From a960649dae28e6bcdf95ae1dd6cf8e149eb406a1 Mon Sep 17 00:00:00 2001
From: Carlos Scheidegger <carlos.scheidegger@posit.co>
Date: Fri, 10 Jul 2026 19:54:21 -0500
Subject: [PATCH 1/3] Fix keep-md cleanup deleting another format's markdown
 output (#14669)

When output-file has an .html extension and an html format is paired
with a markdown format (e.g. output-file: index.html with html +
commonmark, as nbdev sets up for llms.txt workflows), the markdown
output is named index.html.md -- the same path the keep-md intermediate
convention (<input-stem>.<base-format>.md) assigns to the html format.
The html render's cleanup removed the "stale intermediate", deleting
the freshly written markdown output: website renders then failed at
the output-move step, and other project types silently lost the file.

Compute the projected output paths of the formats being rendered and
attach them to each RenderContext; render cleanup now never deletes a
path that a format owns, and a keep-md: true render whose intermediate
location collides warns and skips saving the intermediate instead of
overwriting the output.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
---
 news/changelog-1.10.md                        |   1 +
 src/command/render/render-files.ts            |  35 +++++-
 src/command/render/render.ts                  |  12 +-
 src/command/render/types.ts                   |   3 +
 src/core/render.ts                            |  17 ++-
 .../output-file-collision/default/.gitignore  |   7 ++
 .../output-file-collision/default/_quarto.yml |   6 +
 .../output-file-collision/default/index.qmd   |   6 +
 .../output-file-collision/keepmd/.gitignore   |   6 +
 .../output-file-collision/keepmd/_quarto.yml  |   9 ++
 .../output-file-collision/keepmd/index.qmd    |   6 +
 .../output-file-collision/website/.gitignore  |   6 +
 .../output-file-collision/website/_quarto.yml |   6 +
 .../output-file-collision/website/index.qmd   |   6 +
 .../render-output-file-collision.test.ts      | 114 ++++++++++++++++++
 15 files changed, 236 insertions(+), 4 deletions(-)
 create mode 100644 tests/docs/output-file-collision/default/.gitignore
 create mode 100644 tests/docs/output-file-collision/default/_quarto.yml
 create mode 100644 tests/docs/output-file-collision/default/index.qmd
 create mode 100644 tests/docs/output-file-collision/keepmd/.gitignore
 create mode 100644 tests/docs/output-file-collision/keepmd/_quarto.yml
 create mode 100644 tests/docs/output-file-collision/keepmd/index.qmd
 create mode 100644 tests/docs/output-file-collision/website/.gitignore
 create mode 100644 tests/docs/output-file-collision/website/_quarto.yml
 create mode 100644 tests/docs/output-file-collision/website/index.qmd
 create mode 100644 tests/smoke/render/render-output-file-collision.test.ts

