Git State Safety

The failure mode this prevents

During a merge/rebase/cherry-pick, the index holds a carefully constructed
mid-state: files from both sides, deletion markers, unresolved paths.
Any mutation of the index before commit silently corrupts that state.

Example: git checkout origin/main -- src/some-file.ts overwrites that path's index entry and can silently reset a sibling's deletion marker too — the failure only surfaces at commit.

Safe read-only inspection

Use these during any fragile state. All are read-only — zero index / working-tree effect:

Need	Command
See a file's content on another ref	git show <ref>:<path>
Same, piped for scripting	git cat-file -p <ref>:<path>
Log for a path on another ref	git log <ref> -- <path>
Diff between two refs	git diff <ref-a> <ref-b> -- <path>
Who last touched a line	git blame <ref> -- <path>
Full tree inspection	git ls-tree -r <ref>
Inspect unmerged stages without touching the index	git ls-files -u
Genuinely need working files from another ref	git worktree add <path> <ref>

The worktree option is the escape hatch when you need working files: create a temporary worktree for reading/testing, investigate there, remove with git worktree remove <path>. The worktree is for reading — do not run a test-merge inside it.

Stage numbering

Mid-merge, the index holds up to three versions of each conflicted path:

• Stage 1 — common ancestor ("base")
• Stage 2 — current branch ("ours")
• Stage 3 — incoming branch ("theirs")

git ls-files -u prints <mode> <sha> <stage>\t<path> for every conflicted entry. These are what git checkout --ours <path> and git checkout --theirs <path> select from.

Unsafe mutations during fragile state

Never run these while merge/rebase/cherry-pick state exists, or while a conflict is partially resolved:

• git checkout <ref> -- <path> — overwrites the index entry. Can silently cancel staged deletions, modifications, or unresolved markers.
• git restore --source=<ref> <path> / git restore --staged <path> — modern equivalents; same failure mode.
• git add <path> / git add -p on a conflicted path — collapses stages 1/2/3 into stage 0. If the worktree still has <<<<<<< markers, you commit literal conflict markers.
• git update-index (any form) — direct index mutation, same or worse blast radius.
• git rm <path> on a conflicted path — resolves-by-deletion; easy to do accidentally.
• git clean — wipes untracked files, including merge leftovers and *.orig notes.
• git commit -a / git commit --all during a merge — pulls in unresolved worktree state wholesale.
• git checkout <ref> (branch switch) — blocked by git if conflicts are present, but succeeds and throws away merge state if forced.
• git reset — always destructive to index/working tree state. Even git reset HEAD <path> can unstage a merge resolution.
• git stash — refuses mid-merge by default; with -f / --all or on older Git it resets .git/MERGE_HEAD. No supported stash pop path restores merge state. Treat as unrecoverable.
• git switch — same hazard as git checkout <ref>.

To abandon and restart a merge, use git merge --abort (or git rebase --abort, git cherry-pick --abort). Note: git merge --abort requires ORIG_HEAD to point at the pre-merge tip — if you have already run a git reset or started a second merge, --abort may refuse or restore the wrong state.

Safe per-path conflict resolution

These are safe mid-merge:

• git checkout --ours <path> — resolve using stage 2 (current branch's version). Stages the resolution.
• git checkout --theirs <path> — resolve using stage 3 (incoming branch's version). Stages the resolution.

These differ from git checkout <ref> -- <path> (unsafe) because they operate on conflict stages already in the index.

Cheap insurance: cp .git/index .git/index.bak before any risky operation. Restore with cp .git/index.bak .git/index.

Recovery when a bad merge already landed

If the bad merge is local-only (not yet pushed): git reset --hard ORIG_HEAD — git merge writes ORIG_HEAD to the pre-merge tip. Only works pre-push and only if no subsequent merge/reset has run.

If the bad merge is already pushed and no-force-push applies, reverse the effect with a follow-on commit. This assumes git status shows a clean tree (the merge is committed; fragile-index rules above no longer apply).

For the rest of this section, <upstream> = the ref whose state the merge was intended to produce.

Recipe

1. Confirm the damage: git diff <upstream>...<your-branch> --name-status

2. Partition and fix by diff filter:

   # Files the branch kept that upstream DELETED — remove them
   git diff <upstream>...<your-branch> --diff-filter=A --name-only \
     | xargs git rm
   
   # Files that diverged in CONTENT — restore upstream content
   git diff <upstream>...<your-branch> --diff-filter=M --name-only \
     | xargs -I{} git checkout <upstream> -- {}
   
   # Files the branch DELETED that upstream kept — restore from upstream
   git diff <upstream>...<your-branch> --diff-filter=D --name-only \
     | xargs -I{} git checkout <upstream> -- {}

3. Verify: git diff <upstream>...<your-branch> --name-status should list only files your change actually touches.

4. Commit the recovery as its own commit — do not amend the merge commit and do not force-push. The bad merge stays in history but its effect is reversed.

5. Pre-commit hooks may complain about pre-existing warnings in restored files. Request explicit engineer approval before using --no-verify.

If GitHub's PR diff still shows restored files

GitHub's three-dot diff (merge-base→tip) still lists files as changed even after their content is reverted to match <upstream> — the only clean fix is a fresh branch off current upstream with just the intended changes.

Rule of thumb

If git status shows MERGING, REBASING, CHERRY-PICKING, or any UU / DU / UD / AU / UA / AA / DD entries, treat the index as read-only.

Detection in scripts (locale-independent):

• test -e "$(git rev-parse --git-path MERGE_HEAD)" — active merge
• test -d "$(git rev-parse --git-path rebase-merge)" — active interactive/merge rebase
• test -d "$(git rev-parse --git-path rebase-apply)" — active apply-based rebase
• test -e "$(git rev-parse --git-path CHERRY_PICK_HEAD)" — active cherry-pick

git reflog retains every ref movement for 90 days (gc.reflogExpire) — recover an accidental reset --hard via git reset --hard HEAD@{1} before git gc reaps the orphaned commits.