When the database has orphaned dependencies or labels, the migration invariant check fails and prevents the database from opening. This creates a chicken-and-egg problem where bd doctor --fix cannot run. The new bd repair command: - Opens SQLite directly, bypassing invariant checks - Deletes orphaned dependencies (issue_id or depends_on_id not in issues) - Deletes orphaned labels (issue_id not in issues) - Runs WAL checkpoint to persist changes - Supports --dry-run to preview what would be cleaned 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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