
       }
-      const markdown = await Bun.file(source).text()
       const body = await marked.parse(markdown, { gfm: true, renderer })
       const base = `${path.relative(folder, path.dirname(source)).split(path.sep).join("/") || "."}/`
       const title = path.basename(source, path.extname(source))
@@ -170,9 +178,11 @@ ${body}
         ...(review ? { review_id: review.id } : {}),
       })
     }
+    const snapshotFile = path.join(folder, `.openscience-publication-${nonce}.md`)
+    await Bun.write(snapshotFile, snapshot)
     const args = [
       "pandoc",
-      source,
+      snapshotFile,
       "--standalone",
       `--resource-path=${path.dirname(source)}${path.delimiter}${root}`,
       "--output",
@@ -190,7 +200,7 @@ ${body}
       proc.exited,
       new Response(proc.stdout).text(),
       new Response(proc.stderr).text(),
-    ])
+    ]).finally(() => fs.rm(snapshotFile, { force: true }))
     if (code !== 0) {
       await fs.rm(target, { force: true })
       throw new Error(stderr.trim() || stdout.trim() || `Pandoc exited with code ${code}`)
@@ -224,4 +234,9 @@ ${body}
     if (image && scheme === "data" && /^data:image\//i.test(value)) return value
     return undefined
   }
+
+  async function hash(value: ArrayBuffer) {
+    const digest = await crypto.subtle.digest("SHA-256", value)
+    return [...new Uint8Array(digest)].map((byte) => byte.toString(16).padStart(2, "0")).join("")
+  }
 }
diff --git a/backend/cli/src/file/review.ts b/backend/cli/src/file/review.ts
index d6d67634..9c64618a 100644
--- a/backend/cli/src/file/review.ts
+++ b/backend/cli/src/file/review.ts
@@ -244,11 +244,11 @@ export namespace PublicationReview {
     )
   }
 
-  export async function assertReady(filepath: string, id: string): Promise<Report> {
+  export async function assertReady(filepath: string, id: string, artifactHash?: string): Promise<Report> {
     const report = await get(id)
     const source = await target(filepath)
     if (report.path !== source.relative) throw new Error("The publication review belongs to a different manuscript")
-    await assertCurrent(report)
+    await assertCurrent(report, artifactHash)
     if (!report.finalized) throw new Error("The publication review has not been finalized")
     if (report.findings.some((finding) => finding.severity === "blocking" && finding.status === "open")) {
       throw new Error("The publication review still has open blocking findings")
@@ -527,13 +527,13 @@ export namespace PublicationReview {
     }
   }
 
-  async function assertCurrent(report: Report) {
+  async function assertCurrent(report: Report, artifactHash?: string) {
     const absolute = path.resolve(Instance.worktree, report.path)
     if (!(await Instance.containsCanonicalPath(absolute))) {
       throw new Error("The reviewed manuscript is outside the current project")
     }
     if (!(await Bun.file(absolute).exists())) throw new Error("The reviewed manuscript no longer exists")
-    if ((await digest(absolute)) !== report.artifactHash) {
+    if ((artifactHash ?? (await digest(absolute))) !== report.artifactHash) {
       throw new Error("The manuscript changed after this publication review was generated")
     }
   }
diff --git a/backend/cli/test/compute/jobs.test.ts b/backend/cli/test/compute/jobs.test.ts
index 66da8ac5..584b7632 100644
--- a/backend/cli/test/compute/jobs.test.ts
+++ b/backend/cli/test/compute/jobs.test.ts
@@ -69,6 +69,43 @@ describe("ComputeJobs command adapters", () => {
 })
 
