- Updated molecules.md to reflect actual JSONL storage format
- Updated architecture.md molecule sections with ASCII diagrams
- Replaced markdown "## Step:" format with tree diagrams
- Changed plugin system from directory-based to molecule-based
- Plugins now use labels for metadata (tier, phase, role)
- Mol Mall distributes molecules.jsonl fragments
Related: gt-u818, gt-9za0
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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