feat(mol): spawn molecules as ephemeral by default (bd-2vh3.2)

Molecule spawning now creates ephemeral issues that can be bulk-deleted
when closed using `bd cleanup --ephemeral`. This supports the ephemeral
molecule workflow pattern where execution traces are cleaned up while
outcomes persist.

Changes:
- Add `ephemeral` parameter to cloneSubgraph() and spawnMolecule()
- mol spawn: ephemeral=true by default, add --persistent flag to opt out
- mol run: ephemeral=true (molecule execution)
- mol bond: ephemeral=true (bonded protos)
- template instantiate: ephemeral=false (deprecated, backwards compat)

This is Tier 1 of the ephemeral molecule workflow epic (bd-2vh3).

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

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

cmd/bd/mol.go

@@ -62,8 +62,9 @@ Commands:
 // spawnMolecule creates new issues from the proto with variable substitution.
 // This instantiates a proto (template) into a molecule (real issues).
 // Wraps cloneSubgraph from template.go and returns InstantiateResult.
-func spawnMolecule(ctx context.Context, s storage.Storage, subgraph *MoleculeSubgraph, vars map[string]string, assignee string, actorName string) (*InstantiateResult, error) {
+// If ephemeral is true, spawned issues are marked for bulk deletion when closed.
-	return cloneSubgraph(ctx, s, subgraph, vars, assignee, actorName)
+func spawnMolecule(ctx context.Context, s storage.Storage, subgraph *MoleculeSubgraph, vars map[string]string, assignee string, actorName string, ephemeral bool) (*InstantiateResult, error) {
+	return cloneSubgraph(ctx, s, subgraph, vars, assignee, actorName, ephemeral)
 }
 
 // printMoleculeTree prints the molecule structure as a tree

cmd/bd/mol_bond.go

@@ -283,8 +283,8 @@ func bondProtoMol(ctx context.Context, s storage.Storage, proto, mol *types.Issu
 		return nil, fmt.Errorf("missing required variables: %s (use --var)", strings.Join(missingVars, ", "))
 	}
 
-	// Spawn the proto
+	// Spawn the proto (ephemeral by default for molecule execution - bd-2vh3)
-	spawnResult, err := spawnMolecule(ctx, s, subgraph, vars, "", actorName)
+	spawnResult, err := spawnMolecule(ctx, s, subgraph, vars, "", actorName, true)
 	if err != nil {
 		return nil, fmt.Errorf("spawning proto: %w", err)
 	}

cmd/bd/mol_run.go

@@ -89,8 +89,8 @@ func runMolRun(cmd *cobra.Command, args []string) {
 		os.Exit(1)
 	}
 
-	// Spawn the molecule with actor as assignee
+	// Spawn the molecule with actor as assignee (ephemeral for cleanup - bd-2vh3)
-	result, err := spawnMolecule(ctx, store, subgraph, vars, actor, actor)
+	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)

cmd/bd/mol_spawn.go

@@ -53,6 +53,7 @@ func runMolSpawn(cmd *cobra.Command, args []string) {
 	assignee, _ := cmd.Flags().GetString("assignee")
 	attachFlags, _ := cmd.Flags().GetStringSlice("attach")
 	attachType, _ := cmd.Flags().GetString("attach-type")
+	persistent, _ := cmd.Flags().GetBool("persistent")
 
 	// Parse variables
 	vars := make(map[string]string)
@@ -181,7 +182,9 @@ func runMolSpawn(cmd *cobra.Command, args []string) {
 	}
 
 	// Clone the subgraph (spawn the molecule)
-	result, err := spawnMolecule(ctx, store, subgraph, vars, assignee, actor)
+	// Spawned molecules are ephemeral by default (bd-2vh3) - use --persistent to opt out
+	ephemeral := !persistent
+	result, err := spawnMolecule(ctx, store, subgraph, vars, assignee, actor, ephemeral)
 	if err != nil {
 		fmt.Fprintf(os.Stderr, "Error spawning molecule: %v\n", err)
 		os.Exit(1)
@@ -233,6 +236,7 @@ func init() {
 	molSpawnCmd.Flags().String("assignee", "", "Assign the root issue to this agent/user")
 	molSpawnCmd.Flags().StringSlice("attach", []string{}, "Proto to attach after spawning (repeatable)")
 	molSpawnCmd.Flags().String("attach-type", types.BondTypeSequential, "Bond type for attachments: sequential, parallel, or conditional")
+	molSpawnCmd.Flags().Bool("persistent", false, "Create non-ephemeral issues (default: ephemeral for cleanup)")
 
