feat(molecules): add bd molecule commands and template protection (beads-1ra)

- Add `bd molecule list` to list template molecules
- Add `bd molecule show` to show molecule details
- Add `bd molecule instantiate` to create work items from templates
- Exclude templates from `bd list` by default (use --include-templates)
- Reject mutations (update/close/delete) to template issues
- Add IncludeTemplates to RPC ListArgs for daemon mode

Templates are marked with is_template=true and are read-only.
Use `bd molecule instantiate` to create editable work items.

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

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

cmd/bd/list.go

@@ -141,6 +141,9 @@ var listCmd = &cobra.Command{
 		pinnedFlag, _ := cmd.Flags().GetBool("pinned")
 		noPinnedFlag, _ := cmd.Flags().GetBool("no-pinned")
 
+		// Template filtering (beads-1ra)
+		includeTemplates, _ := cmd.Flags().GetBool("include-templates")
+
 		// Use global jsonOutput set by PersistentPreRun
 
 		// Normalize labels: trim, dedupe, remove empty
@@ -290,6 +293,13 @@ var listCmd = &cobra.Command{
 			filter.Pinned = &pinned
 		}
 
+		// Template filtering (beads-1ra): exclude templates by default
+		// Use --include-templates to show all issues including templates
+		if !includeTemplates {
+			isTemplate := false
+			filter.IsTemplate = &isTemplate
+		}
+
 		// Check database freshness before reading (bd-2q6d, bd-c4rq)
 		// Skip check when using daemon (daemon auto-imports on staleness)
 		ctx := rootCtx
@@ -368,6 +378,9 @@ var listCmd = &cobra.Command{
 			// Pinned filtering (bd-p8e)
 			listArgs.Pinned = filter.Pinned
 
+			// Template filtering (beads-1ra)
+			listArgs.IncludeTemplates = includeTemplates
+
 			 resp, err := daemonClient.List(listArgs)
 			if err != nil {
 				fmt.Fprintf(os.Stderr, "Error: %v\n", err)
@@ -585,6 +598,9 @@ func init() {
 	listCmd.Flags().Bool("pinned", false, "Show only pinned issues")
 	listCmd.Flags().Bool("no-pinned", false, "Exclude pinned issues")
 
+	// Template filtering (beads-1ra): exclude templates by default
+	listCmd.Flags().Bool("include-templates", false, "Include template molecules in output")
+
 	// Note: --json flag is defined as a persistent flag in main.go, not here
 	rootCmd.AddCommand(listCmd)
 }

