Temp *.quarto_ipynb files are not deleted after publishing

[cbrnr]

I have a weird issue that unfortunately I cannot reproduce with a minimal example, so I'll try to describe what's happening as best as I can.

I have a project-like folder structure with an empty _quarto.yml in the root. There are several subfolders, each of which contains two .qmd files, e.g., 01/01.qmd, 01/01-a.qmd, 02/02.qmd, 02/02-a.qmd, and so on.

When publishing a document (I only tried Netlify), I run the following command from the project root:

quarto publish netlify 01/01.qmd

This works, but somehow this single step adds temporary *.quarto_ipynb files in all subfolders (e.g., 01/01.quarto_ipynb, 01/01-a.quarto_ipynb, 02/02.quarto_ipynb, 02/02-a.quarto_ipynb, ...). Furthermore, these temporary files remain in the folders even when the publishing process has completed.

❯ quarto check

Quarto 1.6.36
[✓] Checking environment information...
      Quarto cache location: /Users/clemens/Library/Caches/quarto
[✓] Checking versions of quarto binary dependencies...
      Pandoc version 3.4.0: OK
      Dart Sass version 1.70.0: OK
      Deno version 1.46.3: OK
      Typst version 0.11.0: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
      Version: 1.6.36
      Path: /Users/clemens/Applications/quarto/bin

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

[✓] Checking LaTeX....................OK
      Using: TinyTex
      Path: /Users/clemens/Library/TinyTeX/bin/universal-darwin
      Version: 2024

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

[✓] Checking Python 3 installation....OK
      Version: 3.12.7
      Path: /Users/clemens/Projects/python-intro/.venv/bin/python
      Jupyter: 5.7.2
      Kernels: python3

[✓] Checking Jupyter engine render....OK

[✓] Checking R installation...........OK
      Version: 4.4.2
      Path: /Library/Frameworks/R.framework/Resources
      LibPaths:
        - /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library
      knitr: 1.49
      rmarkdown: 2.29

[✓] Checking Knitr engine render......OK

[mcanouil]

Do you observe the same behaviour using quarto render?

I'll move this as a discussion for now.

[mcanouil]

Yes, it's because single file are now projects but I would still not expect to Quarto to create .quarto_ipynb files for all inputs in the project. quarto render/preview does not do that for instance.

[cbrnr]

OK, so you are saying this is still a bug then?

[mcanouil]

In my opinion but I am not the developer/designer of the initial behaviour and the change when single file became project, so I let mostly Carlos see what is what here.

[cscheid]

Yes, now that we have @mcanouil's repro I'm positive this is a bug.