Steve Yegge f3c663d31c feat: add bd doctor --deep for full graph integrity validation (bd-cwpl) ...

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.

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

2025-12-28 02:13:34 -08:00

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