The sync.branch workflow copies JSONL to main working dir without committing, which blocked bd sync --merge (required clean working dir). Changes: - Exclude .beads/ from dirty check in mergeSyncBranch - Restore .beads/ to HEAD before merge to prevent conflicts 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>