Fix bd-51: Add git hooks to eliminate auto-flush race condition

- Added --flush-only flag to bd sync command
- Created pre-commit hook to flush pending changes before commit
- Created post-merge hook to import changes after pull/merge
- Added install script for easy setup
- Updated AGENTS.md with git hooks workflow
- Resolves race condition where daemon auto-flush fires after commit

Amp-Thread-ID: https://ampcode.com/threads/T-00b80d3a-4194-4c75-a60e-25a318cf9f91
Co-authored-by: Amp <amp@ampcode.com>

AGENTS.md

@@ -344,7 +344,24 @@ git pull  # bd commands will auto-import the updated JSONL
 bd ready  # Fresh data from git!
 ```
 
-**Optional**: Use the git hooks in `examples/git-hooks/` for immediate export (no 5-second wait) and guaranteed import after git operations. Not required with auto-sync enabled.
+**Recommended**: Install git hooks to eliminate the race condition between auto-flush and commits:
+
+```bash
+# One-time setup
+./examples/git-hooks/install.sh
+```
+
+This installs:
+- **pre-commit** - Flushes pending changes immediately before commit (eliminates 5-second wait)
+- **post-merge** - Imports updated JSONL after pull/merge (guaranteed sync)
+
+Benefits:
+- ✅ No more dirty working tree after commits
+- ✅ Immediate flush (no 5-second debounce wait)
+- ✅ Automatic collision resolution on merge
+- ✅ Works alongside auto-sync
+
+See [examples/git-hooks/README.md](examples/git-hooks/README.md) for details.
 
 ### Git Worktrees