Verified against pre-commit 4.6.0 source (site-packages/pre_commit/): commands/run.py:344 sets stash = not args.all_files and not args.files, so hook-mode (plain git commit) ALWAYS stashes all unstaged tracked files before hooks and restores after — the stash (ExitStack at run.py:419) happens BEFORE hook selection (load_config at :423), so it fires even when zero hooks match, and no config/env opt-out exists (SKIP= filters hooks after the stash; .pre-commit-config.yaml cannot prevent it). staged_files_only.py:95: on patch-apply conflict, git checkout -- . runs a second time, so a concurrent write landing mid-hook-window is silently lost. staged_files_only.py:58: empty unstaged diff means no stash, so clean-tree commits are safe.
Consequence: if another process/session has in-progress unstaged edits in the same worktree, a hook-running git commit mutates their tree mid-flight and can destroy their writes. The hook-equivalent, stash-free recipe is: pre-commit run --files <staged paths> && git commit --no-verify … — same hook checks (run --files checks worktree content and never stashes), no tree mutation. Untracked files are never stashed (diff-index vs write-tree), so only tracked modifications matter.
Secondary gotcha from the same work: on macOS, git rev-parse --show-toplevel returns the symlink-resolved path (/tmp → /private/tmp), so comparing paths resolved from a raw cwd against the git root silently fails; realpath the cwd before relativizing pathspecs.