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

docs/polecat-wisp-architecture.md

@@ -285,8 +285,8 @@ bd mol detach
 
 ### Phase 1: Core Infrastructure (P0)
 
-1. Add `mol-crew-session` to builtin_molecules.go
-2. Add `mol-polecat-session` to builtin_molecules.go
+1. Create `mol-crew-session.formula.json` in `.beads/formulas/`
+2. Create `mol-polecat-session.formula.json` in `.beads/formulas/`
 3. Add wisp attachment mechanism to beads
 4. Update spawn.go for polecat session wisps
 

internal/beads/builtin_molecules.go

@@ -1,28 +0,0 @@
-// Package beads provides a wrapper for the bd (beads) CLI.
-package beads
-
-// BuiltinMolecule defines a built-in molecule template.
-// Deprecated: Molecules are now defined as formula files in .beads/formulas/
-// and cooked into proto beads via `bd cook`. This type remains for backward
-// compatibility but is no longer used.
-type BuiltinMolecule struct {
-	ID          string // Well-known ID (e.g., "mol-engineer-in-box")
-	Title       string
-	Description string
-}
-
-// BuiltinMolecules returns all built-in molecule definitions.
-// Deprecated: Molecules are now defined as formula files (.beads/formulas/*.formula.json)
-// and cooked into proto beads via `bd cook`. This function returns an empty slice.
-// Use `bd cook` to create proto beads from formulas instead.
-func BuiltinMolecules() []BuiltinMolecule {
-	return []BuiltinMolecule{}
-}
-
-// SeedBuiltinMolecules is deprecated and does nothing.
-// Molecules are now created by cooking formula files with `bd cook`.
-// This function remains for backward compatibility with existing installations.
-func (b *Beads) SeedBuiltinMolecules() (int, error) {
-	// No-op: formulas are cooked on-demand, not seeded at install time
-	return 0, nil
-}

internal/beads/catalog.go

@@ -16,15 +16,14 @@ type CatalogMolecule struct {
 	ID          string `json:"id"`
 	Title       string `json:"title"`
 	Description string `json:"description"`
-	Source      string `json:"source,omitempty"` // "builtin", "town", "rig", "project"
+	Source      string `json:"source,omitempty"` // "town", "rig", "project"
 }
 
 // MoleculeCatalog provides hierarchical molecule template loading.
 // It loads molecules from multiple sources in priority order:
-// 1. Built-in molecules (shipped with the binary)
-// 2. Town-level: <town>/.beads/molecules.jsonl
-// 3. Rig-level: <town>/<rig>/.beads/molecules.jsonl
-// 4. Project-level: .beads/molecules.jsonl in current directory
+// 1. Town-level: <town>/.beads/molecules.jsonl
+// 2. Rig-level: <town>/<rig>/.beads/molecules.jsonl
+// 3. Project-level: .beads/molecules.jsonl in current directory
 //
 // Later sources can override earlier ones by ID.
 type MoleculeCatalog struct {
@@ -46,21 +45,11 @@ func NewMoleculeCatalog() *MoleculeCatalog {
 //   - rigPath: Path to the rig directory (e.g., ~/gt/gastown). Empty to skip rig-level.
 //   - projectPath: Path to the project directory. Empty to skip project-level.
 //
-// Built-in molecules are always loaded first.
+// Molecules are loaded from town, rig, and project levels (no builtin molecules).
 func LoadCatalog(townRoot, rigPath, projectPath string) (*MoleculeCatalog, error) {
 	catalog := NewMoleculeCatalog()
 
-	// 1. Load built-in molecules
-	for _, builtin := range BuiltinMolecules() {
-		catalog.Add(&CatalogMolecule{
-			ID:          builtin.ID,
-			Title:       builtin.Title,
-			Description: builtin.Description,
-			Source:      "builtin",
-		})
-	}
-
-	// 2. Load town-level molecules
+	// 1. Load town-level molecules
 	if townRoot != "" {
 		townMolsPath := filepath.Join(townRoot, ".beads", "molecules.jsonl")
 		if err := catalog.LoadFromFile(townMolsPath, "town"); err != nil && !os.IsNotExist(err) {
@@ -68,7 +57,7 @@ func LoadCatalog(townRoot, rigPath, projectPath string) (*MoleculeCatalog, error
 		}
 	}
 
