Adds the gt molecule seed subcommand that creates built-in molecule
definitions (engineer-in-box, quick-fix, research) in the beads database.
- Brings molecule.go from main (with list, show, parse, instantiate, instances)
- Adds builtin_molecules.go with 3 built-in workflow templates
- SeedBuiltinMolecules() writes directly to JSONL to bypass bd CLI type validation
- Molecules use well-known IDs (mol-engineer-in-box, mol-quick-fix, mol-research)
- Command is idempotent - skips molecules that already exist
Note: bd CLI does not yet support molecule as a valid issue type.
Filed beads-1 to add molecule type support. Until then, use bd --no-db.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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