cmd/bd/molecule.go

@@ -0,0 +1,355 @@
+package main
+
+import (
+	"encoding/json"
+	"fmt"
+	"os"
+	"time"
+
+	"github.com/fatih/color"
+	"github.com/spf13/cobra"
+	"github.com/steveyegge/beads/internal/hooks"
+	"github.com/steveyegge/beads/internal/rpc"
+	"github.com/steveyegge/beads/internal/types"
+)
+
+var moleculeCmd = &cobra.Command{
+	Use:   "molecule",
+	Short: "Manage template molecules",
+	Long: `Manage template molecules for issue instantiation.
+
+Molecules are template issues that can be instantiated to create work items.
+They are stored in molecules.jsonl and marked with is_template=true.
+
+Examples:
+  bd molecule list                    # List all available molecules
+  bd molecule show mol-123            # Show details of a molecule
+`,
+}
+
+var moleculeListCmd = &cobra.Command{
+	Use:   "list",
+	Short: "List available molecules",
+	Long: `List all available template molecules.
+
+Templates are read-only issues that can be instantiated to create work items.
+Use --all to include closed molecules.
+
+Examples:
+  bd molecule list                    # List open molecules
+  bd molecule list --all              # List all molecules including closed
+`,
+	Run: func(cmd *cobra.Command, args []string) {
+		showAll, _ := cmd.Flags().GetBool("all")
+
+		ctx := rootCtx
+		if daemonClient == nil {
+			if err := ensureDatabaseFresh(ctx); err != nil {
+				fmt.Fprintf(os.Stderr, "Error: %v\n", err)
+				os.Exit(1)
+			}
+		}
+
+		// Build filter for template molecules
+		isTemplate := true
+		filter := types.IssueFilter{
+			IsTemplate: &isTemplate,
+		}
+
+		if !showAll {
+			// Default to non-closed
+			status := types.StatusOpen
+			filter.Status = &status
+		}
+
+		// Direct mode only for now
+		if store == nil {
+			fmt.Fprintf(os.Stderr, "Error: database not available\n")
+			os.Exit(1)
+		}
+
+		issues, err := store.SearchIssues(ctx, "", filter)
+		if err != nil {
+			fmt.Fprintf(os.Stderr, "Error: %v\n", err)
+			os.Exit(1)
+		}
+
+		if len(issues) == 0 {
+			fmt.Println("No molecules found")
+			return
+		}
+
+		if jsonOutput {
+			outputJSON(issues)
+			return
+		}
+
+		// Print molecule list
+		for _, issue := range issues {
+			priorityStr := fmt.Sprintf("P%d", issue.Priority)
+			fmt.Printf("%s [%s] %s\n", issue.ID, priorityStr, issue.Title)
+		}
+		fmt.Printf("\n%d molecule(s)\n", len(issues))
+	},
+}
+
+var moleculeShowCmd = &cobra.Command{
+	Use:   "show <molecule-id>",
+	Short: "Show molecule details",
+	Long: `Show detailed information about a template molecule.
+
+Examples:
+  bd molecule show mol-123
+`,
+	Args: cobra.ExactArgs(1),
+	Run: func(cmd *cobra.Command, args []string) {
+		moleculeID := args[0]
+
+		ctx := rootCtx
+		if daemonClient == nil {
+			if err := ensureDatabaseFresh(ctx); err != nil {
+				fmt.Fprintf(os.Stderr, "Error: %v\n", err)
+				os.Exit(1)
+			}
+		}
+
+		if store == nil {
+			fmt.Fprintf(os.Stderr, "Error: database not available\n")
+			os.Exit(1)
+		}
+
+		issue, err := store.GetIssue(ctx, moleculeID)
+		if err != nil {
+			fmt.Fprintf(os.Stderr, "Error: %v\n", err)
+			os.Exit(1)
+		}
+
+		if issue == nil {
+			fmt.Fprintf(os.Stderr, "Error: molecule %s not found\n", moleculeID)
+			os.Exit(1)
+		}
+
+		if !issue.IsTemplate {
+			fmt.Fprintf(os.Stderr, "Warning: %s is not a template molecule\n", moleculeID)
+		}
+
+		if jsonOutput {
+			outputJSON(issue)
+			return
+		}
+
+		// Print molecule details
+		fmt.Printf("%s: %s\n", issue.ID, issue.Title)
+		fmt.Printf("Type: %s\n", issue.IssueType)
+		fmt.Printf("Priority: P%d\n", issue.Priority)
+		fmt.Printf("Status: %s\n", issue.Status)
+		fmt.Printf("Template: %v\n", issue.IsTemplate)
+
+		if issue.Description != "" {
+			fmt.Printf("\nDescription:\n%s\n", issue.Description)
+		}
+
+		if issue.Design != "" {
+			fmt.Printf("\nDesign:\n%s\n", issue.Design)
+		}
+
+		if issue.AcceptanceCriteria != "" {
+			fmt.Printf("\nAcceptance Criteria:\n%s\n", issue.AcceptanceCriteria)
+		}
+	},
+}
+
+var moleculeInstantiateCmd = &cobra.Command{
+	Use:   "instantiate <molecule-id>",
+	Short: "Create a work item from a template molecule",
+	Long: `Create a new work item based on a template molecule.
+
+The new issue will inherit the template's title, description, design,
+acceptance criteria, priority, and issue type. The new issue will have
+is_template=false and will be linked to the template via a discovered-from
+dependency.
+
+Examples:
+  bd molecule instantiate mol-123              # Create work item from template
+  bd molecule instantiate mol-123 --title "Custom title"  # Override title
+`,
+	Args: cobra.ExactArgs(1),
+	Run: func(cmd *cobra.Command, args []string) {
+		CheckReadonly("instantiate")
+		moleculeID := args[0]
+
+		// Get flag overrides
+		titleOverride, _ := cmd.Flags().GetString("title")
+		assignee, _ := cmd.Flags().GetString("assignee")
+
+		ctx := rootCtx
+		if daemonClient == nil {
+			if err := ensureDatabaseFresh(ctx); err != nil {
+				fmt.Fprintf(os.Stderr, "Error: %v\n", err)
