065-rebuild: re-extract all sources through current lenses

[ahoward]

Summary

brane rebuild — clear extracted knowledge and re-digest all stashed sources through current active lenses. The nuclear refresh button.

Why

When you change lenses (activate security, deactivate performance), your existing knowledge was extracted under the old lens configuration. Rebuild re-processes everything with the new perspective. Bunny has this and it's essential after lens changes.

What

CLI

brane rebuild                  # re-digest all sources
brane rebuild --dry-run        # show what would happen
brane rebuild --lens security  # rebuild through a specific lens

Flow

1. List all stashed sources (from body.db digest history)
2. Dry-run: show count and total size
3. Confirm (destructive: clears extracted concepts/edges/episodes from digested sources)
4. For each source chronologically:
   • Load raw stashed content
   • Run through current digest pipeline with active lenses
   • Apply results
5. Each source sees accumulated state from previous sources (order matters)

Key Detail

Rebuild doesn't delete manually-created concepts/edges/episodes — only those tagged with a source provenance from digest. Manual knowledge survives.

MCP Tool

rebuild: { dry_run?: boolean, lens?: string }

Depends On

• 059-digest: consume URLs, files, directories, stdin into knowledge graph #82 (059-digest) — rebuild calls digest for each source
• 063-active-lenses: lens prompts that shape LLM extraction #86 (063-active-lenses) — rebuild is motivated by lens changes

Acceptance

• Clears digest-sourced knowledge
• Re-digests all stashed sources chronologically
• Preserves manually-created knowledge
• Dry-run shows what would happen
• Order-dependent accumulation (each source sees previous results)
• MCP tool exposed
• Spike test passes