Quarto documents cannot render to gfm in a Quarto manuscript project

I have:

• searched the issue tracker for similar issues
• installed the latest version of Quarto CLI
• formatted my issue following the Bug Reports guide

Bug description

In a Quarto manuscript project, I get an error whenever I try to render an individual notebook to GitHub Flavored Markdown. I can render to other formats (e.g. html) without issue. This only seems to happen in a manuscript project, not in other projects (e.g. default, website), or outside of a project.

Steps to reproduce

Create a new manuscript project. Inside the project, add a new Quarto document. Set the output to gfm and render/preview.

Actual behavior

ERROR: No output created by quarto render Untitled-1.qmd

Stack trace:
    at handleRenderResult (file:///Applications/Positron.app/Contents/Resources/app/quarto/bin/quarto.js:92852:15)
    at renderForPreview (file:///Applications/Positron.app/Contents/Resources/app/quarto/bin/quarto.js:92868:25)
    at eventLoopTick (ext:core/01_core.js:175:7)
    at async render (file:///Applications/Positron.app/Contents/Resources/app/quarto/bin/quarto.js:92741:29)
    at async preview (file:///Applications/Positron.app/Contents/Resources/app/quarto/bin/quarto.js:92752:21)
    at async Command.actionHandler (file:///Applications/Positron.app/Contents/Resources/app/quarto/bin/quarto.js:109437:9)
    at async Command.execute (file:///Applications/Positron.app/Contents/Resources/app/quarto/bin/quarto.js:8253:13)
    at async Command.parseCommand (file:///Applications/Positron.app/Contents/Resources/app/quarto/bin/quarto.js:8143:20)
    at async quarto (file:///Applications/Positron.app/Contents/Resources/app/quarto/bin/quarto.js:133948:9)
    at async file:///Applications/Positron.app/Contents/Resources/app/quarto/bin/quarto.js:133978:9

Expected behavior

No response

Your environment

• IDE: Positron Version: 2025.10.0 build 199
• OS: MacOS 15.7.1 (Sequoia)

Quarto check output

Quarto 1.7.32
[✓] Checking environment information...
      Quarto cache location: /Users/leonreteig/Library/Caches/quarto
[✓] Checking versions of quarto binary dependencies...
      Pandoc version 3.6.3: OK
      Dart Sass version 1.85.1: OK
      Deno version 1.46.3: OK
      Typst version 0.13.0: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
      Version: 1.7.32
      Path: /Applications/Positron.app/Contents/Resources/app/quarto/bin

[✓] Checking tools....................OK
      TinyTeX: (not installed)
      Chromium: (not installed)

[✓] Checking LaTeX....................OK
      Tex:  (not detected)

[✓] Checking Chrome Headless....................OK
      Using: Chrome found on system
      Path: /Applications/Google Chrome.app/Contents/MacOS/Google Chrome
      Source: MacOS known location

[✓] Checking basic markdown render....OK

[✓] Checking Python 3 installation....OK
      Version: 3.9.6
      Path: /Library/Developer/CommandLineTools/usr/bin/python3
      Jupyter: (None)

      Jupyter is not available in this Python installation.
      Install with python3 -m pip install jupyter

[✓] Checking R installation...........OK
      Version: 4.5.1
      Path: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources
      LibPaths:
        - /Users/leonreteig/Library/R/arm64/4.5/library
        - /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library
      knitr: (None)
      rmarkdown: (None)

      The knitr package is not available in this R installation.
      Install with install.packages("knitr")
      The rmarkdown package is not available in this R installation.
      Install with install.packages("rmarkdown")

Reproduce the issue by creating a manuscript project, adding a Quarto document with gfm output, and running render or preview. Start with the render/preview path named in the stack trace, including handleRenderResult, and compare manuscript handling with formats that work. Done means an individual manuscript document renders to GitHub Flavored Markdown without the no-output error.