Restrict update --sync pruning to entries missing on disk

[ChanTsune]

Summary

update --sync now prunes an archive entry only when its path no longer exists on disk. Previously any entry absent from the collected set was pruned, so entries filtered out by --exclude/--include or time filters were deleted even though their files still exist.

Notes

• --sync is a stable option, so this changes stable-surface behavior.
• Ambiguous stat errors (e.g. PermissionDenied) keep the entry to avoid data loss; only NotFound/NotADirectory/InvalidFilename prune.
• Names produced by -s/--transform/--strip-components do not correspond to filesystem paths and are still pruned, as before.
• Stacked on Unify missing-time options into a single --missing-time option #3164.

Summary by CodeRabbit

• Bug Fixes
  • --sync now avoids removing archive entries just because they were skipped by filters, as long as the source files still exist on disk.
  • Improved handling of missing-file checks to reduce accidental pruning when file access fails for reasons other than “not found.”
• Tests
  • Added coverage for --sync with excluded files and time-based filters to confirm existing files remain in the archive.

[coderabbitai]

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Review details

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: ff4b53ab-f3c7-4b2b-a046-4ad41933263b

📥 Commits

Reviewing files that changed from the base of the PR and between 5bc874d and 8b3731f.

📒 Files selected for processing (2)

• cli/src/command/update.rs
• cli/tests/cli/update/option_sync.rs

📝 Walkthrough

Walkthrough

Changes --sync pruning logic in run_update_archive to only prune archive entries when they are absent from disk, using a new exists_on_disk helper that treats specific IO errors as missing. Adds two integration tests validating this behavior.

Changes

Sync pruning fix

Layer / File(s)	Summary
Sync pruning logic and disk-existence helper cli/src/command/update.rs	Pruning during --sync now requires the entry to be absent on disk (checked via new exists_on_disk helper using symlink_metadata), rather than pruning unconditionally when sync is set; also reformats std imports.
Integration tests for sync pruning behavior cli/tests/cli/update/option_sync.rs	Adds tests confirming excluded-but-existing files and files skipped due to --newer-mtime filtering remain in the archive after --sync.

Estimated code review effort: 3 (Moderate) | ~20 minutes

Possibly related PRs

• ChanTsune/Portable-Network-Archive#2512: Both PRs modify the same --sync pruning logic in run_update_archive.
• ChanTsune/Portable-Network-Archive#2873: The pruning-only-if-missing logic introduced here directly underpins a disk-deletion sync test in that PR.
• ChanTsune/Portable-Network-Archive#3014: Also changes --sync conditional pruning/replacement behavior in run_update_archive.

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title clearly and accurately summarizes the main change to update --sync pruning behavior.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch cli/update/sync-prune-missing-on-disk

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[gemini-code-assist]

Code Review

This pull request refactors the --sync update behavior to only prune archive entries that no longer exist on disk, preventing entries filtered out by exclusions or time filters from being deleted. A helper function exists_on_disk is introduced along with corresponding integration tests. Feedback highlights a potential cross-platform data loss issue and MSRV compilation risk caused by matching io::ErrorKind::InvalidFilename in the exists_on_disk function, suggesting its removal.

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