Remove bd mol run - orchestration belongs in gt

bd mol run was a convenience combo (pour + assign + pin + start) that
felt like orchestration but lived in the data layer. This blurred the
architectural boundary between bd (data) and gt (orchestration).

- Delete cmd/bd/mol_run.go entirely
- Update mol.go help text to remove run reference
- Update mol_current.go to suggest bd pour instead

gt spawn will implement the orchestration combo by calling the atomic
bd commands (pour, update, pin) directly.

Closes bd-00u3

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

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

cmd/bd/mol.go

@@ -51,7 +51,6 @@ Commands:
   catalog  List available protos
   show     Show proto/molecule structure and variables
   bond     Polymorphic combine: proto+proto, proto+mol, mol+mol
-  run      Pour + assign + pin for durable execution
   distill  Extract proto from ad-hoc epic
 
 See also:

cmd/bd/mol_current.go

@@ -100,7 +100,7 @@ The output shows all steps with status indicators:
 				}
 				fmt.Println(".")
 				fmt.Println("\nTo start work on a molecule:")
-				fmt.Println("  bd mol run <proto-id>       # Spawn and start a new molecule")
+				fmt.Println("  bd pour <proto-id>          # Instantiate a molecule from template")
 				fmt.Println("  bd update <step-id> --status in_progress  # Claim a step")
 				return
 			}

cmd/bd/mol_run.go

@@ -1,177 +0,0 @@
-package main
-
-import (
-	"fmt"
-	"os"
-	"strings"
-
-	"github.com/spf13/cobra"
-	"github.com/steveyegge/beads/internal/beads"
-	"github.com/steveyegge/beads/internal/storage/sqlite"
-	"github.com/steveyegge/beads/internal/types"
-	"github.com/steveyegge/beads/internal/ui"
-)
-
-var molRunCmd = &cobra.Command{
-	Use:   "run <proto-id-or-title>",
-	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
-
-The proto can be specified by ID or title. Title matching is case-insensitive
-and supports partial matches (e.g., "polecat" matches "mol-polecat-work").
-
-After a crash or session reset, the pinned root issue ensures the agent
-can resume from where it left off by checking 'bd ready'.
-
-The --template-db flag enables cross-database spawning: read templates from
-one database (e.g., main) while writing spawned instances to another (e.g., wisp).
-This is essential for wisp molecule spawning where templates exist in the main
-database but instances should be ephemeral.
-
-Example:
-  bd mol run mol-polecat-work --var issue=gt-xxx     # By title
-  bd mol run gt-lwuu --var issue=gt-xxx              # By ID
-  bd mol run polecat --var issue=gt-xxx              # By partial title
-  bd --db .beads-wisp/beads.db mol run mol-patrol --template-db .beads/beads.db`,
-	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")
-	templateDB, _ := cmd.Flags().GetString("template-db")
-
-	// 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]
-	}
-
-	// Determine which store to use for reading the template
-	// If --template-db is set, open a separate connection for reading the template
-	// This enables cross-database spawning (read from main, write to wisp)
-	//
-	// Auto-discovery: if --db contains ".beads-wisp" (wisp storage) but --template-db
-	// is not set, automatically use the main database for templates. This handles the
-	// common case of spawning patrol molecules from main DB into wisp storage.
-	templateStore := store
-	if templateDB == "" && strings.Contains(dbPath, ".beads-wisp") {
-		// Auto-discover main database for templates
-		templateDB = beads.FindDatabasePath()
-		if templateDB == "" {
-			fmt.Fprintf(os.Stderr, "Error: cannot find main database for templates\n")
-			fmt.Fprintf(os.Stderr, "Hint: specify --template-db explicitly\n")
-			os.Exit(1)
-		}
-	}
-	if templateDB != "" {
-		var err error
-		templateStore, err = sqlite.NewWithTimeout(ctx, templateDB, lockTimeout)
-		if err != nil {
-			fmt.Fprintf(os.Stderr, "Error opening template database %s: %v\n", templateDB, err)
-			os.Exit(1)
-		}
-		defer func() { _ = templateStore.Close() }()
-	}
-
-	// Resolve molecule ID from template store (supports both ID and title - bd-drcx)
-	moleculeID, err := resolveProtoIDOrTitle(ctx, templateStore, args[0])
-	if err != nil {
-		fmt.Fprintf(os.Stderr, "Error resolving molecule %s: %v\n", args[0], err)
-		os.Exit(1)
-	}
-
-	// Load the molecule subgraph from template store
-	subgraph, err := loadTemplateSubgraph(ctx, templateStore, 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 (wisp for cleanup - bd-2vh3)
-	result, err := spawnMolecule(ctx, store, subgraph, vars, actor, actor, true)
-	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)
-}
-
-func init() {
-	molRunCmd.Flags().StringSlice("var", []string{}, "Variable substitution (key=value)")
-	molRunCmd.Flags().String("template-db", "", "Database to read templates from (enables cross-database spawning)")
-
-	molCmd.AddCommand(molRunCmd)
-}