diff --git a/news/changelog-1.10.md b/news/changelog-1.10.md
index e10a2250d0a..efbd8a5346c 100644
--- a/news/changelog-1.10.md
+++ b/news/changelog-1.10.md
@@ -114,3 +114,4 @@ All changes included in 1.10:
 - ([#14582](https://github.com/quarto-dev/quarto-cli/issues/14582)): Fix format detection for extension formats (e.g. `acm-pdf`) in project preview, manuscript notebooks, MECA bundles, and website format ordering.
 - ([#14583](https://github.com/quarto-dev/quarto-cli/issues/14583)): Fix a shortcode used as an image source (e.g. `![]({{< meta logo >}})`) getting the `default-image-extension` appended, producing a doubled extension once the shortcode resolves.
 - ([#14595](https://github.com/quarto-dev/quarto-cli/issues/14595)): Fix reload preview in code-server environment
+- ([#14669](https://github.com/quarto-dev/quarto-cli/issues/14669)): Fix the markdown output being deleted when `output-file` has an `.html` extension and an html format is paired with a markdown format (e.g. `output-file: index.html` with `format: html` + `commonmark`, as nbdev sets up for llms.txt workflows). The markdown output's name (`index.html.md`) coincides with the conventional `keep-md` intermediate location for the html format, and render cleanup deleted it — failing website renders at the output-move step and silently dropping the file in other project types. Renders now never clean up (or write a `keep-md` intermediate over) a path that belongs to another format's output; a `keep-md: true` render whose intermediate location collides warns and skips saving the intermediate.
diff --git a/src/command/render/render-files.ts b/src/command/render/render-files.ts
index 171cffec591..7423eec6253 100644
--- a/src/command/render/render-files.ts
+++ b/src/command/render/render-files.ts
@@ -62,7 +62,7 @@ import {
   RenderFlags,
   RenderOptions,
 } from "./types.ts";
-import { error, info } from "../../deno_ral/log.ts";
+import { error, info, warning } from "../../deno_ral/log.ts";
 import * as ld from "../../core/lodash.ts";
 import { basename, dirname, join, relative } from "../../deno_ral/path.ts";
 import { Format } from "../../config/types.ts";
@@ -71,9 +71,11 @@ import {
   inputFilesDir,
   isServerShiny,
   isServerShinyKnitr,
+  projectedOutputFile,
 } from "../../core/render.ts";
 import {
   normalizePath,
+  pathsEqual,
   removeIfEmptyDir,
   removeIfExists,
 } from "../../core/path.ts";
@@ -460,6 +462,20 @@ async function renderFileInternal(
       files,
       options,
     );
+
+    // let each context know the projected outputs of the formats being
+    // rendered: keep-md intermediate handling must not write to or delete
+    // a path that a format owns (e.g. output-file: index.html plus a
+    // markdown format yields index.html.md, which is also the conventional
+    // keep-md location for the html format) (#14669)
+    const formatOutputs = Object.values(contexts)
+      .filter((context) => context.active)
+      .map((context) =>
+        projectedOutputFile(context.target.input, context.format)
+      );
+    for (const context of Object.values(contexts)) {
+      context.siblingFormatOutputs = formatOutputs;
+    }
   } catch (e) {
     // bad YAML can cause failure before validation. We
     // reconstruct the context as best we can and try to validate.
@@ -670,7 +686,22 @@ async function renderFileInternal(
           // keep md if requested
           const keepMd = executionEngineKeepMd(context);
           if (keepMd && context.format.execute[kKeepMd]) {
-            Deno.writeTextFileSync(keepMd, executeResult.markdown.value);
+            if (
+              context.siblingFormatOutputs?.some((output) =>
+                pathsEqual(output, keepMd)
+              )
+            ) {
+              warning(
+                `${
+                  basename(context.target.input)
+                }: not saving the keep-md intermediate because its ` +
+                  `conventional location (${
+                    basename(keepMd)
+                  }) is the output file of another format`,
+              );
+            } else {
+              Deno.writeTextFileSync(keepMd, executeResult.markdown.value);
+            }
           }
 
           // now get "unmapped" execute result back to send to pandoc
diff --git a/src/command/render/render.ts b/src/command/render/render.ts
index 3da6c73f04d..826316c608a 100644
--- a/src/command/render/render.ts
+++ b/src/command/render/render.ts
@@ -15,6 +15,7 @@ import { resourcePath } from "../../core/resources.ts";
 import { inputFilesDir } from "../../core/render.ts";
 import {
   normalizePath,
+  pathsEqual,
   pathWithForwardSlashes,
   safeExistsSync,
 } from "../../core/path.ts";
@@ -374,6 +375,15 @@ export async function renderPandoc(
       }
 
       if (cleanup !== false) {
+        // the conventional keep-md location can coincide with the declared
+        // output of another format (e.g. output-file: index.html plus a
+        // markdown format yields index.html.md) -- never clean up a path
+        // that a format owns (#14669)
+        const keepMd = executionEngineKeepMd(context);
+        const keepMdIsFormatOutput = keepMd !== undefined &&
+          context.siblingFormatOutputs?.some((output) =>
+            pathsEqual(output, keepMd)
+          );
         withTiming("render-cleanup", () =>
           renderCleanup(
             context.target.input,
@@ -381,7 +391,7 @@ export async function renderPandoc(
             format,
             file.context.project,
             cleanupSelfContained,
-            executionEngineKeepMd(context),
+            keepMdIsFormatOutput ? undefined : keepMd,
           ));
       }
 
