Major refactor of molecular chemistry to make protos ephemeral:
- Formulas are now cooked directly to in-memory TemplateSubgraph
- No more proto beads stored in the database
Changes:
- cook.go: Add cookFormulaToSubgraph() and resolveAndCookFormula()
for in-memory formula cooking
- template.go: Add VarDefs field to TemplateSubgraph for default
value handling, add extractRequiredVariables() and
applyVariableDefaults() helpers
- pour.go: Try formula loading first for any name (not just mol-)
- wisp.go: Same pattern as pour
- mol_bond.go: Use resolveOrCookToSubgraph() for in-memory subgraphs
- mol_catalog.go: List formulas from disk instead of DB proto beads
- mol_distill.go: Output .formula.json files instead of proto beads
Flow: Formula (.formula.json) -> pour/wisp (cook inline) -> Mol/Wisp
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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