Remove deprecated builtin molecules infrastructure

- Delete builtin_molecules.go (empty stubs)
- Remove `mol export` command (exported 0 molecules)
- Clean dead code in catalog.go iterating empty BuiltinMolecules()
- Update docs to reference formula files instead of Go code

Molecules are now defined as .beads/formulas/*.formula.json files
and cooked into proto beads via `bd cook`.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

docs/architecture.md

@@ -705,9 +705,9 @@ gt spawn --issue gt-xyz --molecule mol-engineer-in-box
 - Each instance has an `instantiated_from` edge to the source molecule
 - Enables querying: "show all instances of mol-engineer-in-box"
 
-### Built-in Molecules
+### Standard Molecules
 
-Gas Town ships with three built-in molecules:
+Gas Town includes formula files (`.beads/formulas/`) for standard molecules:
 
 **mol-engineer-in-box** (5 steps):
 ```
@@ -727,9 +727,9 @@ investigate → document
 ```
 Exploration workflow for understanding problems.
 
-Seed built-in molecules with:
+Cook formula files into proto beads:
 ```bash
-gt molecule seed
+bd cook <formula-id>
 ```
 
 ### Usage