+				os.Exit(1)
+			}
+		}
+
+		if store == nil && daemonClient == nil {
+			fmt.Fprintf(os.Stderr, "Error: database not available\n")
+			os.Exit(1)
+		}
+
+		// Get the template molecule
+		var template *types.Issue
+		var err error
+
+		if daemonClient != nil {
+			showArgs := &rpc.ShowArgs{ID: moleculeID}
+			resp, showErr := daemonClient.Show(showArgs)
+			if showErr != nil {
+				fmt.Fprintf(os.Stderr, "Error: %v\n", showErr)
+				os.Exit(1)
+			}
+			template = &types.Issue{}
+			if jsonErr := json.Unmarshal(resp.Data, template); jsonErr != nil {
+				fmt.Fprintf(os.Stderr, "Error parsing response: %v\n", jsonErr)
+				os.Exit(1)
+			}
+		} else {
+			template, err = store.GetIssue(ctx, moleculeID)
+			if err != nil {
+				fmt.Fprintf(os.Stderr, "Error: %v\n", err)
+				os.Exit(1)
+			}
+		}
+
+		if template == nil {
+			fmt.Fprintf(os.Stderr, "Error: molecule %s not found\n", moleculeID)
+			os.Exit(1)
+		}
+
+		if !template.IsTemplate {
+			fmt.Fprintf(os.Stderr, "Warning: %s is not a template molecule (is_template=false)\n", moleculeID)
+		}
+
+		// Build title (use override or template title)
+		title := template.Title
+		if titleOverride != "" {
+			title = titleOverride
+		}
+
+		// Create the new work item
+		if daemonClient != nil {
+			// Daemon mode
+			createArgs := &rpc.CreateArgs{
+				Title:              title,
+				Description:        template.Description,
+				IssueType:          string(template.IssueType),
+				Priority:           template.Priority,
+				Design:             template.Design,
+				AcceptanceCriteria: template.AcceptanceCriteria,
+				Assignee:           assignee,
+				Dependencies:       []string{"discovered-from:" + moleculeID},
+			}
+
+			resp, createErr := daemonClient.Create(createArgs)
+			if createErr != nil {
+				fmt.Fprintf(os.Stderr, "Error: %v\n", createErr)
+				os.Exit(1)
+			}
+
+			var issue types.Issue
+			if jsonErr := json.Unmarshal(resp.Data, &issue); jsonErr != nil {
+				fmt.Fprintf(os.Stderr, "Error parsing response: %v\n", jsonErr)
+				os.Exit(1)
+			}
+
+			// Run create hook
+			if hookRunner != nil {
+				hookRunner.Run(hooks.EventCreate, &issue)
+			}
+
+			if jsonOutput {
+				outputJSON(&issue)
+			} else {
+				green := color.New(color.FgGreen).SprintFunc()
+				fmt.Printf("%s Created work item: %s (from template %s)\n", green("✓"), issue.ID, moleculeID)
+				fmt.Printf("  Title: %s\n", issue.Title)
+				fmt.Printf("  Priority: P%d\n", issue.Priority)
+				fmt.Printf("  Status: %s\n", issue.Status)
+			}
+			return
+		}
+
+		// Direct mode
+		now := time.Now()
+		issue := &types.Issue{
+			Title:              title,
+			Description:        template.Description,
+			Design:             template.Design,
+			AcceptanceCriteria: template.AcceptanceCriteria,
+			Status:             types.StatusOpen,
+			Priority:           template.Priority,
+			IssueType:          template.IssueType,
+			Assignee:           assignee,
+			IsTemplate:         false, // Work items are not templates
+			CreatedAt:          now,
+			UpdatedAt:          now,
+		}
+
+		if err := store.CreateIssue(ctx, issue, actor); err != nil {
+			fmt.Fprintf(os.Stderr, "Error creating issue: %v\n", err)
+			os.Exit(1)
+		}
+
+		// Get the created issue (ID is set by CreateIssue)
+		createdIssue, err := store.GetIssue(ctx, issue.ID)
+		if err != nil || createdIssue == nil {
+			fmt.Fprintf(os.Stderr, "Error getting created issue: %v\n", err)
+			os.Exit(1)
+		}
+
+		// Add discovered-from dependency to template
+		dep := &types.Dependency{
+			IssueID:     createdIssue.ID,
+			DependsOnID: moleculeID,
+			Type:        types.DepDiscoveredFrom,
+			CreatedAt:   now,
+			CreatedBy:   actor,
+		}
+		if err := store.AddDependency(ctx, dep, actor); err != nil {
+			fmt.Fprintf(os.Stderr, "Warning: failed to add dependency to template: %v\n", err)
+		}
+
+		// Run create hook
+		if hookRunner != nil {
+			hookRunner.Run(hooks.EventCreate, createdIssue)
+		}
+
+		// Schedule auto-flush
+		markDirtyAndScheduleFlush()
+
+		if jsonOutput {
+			outputJSON(createdIssue)
+		} else {
+			green := color.New(color.FgGreen).SprintFunc()
+			fmt.Printf("%s Created work item: %s (from template %s)\n", green("✓"), createdIssue.ID, moleculeID)
+			fmt.Printf("  Title: %s\n", createdIssue.Title)
+			fmt.Printf("  Priority: P%d\n", createdIssue.Priority)
+			fmt.Printf("  Status: %s\n", createdIssue.Status)
+		}
+	},
+}
+
+func init() {
+	// Add subcommands
+	moleculeCmd.AddCommand(moleculeListCmd)
+	moleculeCmd.AddCommand(moleculeShowCmd)
+	moleculeCmd.AddCommand(moleculeInstantiateCmd)
+
+	// Flags for list command
+	moleculeListCmd.Flags().Bool("all", false, "Include closed molecules")
+
+	// Flags for instantiate command
+	moleculeInstantiateCmd.Flags().String("title", "", "Override the template title")
+	moleculeInstantiateCmd.Flags().StringP("assignee", "a", "", "Assign the new work item")
+
+	// Add molecule command to root
+	rootCmd.AddCommand(moleculeCmd)
+}