diff --git a/src/command/render/types.ts b/src/command/render/types.ts
index cdc576ea53c..2826cdf9f6e 100644
--- a/src/command/render/types.ts
+++ b/src/command/render/types.ts
@@ -61,6 +61,9 @@ export interface RenderContext {
   libDir: string;
   project: ProjectContext;
   active: boolean;
+  // projected output paths of the input's other formats; keep-md intermediate
+  // handling must not write to or delete paths a format owns (#14669)
+  siblingFormatOutputs?: string[];
 }
 
 export interface RunPandocResult {
diff --git a/src/core/render.ts b/src/core/render.ts
index 313445eaed3..7c652f6e158 100644
--- a/src/core/render.ts
+++ b/src/core/render.ts
@@ -8,7 +8,7 @@ import { kOutputExt, kOutputFile, kServer } from "../config/constants.ts";
 import { Format, Metadata } from "../config/types.ts";
 import { kJupyterEngine, kKnitrEngine } from "../execute/types.ts";
 import { dirAndStem } from "./path.ts";
-import { extname } from "../deno_ral/path.ts";
+import { dirname, extname, join } from "../deno_ral/path.ts";
 
 export function inputFilesDir(input: string) {
   const [_, stem] = dirAndStem(input);
@@ -44,6 +44,21 @@ export function isServerShinyKnitr(
   return isServerShiny(format) && engine === kKnitrEngine;
 }
 
