Root cause, two parts:
- An explicit save (Save All before a checkout, before running, before Commit) also wrote documents that were not modified, running save actions such as stripping trailing whitespace and adding a final newline on them — files the user never touched gained whitespace-only changes. Saves now skip clean documents, as autosave already did.
- After our own VCS operations rewrote files (checkout, rollback, stash, patch, ignore, commit/worktree hooks, Directory Compare), clean editor buffers were only refreshed by the file watcher, which can miss a rewrite that keeps the length and the timestamp's millisecond. Those operations now reload clean buffers synchronously before returning, keeping each document's chosen encoding; modified buffers keep the existing conflict handling.
Fixes#893
Co-Authored-By: Claude Opus 5.5 <[email protected]>
