refactor(mol): split 1218-line mol.go into subcommand files

Split monolithic mol.go into 7 focused files:
- mol.go (76 lines): root command, shared constants
- mol_catalog.go (83): bd mol catalog
- mol_show.go (76): bd mol show
- mol_spawn.go (238): bd mol spawn
- mol_run.go (137): bd mol run
- mol_bond.go (382): bd mol bond + helpers
- mol_distill.go (307): bd mol distill + helpers

Closes bd-cnwx

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

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

cmd/bd/mol_catalog.go

@@ -0,0 +1,83 @@
+package main
+
+import (
+	"encoding/json"
+	"fmt"
+	"os"
+	"strings"
+
+	"github.com/spf13/cobra"
+	"github.com/steveyegge/beads/internal/rpc"
+	"github.com/steveyegge/beads/internal/types"
+	"github.com/steveyegge/beads/internal/ui"
+)
+
+var molCatalogCmd = &cobra.Command{
+	Use:     "catalog",
+	Aliases: []string{"list", "ls"},
+	Short:   "List available molecules",
+	Run: func(cmd *cobra.Command, args []string) {
+		ctx := rootCtx
+		var molecules []*types.Issue
+
+		if daemonClient != nil {
+			resp, err := daemonClient.List(&rpc.ListArgs{})
+			if err != nil {
+				fmt.Fprintf(os.Stderr, "Error loading molecules: %v\n", err)
+				os.Exit(1)
+			}
+			var allIssues []*types.Issue
+			if err := json.Unmarshal(resp.Data, &allIssues); err == nil {
+				for _, issue := range allIssues {
+					for _, label := range issue.Labels {
+						if label == MoleculeLabel {
+							molecules = append(molecules, issue)
+							break
+						}
+					}
+				}
+			}
+		} else if store != nil {
+			var err error
+			molecules, err = store.GetIssuesByLabel(ctx, MoleculeLabel)
+			if err != nil {
+				fmt.Fprintf(os.Stderr, "Error loading molecules: %v\n", err)
+				os.Exit(1)
+			}
+		} else {
+			fmt.Fprintf(os.Stderr, "Error: no database connection\n")
+			os.Exit(1)
+		}
+
+		if jsonOutput {
+			outputJSON(molecules)
+			return
+		}
+
+		if len(molecules) == 0 {
+			fmt.Println("No protos available.")
+			fmt.Println("\nTo create a proto:")
+			fmt.Println("  1. Create an epic with child issues")
+			fmt.Println("  2. Add the 'template' label: bd label add <epic-id> template")
+			fmt.Println("  3. Use {{variable}} placeholders in titles/descriptions")
+			fmt.Println("\nTo spawn (instantiate) a molecule from a proto:")
+			fmt.Println("  bd mol spawn <id> --var key=value")
+			return
+		}
+
+		fmt.Printf("%s\n", ui.RenderPass("Protos (for bd mol spawn):"))
+		for _, mol := range molecules {
+			vars := extractVariables(mol.Title + " " + mol.Description)
+			varStr := ""
+			if len(vars) > 0 {
+				varStr = fmt.Sprintf(" (vars: %s)", strings.Join(vars, ", "))
+			}
+			fmt.Printf("  %s: %s%s\n", ui.RenderAccent(mol.ID), mol.Title, varStr)
+		}
+		fmt.Println()
+	},
+}
+
+func init() {
+	molCmd.AddCommand(molCatalogCmd)
+}