+// the path a format's rendered output is written to before any project
+// output-dir relocation: an explicit output-file (with the format's extension
+// appended by formatOutputFile when it differs), else <input-stem>.<output-ext>.
+// used to detect collisions between declared outputs and the keep-md
+// intermediate naming convention (#14669); doesn't cover recipe special cases
+// (--output flag, md-to-md rename, stdout) which can't produce colliding names
+export function projectedOutputFile(input: string, format: Format): string {
+  const outputFile = formatOutputFile(format);
+  if (outputFile) {
+    return join(dirname(input), outputFile);
+  }
+  const [dir, stem] = dirAndStem(input);
+  return join(dir, `${stem}.${format.render[kOutputExt] || "html"}`);
+}
+
 export function formatOutputFile(format: Format) {
   let outputFile = format.pandoc[kOutputFile];
   if (outputFile) {
diff --git a/tests/docs/output-file-collision/default/.gitignore b/tests/docs/output-file-collision/default/.gitignore
new file mode 100644
index 00000000000..f9ce2b2db87
--- /dev/null
+++ b/tests/docs/output-file-collision/default/.gitignore
@@ -0,0 +1,7 @@
+/.quarto/
+/index.html
+/index.html.md
+/index.commonmark.md
+/index_files/
+/site_libs/
+**/*.quarto_ipynb
diff --git a/tests/docs/output-file-collision/default/_quarto.yml b/tests/docs/output-file-collision/default/_quarto.yml
new file mode 100644
index 00000000000..a98fe5d28de
--- /dev/null
+++ b/tests/docs/output-file-collision/default/_quarto.yml
@@ -0,0 +1,6 @@
+project:
+  type: default
+
+format:
+  html: default
+  commonmark: default
diff --git a/tests/docs/output-file-collision/default/index.qmd b/tests/docs/output-file-collision/default/index.qmd
new file mode 100644
index 00000000000..5cd735cefb7
--- /dev/null
+++ b/tests/docs/output-file-collision/default/index.qmd
@@ -0,0 +1,6 @@
+---
+title: Home
+output-file: index.html
+---
+
+Hello.
diff --git a/tests/docs/output-file-collision/keepmd/.gitignore b/tests/docs/output-file-collision/keepmd/.gitignore
new file mode 100644
index 00000000000..b87288d2f4f
--- /dev/null
+++ b/tests/docs/output-file-collision/keepmd/.gitignore
@@ -0,0 +1,6 @@
+/.quarto/
+/_site/
+/site_libs/
+/index.html
+/index.commonmark.md
+**/*.quarto_ipynb
diff --git a/tests/docs/output-file-collision/keepmd/_quarto.yml b/tests/docs/output-file-collision/keepmd/_quarto.yml
new file mode 100644
index 00000000000..3a5d272c7c2
--- /dev/null
+++ b/tests/docs/output-file-collision/keepmd/_quarto.yml
@@ -0,0 +1,9 @@
+project:
+  type: website
+
+format:
+  html: default
+  commonmark: default
+
+execute:
+  keep-md: true
diff --git a/tests/docs/output-file-collision/keepmd/index.qmd b/tests/docs/output-file-collision/keepmd/index.qmd
new file mode 100644
index 00000000000..5d906ee987f
--- /dev/null
+++ b/tests/docs/output-file-collision/keepmd/index.qmd
@@ -0,0 +1,6 @@
+---
+title: Home
+output-file: index.html
+---
+
+Keep md content.
diff --git a/tests/docs/output-file-collision/website/.gitignore b/tests/docs/output-file-collision/website/.gitignore
new file mode 100644
index 00000000000..b87288d2f4f
--- /dev/null
+++ b/tests/docs/output-file-collision/website/.gitignore
@@ -0,0 +1,6 @@
+/.quarto/
+/_site/
+/site_libs/
+/index.html
+/index.commonmark.md
+**/*.quarto_ipynb
diff --git a/tests/docs/output-file-collision/website/_quarto.yml b/tests/docs/output-file-collision/website/_quarto.yml
new file mode 100644
index 00000000000..3c67c72b26d
--- /dev/null
+++ b/tests/docs/output-file-collision/website/_quarto.yml
@@ -0,0 +1,6 @@
+project:
+  type: website
+
+format:
+  html: default
+  commonmark: default
diff --git a/tests/docs/output-file-collision/website/index.qmd b/tests/docs/output-file-collision/website/index.qmd
new file mode 100644
index 00000000000..5cd735cefb7
--- /dev/null
+++ b/tests/docs/output-file-collision/website/index.qmd
@@ -0,0 +1,6 @@
+---
+title: Home
+output-file: index.html
+---
+
+Hello.
diff --git a/tests/smoke/render/render-output-file-collision.test.ts b/tests/smoke/render/render-output-file-collision.test.ts
new file mode 100644
index 00000000000..9e7826733a0
--- /dev/null
+++ b/tests/smoke/render/render-output-file-collision.test.ts
@@ -0,0 +1,114 @@
+/*
+ * render-output-file-collision.test.ts
+ *
+ * Regression tests for https://github.com/quarto-dev/quarto-cli/issues/14669:
+ * pairing an html format with a markdown format while output-file has an
+ * .html extension (e.g. output-file: index.html, as nbdev sets for llms.txt
+ * workflows) names the markdown output index.html.md — the same path as the
+ * keep-md intermediate convention for the html format. Render cleanup was
+ * deleting the markdown output, failing website renders at the output-move
+ * step and silently losing the file in default-type projects.
+ *
+ * Copyright (C) 2020-2026 Posit Software, PBC
+ *
+ */
+import { existsSync, safeRemoveSync } from "../../../src/deno_ral/fs.ts";
+import { join } from "../../../src/deno_ral/path.ts";
+import { docs } from "../../utils.ts";
+import { testQuartoCmd } from "../../test.ts";
+import {
+  ensureFileRegexMatches,
+  fileExists,
+  pathDoNotExists,
+  printsMessage,
+} from "../../verify.ts";
+
+const cleanup = (dir: string, paths: string[]) => {
+  return () => {
+    for (const path of paths) {
+      const target = join(dir, path);
+      if (existsSync(target)) {
+        safeRemoveSync(target, { recursive: true });
+      }
+    }
+    return Promise.resolve();
+  };
+};
+
+// paths a failed (pre-fix) render strands in the project root; clean them
+// too so a regression doesn't leave debris behind
+const websiteOutputs = [
+  "_site",
+  ".quarto",
+  "index.html",
+  "site_libs",
+  "index.commonmark.md",
+];
+
+// website project: the render errored at the output-move step and left
+// index.html + site_libs stranded in the project root
+const websiteDir = docs("output-file-collision/website");
+testQuartoCmd(
+  "render",
+  [websiteDir],
+  [
+    fileExists(join(websiteDir, "_site", "index.html")),
+    fileExists(join(websiteDir, "_site", "index.html.md")),
+    pathDoNotExists(join(websiteDir, "index.html")),
+    pathDoNotExists(join(websiteDir, "site_libs")),
+  ],
+  {
+    setup: cleanup(websiteDir, websiteOutputs),
+    teardown: cleanup(websiteDir, websiteOutputs),
+  },
+  "#14669 website: output-file index.html + commonmark renders both outputs",
+);
+
+// default-type project: the render exited 0 but the markdown output was
+// silently missing
+const defaultDir = docs("output-file-collision/default");
+const defaultOutputs = [
+  "index.html",
+  "index.html.md",
+  "index_files",
+  "site_libs",
+  "index.commonmark.md",
+];
+testQuartoCmd(
+  "render",
+  [defaultDir],
+  [
+    fileExists(join(defaultDir, "index.html")),
+    fileExists(join(defaultDir, "index.html.md")),
+  ],
+  {
+    setup: cleanup(defaultDir, [...defaultOutputs, ".quarto"]),
+    teardown: cleanup(defaultDir, [...defaultOutputs, ".quarto"]),
+  },
+  "#14669 default project: markdown output is not silently dropped",
+);
+
+// keep-md: true wants to write its intermediate to the same path the
+// markdown format owns: the intermediate write is skipped with a warning and
+// the markdown output wins
+const keepmdDir = docs("output-file-collision/keepmd");
+testQuartoCmd(
+  "render",
+  [keepmdDir],
+  [
+    printsMessage({ level: "WARN", regex: /not saving the keep-md/ }),
+    fileExists(join(keepmdDir, "_site", "index.html.md")),
+    // the markdown twin holds the commonmark render of the document, not the
+    // executed-markdown intermediate (which carries a yaml header)
+    ensureFileRegexMatches(join(keepmdDir, "_site", "index.html.md"), [
+      /Keep md content\./,
+    ], [
+      /^---$/,
+    ]),
+  ],
+  {
+    setup: cleanup(keepmdDir, websiteOutputs),
+    teardown: cleanup(keepmdDir, websiteOutputs),
+  },
+  "#14669 keep-md: intermediate write is skipped with a warning on collision",
+);