cmd/bd/show.go

@@ -673,6 +673,17 @@ var updateCmd = &cobra.Command{
 		// Direct mode
 		updatedIssues := []*types.Issue{}
 		for _, id := range resolvedIDs {
+			// Check if issue is a template (beads-1ra): templates are read-only
+			issue, err := store.GetIssue(ctx, id)
+			if err != nil {
+				fmt.Fprintf(os.Stderr, "Error getting %s: %v\n", id, err)
+				continue
+			}
+			if issue != nil && issue.IsTemplate {
+				fmt.Fprintf(os.Stderr, "Error: cannot update template %s: templates are read-only; use 'bd molecule instantiate' to create a work item\n", id)
+				continue
+			}
+
 			// Apply regular field updates if any
 			regularUpdates := make(map[string]interface{})
 			for k, v := range updates {
@@ -733,14 +744,14 @@ var updateCmd = &cobra.Command{
 			}
 
 			// Run update hook (bd-kwro.8)
-			issue, _ := store.GetIssue(ctx, id)
-			if issue != nil && hookRunner != nil {
-				hookRunner.Run(hooks.EventUpdate, issue)
+			updatedIssue, _ := store.GetIssue(ctx, id)
+			if updatedIssue != nil && hookRunner != nil {
+				hookRunner.Run(hooks.EventUpdate, updatedIssue)
 			}
 
 			if jsonOutput {
-				if issue != nil {
-					updatedIssues = append(updatedIssues, issue)
+				if updatedIssue != nil {
+					updatedIssues = append(updatedIssues, updatedIssue)
 				}
 			} else {
 				green := color.New(color.FgGreen).SprintFunc()
@@ -1002,17 +1013,21 @@ var closeCmd = &cobra.Command{
 		if daemonClient != nil {
 			closedIssues := []*types.Issue{}
 			for _, id := range resolvedIDs {
-				// Check if issue is pinned (bd-6v2)
-				if !force {
+				// Get issue for template and pinned checks
 				showArgs := &rpc.ShowArgs{ID: id}
 				showResp, showErr := daemonClient.Show(showArgs)
 				if showErr == nil {
 					var issue types.Issue
 					if json.Unmarshal(showResp.Data, &issue) == nil {
-							if issue.Status == types.StatusPinned {
-								fmt.Fprintf(os.Stderr, "Error: cannot close pinned issue %s (use --force to override)\n", id)
+						// Check if issue is a template (beads-1ra): templates are read-only
+						if issue.IsTemplate {
+							fmt.Fprintf(os.Stderr, "Error: cannot close template %s: templates are read-only\n", id)
 							continue
 						}
+						// Check if issue is pinned (bd-6v2)
+						if !force && issue.Status == types.StatusPinned {
+							fmt.Fprintf(os.Stderr, "Error: cannot close pinned issue %s (use --force to override)\n", id)
+							continue
 						}
 					}
 				}
@@ -1052,9 +1067,17 @@ var closeCmd = &cobra.Command{
 		// Direct mode
 		closedIssues := []*types.Issue{}
 		for _, id := range resolvedIDs {
+			// Get issue for checks
+			issue, _ := store.GetIssue(ctx, id)
+
+			// Check if issue is a template (beads-1ra): templates are read-only
+			if issue != nil && issue.IsTemplate {
+				fmt.Fprintf(os.Stderr, "Error: cannot close template %s: templates are read-only\n", id)
+				continue
+			}
+
 			// Check if issue is pinned (bd-6v2)
 			if !force {
-				issue, _ := store.GetIssue(ctx, id)
 				if issue != nil && issue.Status == types.StatusPinned {
 					fmt.Fprintf(os.Stderr, "Error: cannot close pinned issue %s (use --force to override)\n", id)
 					continue
@@ -1067,14 +1090,14 @@ var closeCmd = &cobra.Command{
 			}
 
