fix(manuscript): keep knitr figures on Windows on first freeze render

news/changelog-1.10.md

@@ -45,6 +45,10 @@ All changes included in 1.10:
 
 ## Projects
 
+### Manuscripts
+
+- ([#14613](https://github.com/quarto-dev/quarto-cli/issues/14613)): Fix dynamically generated figures missing from the rendered manuscript on Windows on the first render when using the knitr engine with `freeze: auto`.
+
 ### Websites
 
 - ([#13565](https://github.com/quarto-dev/quarto-cli/issues/13565), [#14353](https://github.com/quarto-dev/quarto-cli/issues/14353)): Fix sidebar logo not appearing on secondary sidebars in multi-sidebar website layouts.

src/command/preview/preview-shiny.ts

@@ -33,7 +33,7 @@ import {
 } from "../../core/http.ts";
 import { findOpenPort } from "../../core/port.ts";
 import { handleHttpRequests } from "../../core/http-server.ts";
-import { normalizePath } from "../../core/path.ts";
+import { pathsEqual } from "../../core/path.ts";
 import { previewMonitorResources } from "../../core/quarto.ts";
 import { renderServices } from "../render/render-services.ts";
 import { RenderFlags } from "../render/types.ts";
@@ -123,7 +123,7 @@ function runPreviewControlService(
   // helper to check whether a render request is compatible
   // with the original render
   const isCompatibleRequest = async (prevReq: PreviewRenderRequest) => {
-    return normalizePath(options.input) === normalizePath(prevReq.path) &&
+    return pathsEqual(options.input, prevReq.path) &&
       await previewRenderRequestIsCompatible(
         prevReq,
         options.project,

src/command/preview/preview.ts

@@ -72,6 +72,7 @@ import { projectOutputDir } from "../../project/project-shared.ts";
 import { projectContext } from "../../project/project-context.ts";
 import {
   normalizePath,
+  pathsEqual,
   pathWithForwardSlashes,
   safeExistsSync,
 } from "../../core/path.ts";
@@ -788,7 +789,7 @@ function htmlFileRequestHandlerOptions(
           !invalidateDevServerReRender &&
           prevReq &&
           existsSync(prevReq.path) &&
-          normalizePath(prevReq.path) === normalizePath(inputFile) &&
+          pathsEqual(prevReq.path, inputFile) &&
           await previewRenderRequestIsCompatible(prevReq, project, flags.to)
         ) {
           // don't wait for the promise so the

src/command/render/cleanup.ts

@@ -11,6 +11,7 @@ import * as ld from "../../core/lodash.ts";
 
 import {
   normalizePath,
+  pathsEqual,
   removeIfEmptyDir,
   removeIfExists,
 } from "../../core/path.ts";
@@ -73,7 +74,7 @@ export function renderCleanup(
         filesDir = normalizePath(filesDir);
       }
       supporting = supporting.map((supportingDir) => {
-        if (filesDir === supportingDir) {
+        if (pathsEqual(filesDir, supportingDir)) {
           return join(filesDir, figuresDir(figureFormat));
         } else {
           return supportingDir;

src/core/path.ts

@@ -327,6 +327,14 @@ export function normalizePath(path: string | URL): string {
   return file.replace(/^\w:\\/, (m: string) => m[0].toUpperCase() + ":\\");
 }
 
+// Compares two filesystem paths for equality in a separator-agnostic way by
+// normalizing both sides first. Use this instead of comparing raw path strings:
+// engines (notably knitr) can report paths with forward slashes on Windows even
+// when other paths use the platform separator, so a raw === comparison fails.
+export function pathsEqual(a: string, b: string): boolean {
+  return normalizePath(a) === normalizePath(b);
+}
+
 // Moved here from env.ts to avoid circular dependency
 export function suggestUserBinPaths() {
   if (!isWindows) {

tests/unit/path.test.ts

@@ -11,6 +11,7 @@ import { join, resolve } from "../../src/deno_ral/path.ts";
 import { isWindows } from "../../src/deno_ral/platform.ts";
 import {
   dirAndStem,
+  pathsEqual,
   removeIfEmptyDir,
   removeIfExists,
   resolvePathGlobs,
@@ -90,6 +91,29 @@ unitTest("path - dirAndStem", async () => {
   });
 });
 
