git-add-u-after-async-post-commit-hook

git add -u after async post-commit hook stages tracked-file deletions

Problem

You make a clean commit. The project's post-commit hook prints something like:

[post-commit] Python files changed — running doc update in background...

You then need to amend the commit (typo in message, wrong issue reference, etc.). You reach for the muscle-memory sequence:

git add -u && git commit --amend -m "..."   # ← TRAP

The amend output reports something terrifying:

[your-branch 480e2226] fix(...): your message
 1493 files changed, 4 insertions(+), 368977 deletions(-)
 delete mode 100644 .claude-memory/MEMORY.md
 delete mode 100644 .claude-memory/SESSION_CHECKPOINT_*.md
 delete mode 100644 scripts/...
 ...

If you immediately ran git push --force-with-lease, that catastrophe is now on the remote branch. The remote PR diff shows thousands of unrelated deletions mixed with your intended 6-file fix.

git status afterwards reveals the smoking gun — files that WERE tracked before the amend now show as Untracked:

On branch your-branch
Your branch is up to date with 'origin/your-branch'.

Untracked files:
        .claude-memory/
        .cursor/
        .github/
        MEMORY.md
        PRODUCT.md
        scripts/

Why it happens

The async post-commit hook fires after your first commit and starts a background process that:

1. Reads tracked files (e.g. MEMORY.md, docs/site/*.html).
2. Regenerates / renames / moves / deletes them as part of doc rebuild logic.
3. May run git rm or otherwise mutate the index.

The hook is async (& / nohup), so the commit returns immediately and you get the prompt back. The hook is still running.

When you then run git add -u, git stages every change to tracked files — including all the deletions/modifications the hook performed. When you --amend, those deletions become part of the commit. Force-push propagates them to the remote.

Trigger conditions

ALL of these together:

• Project has a post-commit hook that prints running ... in background, running ... in &, nohup, or similar — visible in git commit output.
• You commit, see the hook log line, and don't wait for the background process.
• You run git add -u (or git add . from repo root) before amending or before staging your next intentional change.
• Your git diff --staged --stat reports far more files than you touched.