Implements Phase 1 of bd-56 (Repair Commands & AI-Assisted Tooling): New commands: - bd repair-deps: Find and fix orphaned dependency references - bd detect-pollution: Detect test issues using pattern matching - bd validate: Comprehensive health check (orphans, duplicates, pollution) Features: - JSON output support for all commands - Safe deletion with backup for detect-pollution - Auto-fix support for orphaned dependencies - Direct storage access (requires BEADS_NO_DAEMON=1) Closes bd-56 (Phase 1 complete) Related: bd-103, bd-105, bd-106 Amp-Thread-ID: https://ampcode.com/threads/T-5822c6d2-d645-4043-9a8d-3c51ac93bbb7 Co-authored-by: Amp <amp@ampcode.com>