Add a --deep flag to bd doctor that runs comprehensive graph integrity
checks on the beads database:
- Parent consistency: verify parent-child deps point to existing issues
- Dependency integrity: all dependencies reference valid issues
- Epic completeness: find epics ready to close (all children closed)
- Agent bead integrity: validate agent beads have valid state values
- Mail thread integrity: verify thread_id references exist
- Molecule integrity: check molecules have valid parent-child structures
The deep validation mode warns about potential slowness on large databases
and provides both human-readable and JSON output formats.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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