- 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 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>