From 2ff3b6ff3c63c0cefd64caa36a4137db461a75ba Mon Sep 17 00:00:00 2001
From: Carlos Scheidegger <carlos.scheidegger@posit.co>
Date: Fri, 10 Jul 2026 19:56:54 -0500
Subject: [PATCH 2/3] Protect declared-but-unrendered format outputs from
 keep-md cleanup (#14669)

A partial render (quarto render --to html) of a document whose other
declared format owns the keep-md-conventional path (output-file:
index.html + a markdown format -> index.html.md) was still deleting
the markdown output a previous full render produced, since outputs
live next to sources in default-type projects.

renderContexts already resolves every declared format (inactive ones
are simply marked active: false), so extending the protection is just
including inactive contexts when collecting the owned output paths.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
---
 src/command/render/render-files.ts            | 12 +++++-----
 .../render-output-file-collision.test.ts      | 22 +++++++++++++++++++
 2 files changed, 28 insertions(+), 6 deletions(-)

diff --git a/src/command/render/render-files.ts b/src/command/render/render-files.ts
index 7423eec6253..213b3d85082 100644
--- a/src/command/render/render-files.ts
+++ b/src/command/render/render-files.ts
@@ -463,13 +463,13 @@ async function renderFileInternal(
       options,
     );
 
