.quarto_ipynb files not cleaned up when preview is killed ungracefully

[cderv]

Reported by @mine-cetinkaya-rundel.

When using Positron and clicking the trash/bin icon on the terminal pane running quarto preview, the process is killed without clean shutdown. The transient .quarto_ipynb file created during render is not cleaned up. On the next preview, a new .quarto_ipynb_1 is created, and this accumulates (_2, _3, ...) each time the user repeats the pattern.

This is distinct from #14281, which fixed accumulation within a single preview session (re-renders). This issue is about accumulation across sessions when the process exits ungracefully.

Steps to reproduce

Create test.qmd with Jupyter engine content:

---
format: html
---

```{python}
1 + 1
```

1. Open in Positron
2. Click the Preview button (opens terminal running quarto preview test.qmd)
3. Wait for render to complete
4. Click the bin/trash icon on the terminal pane (kills terminal)
5. Click Preview again
6. Repeat steps 4-5 a few times

Actual behavior

Files accumulate:

test.quarto_ipynb
test.quarto_ipynb_1
test.quarto_ipynb_2

Expected behavior

No .quarto_ipynb files left behind between preview sessions.

Analysis

In quarto render, the .quarto_ipynb is cleaned up promptly after render completes — cmd.ts calls context.cleanup() which triggers cleanupFileInformationCache() → invalidateForFile() → safeRemoveSync().

In quarto preview, cleanup is deferred: the file sits on disk between renders and is only deleted at process exit (via onCleanup) or before the next re-render (via invalidateForFile). If the process is killed ungracefully (SIGKILL, taskkill, terminal destruction), the exit cleanup never fires.

Historically, cleanupNotebook() in jupyter.ts used to delete the file immediately after execution when keep-ipynb was not set. This was changed in #12793 to integrate with the fileInformationCache system (fixing #12780), but the immediate deletion for the keep-ipynb: false case was dropped as a side effect. The file deletion was fully delegated to the cache cleanup, which only runs at context disposal time.

Suggested fix

Restore immediate deletion in cleanupNotebook() for the keep-ipynb: false case, while preserving the cache integration for keep-ipynb: true:

• When transient && keep-ipynb: mark cache entry as non-transient (existing behavior from Handle keep-ipynb correctly now that fileInformationCache is responsible for the cleaning #12793)
• When transient && !keep-ipynb: delete the file from disk immediately after execute

This restores the original behavior from before #12793 and aligns preview with how quarto render handles cleanup. The execute() function already has a guard that recreates the file if missing (with a comment: "could have been removed by the cleanup step of another render"), so re-renders continue to work.

Related: #14281, #12780, #12793, #11597

[cderv]

Also related on the Positron side: posit-dev/positron#13006 ("Killing Quarto Preview in Terminal should exit Quarto process") — the terminal kill path on Windows uses taskkill which doesn't give quarto a chance to run cleanup handlers.

[cderv]

Reproduction confirmed

Reproduced on Positron Daily 2026.05.0-46, Windows 11, quarto-cli main (23bb687).

Using agent-browser to automate Positron via Chrome DevTools Protocol (Positron is Electron-based):

1. Launch positron-daily --remote-debugging-port=9222 /tmp/test-dir
2. Connect agent-browser connect 9222
3. Open test.qmd (simple {python} 1+1 cell)
4. Click Preview → wait for render → test.quarto_ipynb appears on disk
5. Click Kill Terminal (bin icon)
6. test.quarto_ipynb remains on disk (not cleaned up)
7. Click Preview again → test.quarto_ipynb_1 created (collision avoidance)
8. Repeat → _2, _3, etc.

Three cycles produced:

test.quarto_ipynb        # first preview, never cleaned up
test.quarto_ipynb_1      # second preview
test.quarto_ipynb_2      # third preview

agent-browser commands used for reproduction

Setup a test directory with a simple Python qmd:

mkdir /tmp/quarto-ipynb-test

---
format: html
---

```{python}
1 + 1
```

Then run the following agent-browser commands:

# Close any running Positron, launch with CDP
positron-daily --remote-debugging-port=9222 /tmp/quarto-ipynb-test

# Connect (after Positron finishes loading)
agent-browser connect 9222
agent-browser tab list
agent-browser tab 1  # switch to test folder window

# Open test.qmd - refs come from snapshot
agent-browser snapshot -i  # find treeitem "test.qmd" ref
agent-browser dblclick @eNN  # double-click to open
agent-browser wait 2000

# Click Preview - ref from snapshot
agent-browser snapshot -i  # find button "Preview" ref
agent-browser click @eNN
agent-browser wait 15000

# Verify file exists during preview
ls /tmp/quarto-ipynb-test/*.quarto_ipynb*
# => test.quarto_ipynb

# Kill Terminal - ref from snapshot
agent-browser snapshot -i  # find button "Kill Terminal" ref
agent-browser click @eNN
agent-browser wait 3000

# Check stale file
ls /tmp/quarto-ipynb-test/*.quarto_ipynb*
# => test.quarto_ipynb  (still there - bug!)

# Second preview cycle
agent-browser snapshot -i  # find Preview button again
agent-browser click @eNN
agent-browser wait 15000

ls /tmp/quarto-ipynb-test/*.quarto_ipynb*
# => test.quarto_ipynb
# => test.quarto_ipynb_1  (accumulated!)

Note: @eNN refs are session-specific. Run agent-browser snapshot -i before each
interaction to get the current refs. Key elements to find:

• treeitem "test.qmd" — file in explorer
• button "Preview" — preview button in editor toolbar
• button "Kill Terminal" — bin/trash icon in terminal pane

[cscheid]

There's a good argument to be made about cleaning these up in an existing directory when quarto starts too, so we don't create a large number of these files (or the temporary directories, for that matter).

[cderv]

Yes - I have a fix to delete those at the right time, but I was thinking about adding a cleaner at start for those... I just would like us to handle gracefully .quarto_ipynb there because keep-ipynb: true was set. So I was thinking or removing those per file and not just for all at quarto start.