 describe("ComputeJobs local lifecycle", () => {
+  test("a missing working directory fails durably without crashing the server process", async () => {
+    await using tmp = await tmpdir()
+    const root = path.join(tmp.path, "state")
+    const cwd = path.join(tmp.path, "missing")
+    const cli = path.join(import.meta.dir, "../..")
+    const script = `
+      import { ComputeJobs } from "./src/compute/jobs"
+      const job = await ComputeJobs.start(
+        {
+          name: "missing cwd",
+          command: "printf unreachable",
+          cwd: ${JSON.stringify(cwd)},
+          target: { kind: "local" },
+        },
+        { root: ${JSON.stringify(root)} },
+      )
+      const result = await ComputeJobs.wait(job.id, { root: ${JSON.stringify(root)}, timeout: 5_000 })
+      console.log(JSON.stringify(result))
+    `
+    const proc = Bun.spawn([process.execPath, "-e", script], {
+      cwd: cli,
+      stdout: "pipe",
+      stderr: "pipe",
+    })
+    const [code, stdout, stderr] = await Promise.all([
+      proc.exited,
+      new Response(proc.stdout).text(),
+      new Response(proc.stderr).text(),
+    ])
+
+    expect(code, stderr).toBe(0)
+    const job = ComputeJobs.Job.parse(JSON.parse(stdout.trim()))
+    expect(job.status).toBe("failed")
+    expect(job.exit_code).toBeNull()
+    expect(job.error).toMatch(/ENOENT|no such file or directory/i)
+  })
+
   test("runs a real local job, persists status, and streams its log", async () => {
     await using tmp = await tmpdir()
     const root = path.join(tmp.path, "state")
diff --git a/backend/cli/test/file/publication.test.ts b/backend/cli/test/file/publication.test.ts
index 39d7b806..d2b6846b 100644
--- a/backend/cli/test/file/publication.test.ts
+++ b/backend/cli/test/file/publication.test.ts
@@ -1,5 +1,6 @@
 import { $ } from "bun"
 import { describe, expect, test } from "bun:test"
+import fs from "node:fs/promises"
 import path from "node:path"
 import { PublicationFile } from "../../src/file/publication"
 import { PublicationReview } from "../../src/file/review"
@@ -61,6 +62,21 @@ describe("PublicationFile", () => {
     await expect(PublicationFile.render(tmp.path, { path: "../report.md", format: "html" })).rejects.toThrow("escapes")
   })
 
