refactor: remove bd mol catalog in favor of bd formula list (bd-ctmg)

- Delete mol_catalog.go (duplicate functionality)
- Update mol.go help text to point to bd formula list
- Update CLI_REFERENCE.md and MOLECULES.md docs
- Update deprecated template.go references

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

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

cmd/bd/mol.go

@@ -18,7 +18,6 @@ import (
 //   - Compound: Result of bonding
 //
 // Usage:
-//   bd mol catalog                        # List available protos
 //   bd mol show <id>                      # Show proto/molecule structure
 //   bd mol pour <id> --var key=value      # Instantiate proto → persistent mol
 //   bd mol wisp <id> --var key=value      # Instantiate proto → ephemeral wisp
@@ -48,14 +47,15 @@ The molecule metaphor:
   - Distilling extracts a proto from an ad-hoc epic
 
 Commands:
-  catalog    List available protos
   show       Show proto/molecule structure and variables
   pour       Instantiate proto as persistent mol (liquid phase)
   wisp       Instantiate proto as ephemeral wisp (vapor phase)
   bond       Polymorphic combine: proto+proto, proto+mol, mol+mol
   squash     Condense molecule to digest
   burn       Discard wisp
-  distill    Extract proto from ad-hoc epic`,
+  distill    Extract proto from ad-hoc epic
+
+Use "bd formula list" to list available formulas.`,
 }
 
 // =============================================================================

cmd/bd/mol_catalog.go

@@ -1,134 +0,0 @@
-package main
-
-import (
-	"fmt"
-	"sort"
-	"strings"
-
-	"github.com/spf13/cobra"
-	"github.com/steveyegge/beads/internal/ui"
-)
-
-// CatalogEntry represents a formula in the catalog.
-type CatalogEntry struct {
-	Name        string   `json:"name"`
-	Type        string   `json:"type"`
-	Description string   `json:"description"`
-	Source      string   `json:"source"`
-	Steps       int      `json:"steps"`
-	Vars        []string `json:"vars,omitempty"`
-}
-
-var molCatalogCmd = &cobra.Command{
-	Use:     "catalog",
-	Aliases: []string{"list", "ls"},
-	Short:   "List available molecule formulas",
-	Long: `List formulas available for bd mol pour / bd mol wisp.
-
-Formulas are ephemeral proto definitions stored as .formula.json files.
-They are cooked inline when pouring, never stored as database beads.
-
-Search paths (in priority order):
-  1. .beads/formulas/       (project-level)
-  2. ~/.beads/formulas/     (user-level)
-  3. ~/gt/.beads/formulas/  (Gas Town level)`,
-	Run: func(cmd *cobra.Command, args []string) {
-		typeFilter, _ := cmd.Flags().GetString("type")
-
-		// Get all search paths and scan for formulas
-		searchPaths := getFormulaSearchPaths()
-		seen := make(map[string]bool)
-		var entries []CatalogEntry
-
-		for _, dir := range searchPaths {
-			formulas, err := scanFormulaDir(dir)
-			if err != nil {
-				continue // Skip inaccessible directories
-			}
-
-			for _, f := range formulas {
-				if seen[f.Formula] {
-					continue // Skip shadowed formulas
-				}
-				seen[f.Formula] = true
-
-				// Apply type filter
-				if typeFilter != "" && string(f.Type) != typeFilter {
-					continue
-				}
-
-				// Extract variable names
-				var varNames []string
-				for name := range f.Vars {
-					varNames = append(varNames, name)
-				}
-				sort.Strings(varNames)
-
-				entries = append(entries, CatalogEntry{
-					Name:        f.Formula,
-					Type:        string(f.Type),
-					Description: truncateDescription(f.Description, 60),
-					Source:      f.Source,
-					Steps:       countSteps(f.Steps),
-					Vars:        varNames,
-				})
-			}
-		}
-
-		// Sort by name
-		sort.Slice(entries, func(i, j int) bool {
-			return entries[i].Name < entries[j].Name
-		})
-
-		if jsonOutput {
-			outputJSON(entries)
-			return
-		}
-
-		if len(entries) == 0 {
-			fmt.Println("No formulas found.")
-			fmt.Println("\nTo create a formula, write a .formula.json file:")
-			fmt.Println("  .beads/formulas/my-workflow.formula.json")
-			fmt.Println("\nOr distill from existing work:")
-			fmt.Println("  bd mol distill <epic-id> my-workflow")
-			fmt.Println("\nTo instantiate from formula:")
-			fmt.Println("  bd mol pour <formula-name> --var key=value      # persistent mol")
-			fmt.Println("  bd mol wisp <formula-name> --var key=value      # ephemeral wisp")
-			return
-		}
-
-		fmt.Printf("%s\n\n", ui.RenderPass("Formulas (for bd mol pour / bd mol wisp):"))
-
-		// Group by type for display
-		byType := make(map[string][]CatalogEntry)
-		for _, e := range entries {
-			byType[e.Type] = append(byType[e.Type], e)
-		}
-
-		// Print workflow types first (most common for pour/wisp)
-		typeOrder := []string{"workflow", "expansion", "aspect"}
-		for _, t := range typeOrder {
-			typeEntries := byType[t]
-			if len(typeEntries) == 0 {
-				continue
-			}
-
-			typeIcon := getTypeIcon(t)
-			fmt.Printf("%s %s:\n", typeIcon, strings.Title(t))
-
-			for _, e := range typeEntries {
-				varInfo := ""
-				if len(e.Vars) > 0 {
-					varInfo = fmt.Sprintf(" (vars: %s)", strings.Join(e.Vars, ", "))
-				}
-				fmt.Printf("  %s: %s%s\n", ui.RenderAccent(e.Name), e.Description, varInfo)
-			}
-			fmt.Println()
-		}
-	},
-}
-
-func init() {
-	molCatalogCmd.Flags().String("type", "", "Filter by formula type (workflow, expansion, aspect)")
-	molCmd.AddCommand(molCatalogCmd)
-}

cmd/bd/template.go

@@ -60,7 +60,7 @@ var templateCmd = &cobra.Command{
 	Use:        "template",
 	GroupID:    "setup",
 	Short:      "Manage issue templates",
-	Deprecated: "use 'bd mol' instead (mol catalog, mol show, mol bond)",
+	Deprecated: "use 'bd mol' instead (formula list, mol show, mol bond)",
 	Long: `Manage Beads templates for creating issue hierarchies.
 
 Templates are epics with the "template" label. They can have child issues
@@ -78,7 +78,7 @@ To use a template:
 var templateListCmd = &cobra.Command{
 	Use:        "list",
 	Short:      "List available templates",
-	Deprecated: "use 'bd mol catalog' instead",
+	Deprecated: "use 'bd formula list' instead",
 	Run: func(cmd *cobra.Command, args []string) {
 		ctx := rootCtx
 		var beadsTemplates []*types.Issue