-	// 3. Load rig-level molecules
+	// 2. Load rig-level molecules
 	if rigPath != "" {
 		rigMolsPath := filepath.Join(rigPath, ".beads", "molecules.jsonl")
 		if err := catalog.LoadFromFile(rigMolsPath, "rig"); err != nil && !os.IsNotExist(err) {
@@ -76,7 +65,7 @@ func LoadCatalog(townRoot, rigPath, projectPath string) (*MoleculeCatalog, error
 		}
 	}
 
-	// 4. Load project-level molecules
+	// 3. Load project-level molecules
 	if projectPath != "" {
 		projectMolsPath := filepath.Join(projectPath, ".beads", "molecules.jsonl")
 		if err := catalog.LoadFromFile(projectMolsPath, "project"); err != nil && !os.IsNotExist(err) {
@@ -196,17 +185,3 @@ func (mol *CatalogMolecule) ToIssue() *Issue {
 	}
 }
 
-// ExportBuiltinMolecules writes all built-in molecules to a JSONL file.
-// This is useful for creating a base molecules.jsonl file.
-func ExportBuiltinMolecules(path string) error {
-	catalog := NewMoleculeCatalog()
-	for _, builtin := range BuiltinMolecules() {
-		catalog.Add(&CatalogMolecule{
-			ID:          builtin.ID,
-			Title:       builtin.Title,
-			Description: builtin.Description,
-			Source:      "builtin",
-		})
-	}
-	return catalog.SaveToFile(path)
-}

internal/cmd/molecule.go

@@ -80,22 +80,6 @@ Use --db to show only database molecules.`,
 	RunE: runMoleculeList,
 }
 
-var moleculeExportCmd = &cobra.Command{
-	Use:   "export <path>",
-	Short: "Export built-in molecules to JSONL",
-	Long: `Export built-in molecule templates to a JSONL file.
-
-This creates a molecules.jsonl file containing all built-in molecules.
-You can place this in:
-- <town>/.beads/molecules.jsonl (town-level)
-- <rig>/.beads/molecules.jsonl (rig-level)
-- .beads/molecules.jsonl (project-level)
-
-The file can be edited to customize or add new molecules.`,
-	Args: cobra.ExactArgs(1),
-	RunE: runMoleculeExport,
-}
-
 var moleculeShowCmd = &cobra.Command{
 	Use:   "show <id>",
 	Short: "Show molecule with parsed steps",
@@ -408,7 +392,6 @@ func init() {
 	moleculeCmd.AddCommand(moleculeParseCmd)
 	moleculeCmd.AddCommand(moleculeInstantiateCmd)
 	moleculeCmd.AddCommand(moleculeInstancesCmd)
-	moleculeCmd.AddCommand(moleculeExportCmd)
 	moleculeCmd.AddCommand(moleculeProgressCmd)
 	moleculeCmd.AddCommand(moleculeAttachCmd)
 	moleculeCmd.AddCommand(moleculeDetachCmd)

internal/cmd/molecule_list.go

@@ -130,19 +130,6 @@ func runMoleculeList(cmd *cobra.Command, args []string) error {
 	return nil
 }
 
-func runMoleculeExport(cmd *cobra.Command, args []string) error {
-	path := args[0]
-
-	if err := beads.ExportBuiltinMolecules(path); err != nil {
-		return fmt.Errorf("exporting molecules: %w", err)
-	}
-
-	fmt.Printf("%s Exported %d built-in molecules to %s\n",
-		style.Bold.Render("✓"), len(beads.BuiltinMolecules()), path)
-
-	return nil
-}
-
 func runMoleculeShow(cmd *cobra.Command, args []string) error {
 	molID := args[0]
 

internal/rig/manager.go

@@ -478,7 +478,6 @@ func (m *Manager) createRoleCLAUDEmd(workspacePath string, role string, rigName
 // These molecules define the work loops for Deacon, Witness, and Refinery roles.
 func (m *Manager) seedPatrolMolecules(rigPath string) error {
 	// Use bd command to seed molecules (more reliable than internal API)
-	// The bd mol seed command creates built-in molecules if they don't exist
 	cmd := exec.Command("bd", "mol", "seed", "--patrol")
 	cmd.Dir = rigPath
 	if err := cmd.Run(); err != nil {
@@ -491,7 +490,7 @@ func (m *Manager) seedPatrolMolecules(rigPath string) error {
 
 // seedPatrolMoleculesManually creates patrol molecules using bd create commands.
 func (m *Manager) seedPatrolMoleculesManually(rigPath string) error {
-	// Patrol molecule definitions (subset of builtin_molecules.go for seeding)
+	// Patrol molecule definitions for seeding
 	patrolMols := []struct {
 		title string
 		desc  string