+  test("rejects a Markdown source symlink that escapes the project", async () => {
+    await using outside = await tmpdir({
+      init: async (directory) => {
+        await Bun.write(path.join(directory, "secret.md"), "# External secret\n")
+      },
+    })
+    await using tmp = await tmpdir({
+      init: async (directory) => {
+        await fs.symlink(path.join(outside.path, "secret.md"), path.join(directory, "report.md"))
+      },
+    })
+
+    await expect(PublicationFile.render(tmp.path, { path: "report.md", format: "html" })).rejects.toThrow("escapes")
+  })
+
   test("gates reviewed exports on a finalized report for the exact source bytes", async () => {
     await using tmp = await tmpdir({
       git: true,
@@ -122,4 +138,77 @@ describe("PublicationFile", () => {
       },
     })
   })
+
+  test("a reviewed Pandoc export renders the finalized snapshot when the source changes mid-export", async () => {
+    await using tmp = await tmpdir({
+      git: true,
+      init: async (directory) => {
+        await Bun.write(path.join(directory, "README.md"), "# Publication snapshot fixture\n")
+        await Bun.write(path.join(directory, "uv.lock"), "version = 1\n")
+        await Bun.write(path.join(directory, "pyproject.toml"), '[project]\nname = "publication-snapshot-fixture"\n')
+        await Bun.write(path.join(directory, "report.md"), "# Reviewed result\n\nThe finalized value is 42%.\n")
+        await $`git add README.md uv.lock pyproject.toml report.md`.cwd(directory).quiet()
+        await $`git -c user.name=OpenScience -c user.email=test@openscience.local commit -m "snapshot fixture"`
+          .cwd(directory)
+          .quiet()
+      },
+    })
+
+    await Instance.provide({
+      directory: tmp.path,
+      fn: async () => {
+        const review = await PublicationReview.run({ path: "report.md", actor: "Reviewer" })
+        const finalized = await PublicationReview.finalize(review.id, { actor: "Aayam Bansal" })
+        const original = await Bun.file(path.join(tmp.path, "report.md")).text()
+        const bin = path.join(tmp.path, "bin")
+        const ready = path.join(tmp.path, "pandoc-ready")
+        const resume = path.join(tmp.path, "pandoc-resume")
+        const pandoc = path.join(bin, "pandoc")
+        await fs.mkdir(bin, { recursive: true })
+        await Bun.write(
+          pandoc,
+          `#!/bin/sh
+source="$1"
+shift
+output=""
+while [ "$#" -gt 0 ]; do
+  if [ "$1" = "--output" ]; then
+    shift
+    output="$1"
+  fi
+  shift
+done
+printf ready > ${JSON.stringify(ready)}
+while [ ! -f ${JSON.stringify(resume)} ]; do sleep 0.01; done
+cp "$source" "$output"
+`,
+        )
+        await fs.chmod(pandoc, 0o755)
+        const prior = process.env.PATH
+        process.env.PATH = `${bin}${path.delimiter}${prior ?? ""}`
+        const pending = PublicationFile.render(tmp.path, {
+          path: "report.md",
+          format: "docx",
+          readiness: "reviewed",
+          review_id: finalized.id,
+        })
+        try {
+          await (async () => {
+            for (const _ of Array.from({ length: 200 })) {
+              if (await Bun.file(ready).exists()) return
+              await Bun.sleep(10)
+            }
+            throw new Error("Timed out waiting for the controlled Pandoc process")
+          })()
+          await Bun.write(path.join(tmp.path, "report.md"), "# Changed after validation\n")
+          await Bun.write(resume, "resume")
+          const result = await pending
+          expect(await Bun.file(path.join(tmp.path, result.path)).text()).toBe(original)
+        } finally {
+          process.env.PATH = prior
+          await Bun.write(resume, "resume")
+        }
+      },
+    })
+  })
 })
diff --git a/backend/cli/test/file/science-inspect.test.ts b/backend/cli/test/file/science-inspect.test.ts
index ad9cedc2..6da61ac0 100644
--- a/backend/cli/test/file/science-inspect.test.ts
+++ b/backend/cli/test/file/science-inspect.test.ts
@@ -115,3 +115,26 @@ describe("large binary reads", () => {
     })
   })
 })
+
+describe("large text reads", () => {
+  test("returns a bounded read-only preview instead of loading the whole scientific file", async () => {
+    await using tmp = await tmpdir({
+      init: async (directory) => {
+        const writer = Bun.file(path.join(directory, "variants.vcf")).writer()
+        const chunk = new TextEncoder().encode("chr1\t1\t.\tA\tG\t60\tPASS\tDP=20\n".repeat(32_768))
+        for (const _ of Array.from({ length: 10 })) writer.write(chunk)
+        await writer.end()
+      },
+    })
+
+    await Instance.provide({
+      directory: tmp.path,
+      fn: async () => {
+        const result = await File.read("variants.vcf")
+        expect(result.truncated).toBe(true)
+        expect(result.size).toBeGreaterThan(8 * 1024 * 1024)
+        expect(new TextEncoder().encode(result.content).byteLength).toBeLessThanOrEqual(8 * 1024 * 1024)
+      },
+    })
+  })
+})
diff --git a/frontend/workspace/e2e/compute-jobs.spec.ts b/frontend/workspace/e2e/compute-jobs.spec.ts
index f41e7ad1..b9ee872e 100644
--- a/frontend/workspace/e2e/compute-jobs.spec.ts
+++ b/frontend/workspace/e2e/compute-jobs.spec.ts
@@ -2,6 +2,7 @@ import { mkdtempSync, rmSync } from "node:fs"
 import { tmpdir } from "node:os"
 import path from "node:path"
 import { expect, test } from "./fixtures"
+import { createSdk, promptSelector, sessionPath } from "./utils"
 
