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_run.go

@@ -0,0 +1,137 @@
+package main
+
+import (
+	"fmt"
+	"os"
+	"strings"
+
+	"github.com/spf13/cobra"
+	"github.com/steveyegge/beads/internal/types"
+	"github.com/steveyegge/beads/internal/ui"
+	"github.com/steveyegge/beads/internal/utils"
+)
+
+var molRunCmd = &cobra.Command{
+	Use:   "run <proto-id>",
+	Short: "Spawn proto and start execution (spawn + assign + pin)",
+	Long: `Run a molecule by spawning a proto and setting up for durable execution.
+
+This command:
+  1. Spawns the molecule (creates issues from proto template)
+  2. Assigns the root issue to the caller
+  3. Sets root status to in_progress
+  4. Pins the root issue for session recovery
+
+After a crash or session reset, the pinned root issue ensures the agent
+can resume from where it left off by checking 'bd ready'.
+
+Example:
+  bd mol run mol-version-bump --var version=1.2.0
+  bd mol run bd-qqc --var version=0.32.0 --var date=2025-01-01`,
+	Args: cobra.ExactArgs(1),
+	Run:  runMolRun,
+}
+
+func runMolRun(cmd *cobra.Command, args []string) {
+	CheckReadonly("mol run")
+
+	ctx := rootCtx
+
+	// mol run requires direct store access
+	if store == nil {
+		if daemonClient != nil {
+			fmt.Fprintf(os.Stderr, "Error: mol run requires direct database access\n")
+			fmt.Fprintf(os.Stderr, "Hint: use --no-daemon flag: bd --no-daemon mol run %s ...\n", args[0])
+		} else {
+			fmt.Fprintf(os.Stderr, "Error: no database connection\n")
+		}
+		os.Exit(1)
+	}
+
+	varFlags, _ := cmd.Flags().GetStringSlice("var")
+
+	// Parse variables
+	vars := make(map[string]string)
+	for _, v := range varFlags {
+		parts := strings.SplitN(v, "=", 2)
+		if len(parts) != 2 {
+			fmt.Fprintf(os.Stderr, "Error: invalid variable format '%s', expected 'key=value'\n", v)
+			os.Exit(1)
+		}
+		vars[parts[0]] = parts[1]
+	}
+
+	// Resolve molecule ID
+	moleculeID, err := utils.ResolvePartialID(ctx, store, args[0])
+	if err != nil {
+		fmt.Fprintf(os.Stderr, "Error resolving molecule ID %s: %v\n", args[0], err)
+		os.Exit(1)
+	}
+
+	// Load the molecule subgraph
+	subgraph, err := loadTemplateSubgraph(ctx, store, moleculeID)
+	if err != nil {
+		fmt.Fprintf(os.Stderr, "Error loading molecule: %v\n", err)
+		os.Exit(1)
+	}
+
+	// Check for missing variables
+	requiredVars := extractAllVariables(subgraph)
+	var missingVars []string
+	for _, v := range requiredVars {
+		if _, ok := vars[v]; !ok {
+			missingVars = append(missingVars, v)
+		}
+	}
+	if len(missingVars) > 0 {
+		fmt.Fprintf(os.Stderr, "Error: missing required variables: %s\n", strings.Join(missingVars, ", "))
+		fmt.Fprintf(os.Stderr, "Provide them with: --var %s=<value>\n", missingVars[0])
+		os.Exit(1)
+	}
+
+	// Spawn the molecule with actor as assignee
+	result, err := spawnMolecule(ctx, store, subgraph, vars, actor, actor)
+	if err != nil {
+		fmt.Fprintf(os.Stderr, "Error spawning molecule: %v\n", err)
+		os.Exit(1)
+	}
+
+	// Update root issue: set status=in_progress and pinned=true
+	rootID := result.NewEpicID
+	updates := map[string]interface{}{
+		"status": string(types.StatusInProgress),
+		"pinned": true,
+	}
+	if err := store.UpdateIssue(ctx, rootID, updates, actor); err != nil {
+		fmt.Fprintf(os.Stderr, "Error updating root issue: %v\n", err)
+		os.Exit(1)
+	}
+
+	// Schedule auto-flush
+	markDirtyAndScheduleFlush()
+
+	if jsonOutput {
+		outputJSON(map[string]interface{}{
+			"root_id":    rootID,
+			"created":    result.Created,
+			"id_mapping": result.IDMapping,
+			"pinned":     true,
+			"status":     "in_progress",
+			"assignee":   actor,
+		})
+		return
+	}
+
+	fmt.Printf("%s Molecule running: created %d issues\n", ui.RenderPass("✓"), result.Created)
+	fmt.Printf("  Root issue: %s (pinned, in_progress)\n", rootID)
+	fmt.Printf("  Assignee: %s\n", actor)
+	fmt.Println("\nNext steps:")
+	fmt.Printf("  bd ready                # Find unblocked work in this molecule\n")
+	fmt.Printf("  bd show %s       # View molecule status\n", rootID[:8])
+}
+
+func init() {
+	molRunCmd.Flags().StringSlice("var", []string{}, "Variable substitution (key=value)")
+
+	molCmd.AddCommand(molRunCmd)
+}