 	molCmd.AddCommand(molSpawnCmd)
 }

cmd/bd/template.go

@@ -292,8 +292,8 @@ Example:
 			return
 		}
 
-		// Clone the subgraph
+		// Clone the subgraph (deprecated command, non-ephemeral for backwards compatibility)
-		result, err := cloneSubgraph(ctx, store, subgraph, vars, assignee, actor)
+		result, err := cloneSubgraph(ctx, store, subgraph, vars, assignee, actor, false)
 		if err != nil {
 			fmt.Fprintf(os.Stderr, "Error instantiating template: %v\n", err)
 			os.Exit(1)
@@ -453,7 +453,8 @@ func substituteVariables(text string, vars map[string]string) string {
 
 // cloneSubgraph creates new issues from the template with variable substitution
 // If assignee is non-empty, it will be set on the root epic
-func cloneSubgraph(ctx context.Context, s storage.Storage, subgraph *TemplateSubgraph, vars map[string]string, assignee string, actorName string) (*InstantiateResult, error) {
+// If ephemeral is true, spawned issues are marked for bulk deletion when closed (bd-2vh3)
+func cloneSubgraph(ctx context.Context, s storage.Storage, subgraph *TemplateSubgraph, vars map[string]string, assignee string, actorName string, ephemeral bool) (*InstantiateResult, error) {
 	if s == nil {
 		return nil, fmt.Errorf("no database connection")
 	}
@@ -483,6 +484,7 @@ func cloneSubgraph(ctx context.Context, s storage.Storage, subgraph *TemplateSub
 				IssueType:          oldIssue.IssueType,
 				Assignee:           issueAssignee,
 				EstimatedMinutes:   oldIssue.EstimatedMinutes,
+				Ephemeral:          ephemeral, // bd-2vh3: mark for cleanup when closed
 				CreatedAt:          time.Now(),
 				UpdatedAt:          time.Now(),
 			}

cmd/bd/template_test.go

@@ -268,7 +268,7 @@ func TestCloneSubgraph(t *testing.T) {
 		}
 
 		vars := map[string]string{"version": "2.0.0"}
-		result, err := cloneSubgraph(ctx, s, subgraph, vars, "", "test-user")
+		result, err := cloneSubgraph(ctx, s, subgraph, vars, "", "test-user", false)
 		if err != nil {
 			t.Fatalf("cloneSubgraph failed: %v", err)
 		}
@@ -308,7 +308,7 @@ func TestCloneSubgraph(t *testing.T) {
 		}
 
 		vars := map[string]string{"service": "api-gateway"}
-		result, err := cloneSubgraph(ctx, s, subgraph, vars, "", "test-user")
+		result, err := cloneSubgraph(ctx, s, subgraph, vars, "", "test-user", false)
 		if err != nil {
 			t.Fatalf("cloneSubgraph failed: %v", err)
 		}
@@ -367,7 +367,7 @@ func TestCloneSubgraph(t *testing.T) {
 			t.Fatalf("loadTemplateSubgraph failed: %v", err)
 		}
 
-		result, err := cloneSubgraph(ctx, s, subgraph, nil, "", "test-user")
+		result, err := cloneSubgraph(ctx, s, subgraph, nil, "", "test-user", false)
 		if err != nil {
 			t.Fatalf("cloneSubgraph failed: %v", err)
 		}
@@ -402,7 +402,7 @@ func TestCloneSubgraph(t *testing.T) {
 		}
 
 		// Clone with assignee override
-		result, err := cloneSubgraph(ctx, s, subgraph, nil, "new-assignee", "test-user")
+		result, err := cloneSubgraph(ctx, s, subgraph, nil, "new-assignee", "test-user", false)
 		if err != nil {
 			t.Fatalf("cloneSubgraph failed: %v", err)
 		}