+// Path equality must be separator-agnostic: the knitr engine reports paths
+// with forward slashes on Windows while other paths are normalized to the
+// platform separator. Comparing the raw strings then fails on Windows (#14613).
+// deno-lint-ignore require-await
+unitTest("path - pathsEqual is separator-agnostic (#14613)", async () => {
+  const dir = Deno.makeTempDirSync({ prefix: "quarto-pathsequal-test" });
+  try {
+    const filesDir = join(dir, "index_files");
+    const forwardSlash = filesDir.replaceAll("\\", "/");
+
+    assert(
+      pathsEqual(filesDir, forwardSlash),
+      "same path with different separators must compare equal",
+    );
+    assert(
+      !pathsEqual(filesDir, join(dir, "other_files")),
+      "different paths must not compare equal",
+    );
+  } finally {
+    Deno.removeSync(dir, { recursive: true });
+  }
+});
+
 interface GlobTest {
   name: string;
   globs: string[];

tests/unit/render/cleanup.test.ts

@@ -0,0 +1,84 @@
+/*
+ * cleanup.test.ts
+ *
+ * Copyright (C) 2026 Posit Software, PBC
+ */
+
+import { assert } from "testing/asserts";
+import { ensureDirSync, existsSync } from "../../../src/deno_ral/fs.ts";
+import { join } from "../../../src/deno_ral/path.ts";
+import { unitTest } from "../../test.ts";
+import { renderCleanup } from "../../../src/command/render/cleanup.ts";
+import { Format } from "../../../src/config/types.ts";
+import { createMockProjectContext } from "../project/utils.ts";
+
+// Minimal ipynb format: ipynb is a self-contained (standalone) output, so the
+// self-contained cleanup path in render.ts passes the supporting dirs here.
+function ipynbFormat(): Format {
+  return {
+    pandoc: { to: "ipynb" },
+    execute: {},
+    render: {},
+    metadata: {},
+    language: {},
+  } as unknown as Format;
+}
+
+// Regression test for #14613.
+//
+// On a manuscript first render with freeze:auto, the ipynb completion triggers
+// the self-contained supporting cleanup. The supporting dir reported by the
+// engine uses forward slashes; renderCleanup normalizes the computed filesDir
+// with normalizePath (backslashes on Windows). The separator mismatch made the
+// equality check fail, so the parent index_files dir (instead of the narrowed
+// figure-<to> dir) was handed to safeRemoveDirSync, deleting ALL figures.
+// Subsequent format completions then found no index_files and copied nothing
+// into _manuscript.
+//
+// deno-lint-ignore require-await
+unitTest("renderCleanup - narrows ipynb supporting despite path separator mismatch (#14613)", async () => {
+  const projectDir = Deno.makeTempDirSync({ prefix: "quarto-cleanup-test" });
+  const project = createMockProjectContext({ dir: projectDir });
+  try {
+    const input = join(projectDir, "index.qmd");
+    Deno.writeTextFileSync(input, "");
+
+    const filesDir = join(projectDir, "index_files");
+    const figureHtmlDir = join(filesDir, "figure-html");
+    const figureIpynbDir = join(filesDir, "figure-ipynb");
+    ensureDirSync(figureHtmlDir);
+    ensureDirSync(figureIpynbDir);
+    const figureHtmlPlot = join(figureHtmlDir, "plot.png");
+    Deno.writeTextFileSync(figureHtmlPlot, "html-figure");
+    Deno.writeTextFileSync(join(figureIpynbDir, "plot.png"), "ipynb-figure");
+
+    // Engine reports the supporting dir with forward slashes (as knitr does).
+    const supportingForwardSlash = filesDir.replaceAll("\\", "/");
+
+    renderCleanup(
+      input,
+      join(projectDir, "_manuscript", "index.out.ipynb"),
+      ipynbFormat(),
+      project,
+      [supportingForwardSlash],
+    );
+
+    // Cleanup must narrow to figure-ipynb only; the html figures the other
+    // manuscript formats depend on must survive.
+    assert(
+      existsSync(figureHtmlPlot),
+      "index_files/figure-html must survive ipynb supporting cleanup",
+    );
+    assert(
+      !existsSync(figureIpynbDir),
+      "index_files/figure-ipynb should be removed by narrowed cleanup",
+    );
+  } finally {
+    project.cleanup();
+    try {
+      Deno.removeSync(projectDir, { recursive: true });
+    } catch {
+      // ignore
+    }
+  }
+});