 test("runs a reproducible local job and captures outputs from the right pane", async ({ page, gotoSession }) => {
   const directory = mkdtempSync(path.join(tmpdir(), "openscience-compute-e2e-"))
@@ -41,3 +42,49 @@ test("runs a reproducible local job and captures outputs from the right pane", a
     rmSync(directory, { recursive: true, force: true })
   }
 })
+
+test("defaults a local compute job to the active research project", async ({ page }) => {
+  const first = mkdtempSync(path.join(tmpdir(), "openscience-compute-first-"))
+  const project = mkdtempSync(path.join(tmpdir(), "openscience-compute-project-"))
+  const firstSdk = createSdk(first)
+  const projectSdk = createSdk(project)
+  const firstSession = await firstSdk.session.create({ title: "First compute project" }).then((result) => result.data)
+  const projectSession = await projectSdk.session.create({ title: "Current compute project" }).then((result) => result.data)
+  if (!firstSession?.id || !projectSession?.id) throw new Error("Session create did not return an id")
+  try {
+    await page.goto(sessionPath(first, firstSession.id))
+    await expect(page.locator(promptSelector)).toBeVisible()
+
+    await page
+      .getByRole("tab", { name: "Compute", exact: true })
+      .or(page.getByRole("button", { name: "Compute", exact: true }))
+      .first()
+      .click()
+    const pane = page.locator(".session-right-pane")
+    await pane.getByTitle("new job").click()
+    await page.evaluate((url) => {
+      window.history.pushState({}, "", url)
+      window.dispatchEvent(new PopStateEvent("popstate"))
+    }, sessionPath(project, projectSession.id))
+    await expect(page.locator(promptSelector)).toBeVisible()
+    await page
+      .getByRole("tab", { name: "Compute", exact: true })
+      .or(page.getByRole("button", { name: "Compute", exact: true }))
+      .first()
+      .click()
+    if (!(await pane.getByLabel("Job name").isVisible())) await pane.getByTitle("new job").click()
+
+    await pane.getByLabel("Job name").fill("Project cwd smoke")
+    await pane.getByRole("textbox", { name: "Command", exact: true }).fill("pwd")
+    await pane.getByRole("button", { name: "run job" }).click()
+
+    await expect(pane.getByText("Project cwd smoke", { exact: true }).first()).toBeVisible()
+    await expect(pane.locator("pre")).toContainText(project)
+    await expect(pane.getByText(`cwd · ${project}`, { exact: true })).toBeVisible()
+  } finally {
+    await firstSdk.session.delete({ sessionID: firstSession.id }).catch(() => undefined)
+    await projectSdk.session.delete({ sessionID: projectSession.id }).catch(() => undefined)
+    rmSync(first, { recursive: true, force: true })
+    rmSync(project, { recursive: true, force: true })
+  }
+})
diff --git a/frontend/workspace/src/atlas/ComputeJobs.tsx b/frontend/workspace/src/atlas/ComputeJobs.tsx
index 934c0c14..f1c30925 100644
--- a/frontend/workspace/src/atlas/ComputeJobs.tsx
+++ b/frontend/workspace/src/atlas/ComputeJobs.tsx
@@ -1,6 +1,6 @@
 import { For, Show, createEffect, createMemo, createResource, createSignal, onCleanup, type JSX } from "solid-js"
 import { Dynamic } from "solid-js/web"
-import { useGlobalSDK } from "@/context/global-sdk"
+import { useSDK } from "@/context/sdk"
 import { usePlatform } from "@/context/platform"
 import { settingsApi } from "@/components/settings/api"
 import { FONT_MONO, FONT_SANS } from "@/styles/tokens"
@@ -95,7 +95,7 @@ interface Job {
 const terminal = new Set<Status>(["succeeded", "failed", "cancelled", "interrupted"])
 