-    // let each context know the projected outputs of the formats being
-    // rendered: keep-md intermediate handling must not write to or delete
-    // a path that a format owns (e.g. output-file: index.html plus a
-    // markdown format yields index.html.md, which is also the conventional
-    // keep-md location for the html format) (#14669)
+    // let each context know the projected outputs of every declared format,
+    // including formats not in this render (e.g. quarto render --to html):
+    // keep-md intermediate handling must not write to or delete a path that
+    // a format owns (e.g. output-file: index.html plus a markdown format
+    // yields index.html.md, which is also the conventional keep-md location
+    // for the html format) (#14669)
     const formatOutputs = Object.values(contexts)
-      .filter((context) => context.active)
       .map((context) =>
         projectedOutputFile(context.target.input, context.format)
       );
diff --git a/tests/smoke/render/render-output-file-collision.test.ts b/tests/smoke/render/render-output-file-collision.test.ts
index 9e7826733a0..f360ed0d54e 100644
--- a/tests/smoke/render/render-output-file-collision.test.ts
+++ b/tests/smoke/render/render-output-file-collision.test.ts
@@ -14,6 +14,7 @@
  */
 import { existsSync, safeRemoveSync } from "../../../src/deno_ral/fs.ts";
 import { join } from "../../../src/deno_ral/path.ts";
+import { quarto } from "../../../src/quarto.ts";
 import { docs } from "../../utils.ts";
 import { testQuartoCmd } from "../../test.ts";
 import {
@@ -88,6 +89,27 @@ testQuartoCmd(
   "#14669 default project: markdown output is not silently dropped",
 );
 
+// partial render: a format that is declared but not being rendered still
+// owns its output -- quarto render --to html must not delete the markdown
+// twin a previous full render produced (outputs live in place in
+// default-type projects)
+testQuartoCmd(
+  "render",
+  [join(defaultDir, "index.qmd"), "--to", "html"],
+  [
+    fileExists(join(defaultDir, "index.html")),
+    fileExists(join(defaultDir, "index.html.md")),
+  ],
+  {
+    setup: async () => {
+      await cleanup(defaultDir, [...defaultOutputs, ".quarto"])();
+      await quarto(["render", defaultDir]);
+    },
+    teardown: cleanup(defaultDir, [...defaultOutputs, ".quarto"]),
+  },
+  "#14669 partial render: --to html preserves the existing markdown output",
+);
+
 // keep-md: true wants to write its intermediate to the same path the
 // markdown format owns: the intermediate write is skipped with a warning and
 // the markdown output wins

From 7c288146b63380679e04d2b950ae518b0bd7e404 Mon Sep 17 00:00:00 2001
From: Christophe Dervieux <christophe.dervieux@gmail.com>
Date: Mon, 13 Jul 2026 17:12:58 +0200
Subject: [PATCH 3/3] Extract keep-md/format-output collision check into a
 helper

The collision guard was inlined in both renderCleanup and the keep-md write path; keepMdCollidesWithFormatOutput keeps the invariant (never write to or clean up a path another format owns) in one place. Trim the changelog entry to the user-facing symptom -- the keep-md/output-move mechanism and the nbdev/commonmark example already live in the PR body.
---
 news/changelog-1.10.md             |  2 +-
 src/command/render/render-files.ts |  7 ++++---
 src/command/render/render.ts       | 14 ++++++++------
 src/core/render.ts                 | 13 ++++++++++++-
 4 files changed, 25 insertions(+), 11 deletions(-)

