[asukaminato0721]

Summary

Fixes #3367

# pyrefly: ignore[unused-ignore] now suppresses the display/reporting of the unused-ignore diagnostic for its own ignore comment, including mixed-code directives like # pyrefly: ignore[bad-return, unused-ignore].

The raw unused-ignore collector still returns those errors, so --remove-unused-ignore behavior remains unchanged.

Test Plan

add test

[meta-codesync]

This pull request has been imported. If you are a Meta employee, you can view this in D116160143. (Because this pull request was imported automatically, there will not be any future comments.)

[codspeed]

Merging this PR will not alter performance

✅ 35 untouched benchmarks
⏩ 9 skipped benchmarks¹

---

_{Comparing asukaminato0721:3367 (3c82d7b) with main (c68f2ce)}

Footnotes

1. 9 benchmarks were skipped, so the baseline results were used instead. If they were deleted from the codebase, click here and archive them to remove them from the performance reports. ↩

[stroxler]

Thanks! This needs a rebase before I can merge it; trying to auto-rebase the synced diff failed.

Based on AI review, I think this also needs some fixes... I was considering stacking some fix-forwards, because I think this feature is pretty important, but because we have to rebase anyway I'm passing them off to you:

1. A stale “used” report can silently lose its protection.
   [error/suppress.rs:172–183](https://github.com/meta/pyrefly/blob/71ca65a57395d4908471fd5a20e21c64d81649a9/pyrefly/lib/error/suppress.rs#L172-L183)
   Generate a Windows report where a suppression is used, change only its trailing comment text, then generate a Linux report where it is unused. The records become separate keys; the Windows record is skipped without validation, and cleanup deletes the still-required suppression. I reproduced this with actual platform-specific checks.
   Fix: reject inconsistent source snapshots, including stale records marked used—not just records proposing deletion.

2. Mixing diagnostics JSON and usage reports bypasses usage protection.
   [commands/suppress.rs:74–84](https://github.com/meta/pyrefly/blob/71ca65a57395d4908471fd5a20e21c64d81649a9/pyrefly/lib/commands/suppress.rs#L74-L84)
   Passing an unused-ignore diagnostic alongside a report saying the same suppression was used still deletes it. Diagnostic edits are appended independently, so the report cannot veto them.
   Fix: reject mixed input formats, or reconcile all usage evidence before producing edits.

3. --check-all produces cleanup records for bundled, non-filesystem sources.
   [state/errors.rs:700–704](https://github.com/meta/pyrefly/blob/71ca65a57395d4908471fd5a20e21c64d81649a9/pyrefly/lib/state/errors.rs#L700-L704)
   My minimal check produced 127 bundled-source records with relative paths. Consuming it with --remove-unused=all failed trying to read _collections_abc.pyi, aborting cleanup.
   Fix: restrict actionable reports to ModulePathDetails::FileSystem, matching SerializedError::from_error.

Scope: the summary still promises self-suppression, but the patch deliberately retains those diagnostics and implements report aggregation instead. Update the summary to explain that change in approach.

[github-actions]

According to mypy_primer, this change doesn't affect type check results on a corpus of open source code. ✅

[stroxler]

Looks like this was rebased, but the issues above were not yet addressed.

Also, AI review caught one more potential problem:

[commands/check.rs:1955–1960](https://github.com/meta/pyrefly/blob/3c82d7bf839b872f840a30128fa2005382fefba7/pyrefly/lib/commands/check.rs#L1955-L1960): the suppression report uses BufWriter without explicitly flushing it. For small reports, writing happens during drop, where write errors are discarded.

The AI reviewer reproduced this on the updated version: checking an error-free file with --report-suppressions /dev/full --output-format=omit-errors --summary=none returns exit code 0 with no error, although the report cannot be written.

Fix: call writer.flush()? after writing the newline, and add a regression test for write failure.