 export function ComputeJobs(): JSX.Element {
-  const sdk = useGlobalSDK()
+  const sdk = useSDK()
   const platform = usePlatform()
   const fetchFn = platform.fetch ?? fetch
   const call = <T,>(path: string, init?: RequestInit) =>
@@ -177,7 +177,7 @@ export function ComputeJobs(): JSX.Element {
       body: JSON.stringify({
         name: name().trim(),
         command: command().trim(),
-        cwd: cwd().trim() || undefined,
+        cwd: cwd().trim() || (value === "local" ? sdk.directory : undefined),
         target: value === "local" ? { kind: "local" } : { kind: "ssh", host_id: value.slice(4) },
         resources: hasResources ? resources : undefined,
         modules: listValue(modules()),
diff --git a/frontend/workspace/src/atlas/FilePreview.tsx b/frontend/workspace/src/atlas/FilePreview.tsx
index 458af0f5..d533de02 100644
--- a/frontend/workspace/src/atlas/FilePreview.tsx
+++ b/frontend/workspace/src/atlas/FilePreview.tsx
@@ -170,6 +170,7 @@ export function FileView(props: {
 
   const data = () => file()
   const isBinary = () => data()?.encoding === "base64"
+  const truncated = () => data()?.truncated === true
   const mime = () => data()?.mimeType ?? ""
   const b64 = () => data()?.content ?? ""
   const dataUrl = () => `data:${mime() || "application/octet-stream"};base64,${b64()}`
@@ -242,7 +243,7 @@ export function FileView(props: {
   })
 
   const save = async () => {
-    if (saving() || isBinary() || !dirty()) return
+    if (saving() || isBinary() || truncated() || !dirty()) return
     setSaving(true)
     try {
       // The generated SDK has no file.write; hit the real PUT /file/content
@@ -382,7 +383,7 @@ export function FileView(props: {
           </button>
         </Show>
 
-        <Show when={toggleable()}>
+        <Show when={toggleable() && !truncated()}>
           <button
             type="button"
             onClick={() => setShowSource((v) => !v)}
@@ -500,6 +501,35 @@ export function FileView(props: {
             }}
           >
             <Switch>
+              <Match when={truncated()}>
+                <div
+                  style={{
+                    padding: "16px 18px 28px",
+                    "font-family": FONT_CODE,
+                    "font-size": "12px",
+                    "line-height": 1.65,
+                    color: "var(--color-text)",
+                  }}
+                >
+                  <div
+                    role="status"
+                    style={{
+                      padding: "10px 12px",
+                      "margin-bottom": "14px",
+                      border: "1px solid var(--color-border)",
+                      "border-radius": "6px",
+                      background: "var(--color-bg)",
+                      "font-family": FONT_SANS,
+                      color: "var(--color-text-muted)",
+                      "white-space": "normal",
+                    }}
+                  >
+                    Preview limited to 8 MB of {formatBytes(data()?.size ?? 0)}. Download the file or use a compute tool
+                    for the complete dataset.
+                  </div>
+                  <pre style={{ margin: 0, "white-space": "pre-wrap", "overflow-wrap": "anywhere" }}>{draft()}</pre>
+                </div>
+              </Match>
               {/* markdown */}
               <Match when={kind() === "markdown" && !showSource()}>
                 <ManuscriptWorkbench
@@ -735,6 +765,13 @@ function langFor(k: Kind, x: string): string {
   return LANG[x] ?? "text"
 }
 
+function formatBytes(value: number): string {
+  if (value < 1024) return `${value} B`
+  if (value < 1024 * 1024) return `${(value / 1024).toFixed(1)} KB`
+  if (value < 1024 * 1024 * 1024) return `${(value / (1024 * 1024)).toFixed(1)} MB`
+  return `${(value / (1024 * 1024 * 1024)).toFixed(1)} GB`
+}
+
 // Wrap raw file text in a fenced code block so the shared Markdown renderer
 // (marked + shiki) syntax-highlights it. Guards against content that already
 // contains a triple backtick by widening the fence.

