Bug: pre-commit stash pop creates merge conflicts in working tree

[mrveiss]

Problem

Pre-commit's git stash push/pop cycle corrupted 6 working tree files with merge conflict markers during the #2383 commit. The committed content was correct (hooks passed), but the unstaged working copies had <<<<<<< HEAD conflicts requiring manual resolution.

Discovered During

Committing #2383 — after successful commit, agent_seeder.py, slm_client.py, manager.py, model_constants.py, seed_agents.py, and ssot_config.py all had conflict markers in the working tree.

Root Cause

Known issue #1503 (pre-commit stash risk). The PostToolUse hook (Black + isort) modifies files between the pre-commit stash push and pop, causing the pop to conflict.

Workaround Applied

git checkout HEAD -- <files> to restore committed versions.

Proposed Fix

Add a post-commit hook or adjust the PostToolUse hook workflow:

1. After commit success, run git checkout HEAD -- $(git diff --name-only) to auto-heal
2. Or: disable the PostToolUse auto-format hook and rely solely on pre-commit hooks

Related

#1503 (pre-commit stash risk documentation)

Impact

Medium — requires manual cleanup after every commit that touches files also modified by PostToolUse hook.

[mrveiss]

Fixed in PR #2486 (merged). Added post-commit hook to auto-heal stash-pop conflict markers.