feat: Add file locking and improved chmod handling

[iHildy]

Summary

Introduce a file-based sync lock to coordinate concurrent sync operations and a safe chmod helper to gracefully handle missing files. Refactors across apply, config, and service to adopt the new utilities. Added tests for new features.

Changes

• Add chmodIfExists utility in src/sync/config.ts and use it in writeJsonFile, replacing direct fs.chmod calls; export/import adjusted; tests extend to cover behavior.
• Integrate chmodIfExists into src/sync/apply.ts:
  • Use in copyFileWithMode and copyDirRecursive
  • Use in applyExtraSecrets
• Add new locking layer:
  • New file src/sync/lock.ts with tryAcquireSyncLock, withSyncLock, and related logic
  • New tests src/sync/lock.test.ts covering acquisition, busy state, and stale lock handling
• Refactor src/sync/service.ts:
  • Introduce lock path and locking helpers (runExclusive, skipIfBusy)
  • Wrap key operations (startupSync, init, link, pull, push, enableSecrets, resolve) with locking
  • Provide clear busy-state messaging and behavior
• Tests
  • Add tests for chmodIfExists in src/sync/config.test.ts
  • Ensure imports reflect new chmodIfExists export

Testing

• Run tests: bun test (or mise run test per project setup)
• Specifically verify:
  • chmodIfExists ignores missing paths without error
  • Locking prevents concurrent sync runs and handles stale/busy scenarios
  • Existing sync flows still function with the new locking and chmod handling

Next steps (if you want): I can run the test suite, report results, and adjust any failing tests.

[gemini-code-assist]

Summary of Changes

Hello @iHildy, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request significantly enhances the stability and reliability of the synchronization process. It introduces a robust file-based locking system to prevent concurrent operations from interfering with each other, and refines file permission handling to gracefully manage non-existent paths, thereby improving overall system resilience.

Highlights

• File Locking Mechanism: A new file-based synchronization lock has been introduced to coordinate concurrent sync operations, preventing race conditions and ensuring data integrity. This includes logic for acquiring, releasing, and handling stale locks.
• Improved Chmod Handling: A chmodIfExists utility was added to gracefully handle attempts to change file permissions on non-existent files, preventing errors and making file operations more robust.
• Core Logic Refactoring: Key synchronization operations across src/sync/apply.ts and src/sync/service.ts have been refactored to integrate the new chmodIfExists helper and to wrap critical functions with the file locking mechanism, ensuring exclusive execution.
• New Test Coverage: Dedicated unit tests have been added for both the file locking functionality and the chmodIfExists utility, verifying their correct behavior, including scenarios for busy locks and missing files.

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[gemini-code-assist]

Code Review

This pull request introduces a robust file-based locking mechanism to prevent concurrent sync operations and a chmodIfExists utility for safer file permission changes. The changes are well-structured, with new logic for locking and its tests in dedicated files. The core sync service is cleanly refactored to adopt this locking, using wrapper functions to separate concerns. The new chmodIfExists function is also a good addition for robustness.

I've made a couple of suggestions for minor improvements:

• In src/sync/lock.ts, there's a piece of unreachable code that can be removed.
• In src/sync/service.ts, there's an opportunity to simplify the code by removing some redundant async/await keywords when wrapping service methods with the new locking functions.