From 26d746a38c10691d53477080ac0bfc6574cef976 Mon Sep 17 00:00:00 2001
From: Aayam Bansal <aayambansal@gmail.com>
Date: Wed, 29 Jul 2026 16:09:24 +0800
Subject: [PATCH 39/40] style: format compute project regression

---
 frontend/workspace/e2e/compute-jobs.spec.ts | 15 ++++++++++-----
 1 file changed, 10 insertions(+), 5 deletions(-)

diff --git a/frontend/workspace/e2e/compute-jobs.spec.ts b/frontend/workspace/e2e/compute-jobs.spec.ts
index b9ee872e..c1e98f5f 100644
--- a/frontend/workspace/e2e/compute-jobs.spec.ts
+++ b/frontend/workspace/e2e/compute-jobs.spec.ts
@@ -49,7 +49,9 @@ test("defaults a local compute job to the active research project", async ({ pag
   const firstSdk = createSdk(first)
   const projectSdk = createSdk(project)
   const firstSession = await firstSdk.session.create({ title: "First compute project" }).then((result) => result.data)
-  const projectSession = await projectSdk.session.create({ title: "Current compute project" }).then((result) => result.data)
+  const projectSession = await projectSdk.session
+    .create({ title: "Current compute project" })
+    .then((result) => result.data)
   if (!firstSession?.id || !projectSession?.id) throw new Error("Session create did not return an id")
   try {
     await page.goto(sessionPath(first, firstSession.id))
@@ -62,10 +64,13 @@ test("defaults a local compute job to the active research project", async ({ pag
       .click()
     const pane = page.locator(".session-right-pane")
     await pane.getByTitle("new job").click()
-    await page.evaluate((url) => {
-      window.history.pushState({}, "", url)
-      window.dispatchEvent(new PopStateEvent("popstate"))
-    }, sessionPath(project, projectSession.id))
+    await page.evaluate(
+      (url) => {
+        window.history.pushState({}, "", url)
+        window.dispatchEvent(new PopStateEvent("popstate"))
+      },
+      sessionPath(project, projectSession.id),
+    )
     await expect(page.locator(promptSelector)).toBeVisible()
     await page
       .getByRole("tab", { name: "Compute", exact: true })

From 2ec413b25363c6c4ab3f905a9790cdf494c6e227 Mon Sep 17 00:00:00 2001
From: Aayam Bansal <aayambansal@gmail.com>
Date: Wed, 29 Jul 2026 16:12:09 +0800
Subject: [PATCH 40/40] fix: refresh publication tool discovery

---
 backend/cli/src/file/publication.ts | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/backend/cli/src/file/publication.ts b/backend/cli/src/file/publication.ts
index f13df71e..84fe5060 100644
--- a/backend/cli/src/file/publication.ts
+++ b/backend/cli/src/file/publication.ts
@@ -55,8 +55,10 @@ export namespace PublicationFile {
   }
 
   export async function capabilities(): Promise<Capabilities> {
-    const pandoc = Boolean(Bun.which("pandoc"))
-    const pdf = Bun.which("xelatex") ?? Bun.which("pdflatex") ?? Bun.which("typst") ?? undefined
+    const options = { PATH: process.env.PATH }
+    const pandoc = Boolean(Bun.which("pandoc", options))
+    const pdf =
+      Bun.which("xelatex", options) ?? Bun.which("pdflatex", options) ?? Bun.which("typst", options) ?? undefined
     return Capabilities.parse({
       pandoc,
       pdf_engine: pdf ? path.basename(pdf) : undefined,