diff --git a/news/changelog-1.10.md b/news/changelog-1.10.md
index efbd8a5346c..5f4abd24f67 100644
--- a/news/changelog-1.10.md
+++ b/news/changelog-1.10.md
@@ -114,4 +114,4 @@ All changes included in 1.10:
 - ([#14582](https://github.com/quarto-dev/quarto-cli/issues/14582)): Fix format detection for extension formats (e.g. `acm-pdf`) in project preview, manuscript notebooks, MECA bundles, and website format ordering.
 - ([#14583](https://github.com/quarto-dev/quarto-cli/issues/14583)): Fix a shortcode used as an image source (e.g. `![]({{< meta logo >}})`) getting the `default-image-extension` appended, producing a doubled extension once the shortcode resolves.
 - ([#14595](https://github.com/quarto-dev/quarto-cli/issues/14595)): Fix reload preview in code-server environment
-- ([#14669](https://github.com/quarto-dev/quarto-cli/issues/14669)): Fix the markdown output being deleted when `output-file` has an `.html` extension and an html format is paired with a markdown format (e.g. `output-file: index.html` with `format: html` + `commonmark`, as nbdev sets up for llms.txt workflows). The markdown output's name (`index.html.md`) coincides with the conventional `keep-md` intermediate location for the html format, and render cleanup deleted it — failing website renders at the output-move step and silently dropping the file in other project types. Renders now never clean up (or write a `keep-md` intermediate over) a path that belongs to another format's output; a `keep-md: true` render whose intermediate location collides warns and skips saving the intermediate.
+- ([#14669](https://github.com/quarto-dev/quarto-cli/issues/14669)): Fix markdown output being deleted when `output-file` has an `.html` extension and an html format is paired with a markdown format.
diff --git a/src/command/render/render-files.ts b/src/command/render/render-files.ts
index 213b3d85082..2c578c33c0f 100644
--- a/src/command/render/render-files.ts
+++ b/src/command/render/render-files.ts
@@ -71,11 +71,11 @@ import {
   inputFilesDir,
   isServerShiny,
   isServerShinyKnitr,
+  keepMdCollidesWithFormatOutput,
   projectedOutputFile,
 } from "../../core/render.ts";
 import {
   normalizePath,
-  pathsEqual,
   removeIfEmptyDir,
   removeIfExists,
 } from "../../core/path.ts";
@@ -687,8 +687,9 @@ async function renderFileInternal(
           const keepMd = executionEngineKeepMd(context);
           if (keepMd && context.format.execute[kKeepMd]) {
             if (
-              context.siblingFormatOutputs?.some((output) =>
-                pathsEqual(output, keepMd)
+              keepMdCollidesWithFormatOutput(
+                keepMd,
+                context.siblingFormatOutputs,
               )
             ) {
               warning(
diff --git a/src/command/render/render.ts b/src/command/render/render.ts
index 826316c608a..a7a8510b305 100644
--- a/src/command/render/render.ts
+++ b/src/command/render/render.ts
@@ -12,10 +12,12 @@ import { Document, parseHtml } from "../../core/deno-dom.ts";
 
 import { mergeConfigs } from "../../core/config.ts";
 import { resourcePath } from "../../core/resources.ts";
-import { inputFilesDir } from "../../core/render.ts";
+import {
+  inputFilesDir,
+  keepMdCollidesWithFormatOutput,
+} from "../../core/render.ts";
 import {
   normalizePath,
-  pathsEqual,
   pathWithForwardSlashes,
   safeExistsSync,
 } from "../../core/path.ts";
@@ -380,10 +382,10 @@ export async function renderPandoc(
         // markdown format yields index.html.md) -- never clean up a path
         // that a format owns (#14669)
         const keepMd = executionEngineKeepMd(context);
-        const keepMdIsFormatOutput = keepMd !== undefined &&
-          context.siblingFormatOutputs?.some((output) =>
-            pathsEqual(output, keepMd)
-          );
+        const keepMdIsFormatOutput = keepMdCollidesWithFormatOutput(
+          keepMd,
+          context.siblingFormatOutputs,
+        );
         withTiming("render-cleanup", () =>
           renderCleanup(
             context.target.input,
diff --git a/src/core/render.ts b/src/core/render.ts
index 7c652f6e158..3f41947a5a8 100644
--- a/src/core/render.ts
+++ b/src/core/render.ts
@@ -7,7 +7,7 @@
 import { kOutputExt, kOutputFile, kServer } from "../config/constants.ts";
 import { Format, Metadata } from "../config/types.ts";
 import { kJupyterEngine, kKnitrEngine } from "../execute/types.ts";
-import { dirAndStem } from "./path.ts";
+import { dirAndStem, pathsEqual } from "./path.ts";
 import { dirname, extname, join } from "../deno_ral/path.ts";
 
 export function inputFilesDir(input: string) {
@@ -59,6 +59,17 @@ export function projectedOutputFile(input: string, format: Format): string {
   return join(dir, `${stem}.${format.render[kOutputExt] || "html"}`);
 }
 
+// true when the keep-md intermediate location is a path another declared
+// format owns, so it must not be written to or cleaned up (#14669)
+export function keepMdCollidesWithFormatOutput(
+  keepMd: string | undefined,
+  siblingFormatOutputs: string[] | undefined,
+): boolean {
+  return keepMd !== undefined &&
+    (siblingFormatOutputs?.some((output) => pathsEqual(output, keepMd)) ??
+      false);
+}
+
 export function formatOutputFile(format: Format) {
   let outputFile = format.pandoc[kOutputFile];
   if (outputFile) {