 			// Run close hook (bd-kwro.8)
-			issue, _ := store.GetIssue(ctx, id)
-			if issue != nil && hookRunner != nil {
-				hookRunner.Run(hooks.EventClose, issue)
+			closedIssue, _ := store.GetIssue(ctx, id)
+			if closedIssue != nil && hookRunner != nil {
+				hookRunner.Run(hooks.EventClose, closedIssue)
 			}
 
 			if jsonOutput {
-				if issue != nil {
-					closedIssues = append(closedIssues, issue)
+				if closedIssue != nil {
+					closedIssues = append(closedIssues, closedIssue)
 				}
 			} else {
 				green := color.New(color.FgGreen).SprintFunc()

internal/rpc/protocol.go

@@ -159,6 +159,9 @@ type ListArgs struct {
 
 	// Pinned filtering (bd-p8e)
 	Pinned *bool `json:"pinned,omitempty"`
+
+	// Template filtering (beads-1ra)
+	IncludeTemplates bool `json:"include_templates,omitempty"`
 }
 
 // CountArgs represents arguments for the count operation

internal/rpc/server_issues_epics.go

@@ -337,6 +337,28 @@ func (s *Server) handleUpdate(req *Request) Response {
 	}
 
 	ctx := s.reqCtx(req)
+
+	// Check if issue is a template (beads-1ra): templates are read-only
+	issue, err := store.GetIssue(ctx, updateArgs.ID)
+	if err != nil {
+		return Response{
+			Success: false,
+			Error:   fmt.Sprintf("failed to get issue: %v", err),
+		}
+	}
+	if issue == nil {
+		return Response{
+			Success: false,
+			Error:   fmt.Sprintf("issue %s not found", updateArgs.ID),
+		}
+	}
+	if issue.IsTemplate {
+		return Response{
+			Success: false,
+			Error:   fmt.Sprintf("cannot update template %s: templates are read-only; use 'bd molecule instantiate' to create a work item", updateArgs.ID),
+		}
+	}
+
 	updates := updatesFromArgs(updateArgs)
 	actor := s.reqActor(req)
 
@@ -406,15 +428,15 @@ func (s *Server) handleUpdate(req *Request) Response {
 		s.emitMutation(MutationUpdate, updateArgs.ID)
 	}
 
-	issue, err := store.GetIssue(ctx, updateArgs.ID)
-	if err != nil {
+	updatedIssue, getErr := store.GetIssue(ctx, updateArgs.ID)
+	if getErr != nil {
 		return Response{
 			Success: false,
-			Error:   fmt.Sprintf("failed to get updated issue: %v", err),
+			Error:   fmt.Sprintf("failed to get updated issue: %v", getErr),
 		}
 	}
 
-	data, _ := json.Marshal(issue)
+	data, _ := json.Marshal(updatedIssue)
 	return Response{
 		Success: true,
 		Data:    data,
@@ -439,6 +461,22 @@ func (s *Server) handleClose(req *Request) Response {
 	}
 
 	ctx := s.reqCtx(req)
+
+	// Check if issue is a template (beads-1ra): templates are read-only
+	issue, err := store.GetIssue(ctx, closeArgs.ID)
+	if err != nil {
+		return Response{
+			Success: false,
+			Error:   fmt.Sprintf("failed to get issue: %v", err),
+		}
+	}
+	if issue != nil && issue.IsTemplate {
+		return Response{
+			Success: false,
+			Error:   fmt.Sprintf("cannot close template %s: templates are read-only", closeArgs.ID),
+		}
+	}
+
 	if err := store.CloseIssue(ctx, closeArgs.ID, closeArgs.Reason, s.reqActor(req)); err != nil {
 		return Response{
 			Success: false,
@@ -449,8 +487,8 @@ func (s *Server) handleClose(req *Request) Response {
 	// Emit mutation event for event-driven daemon
 	s.emitMutation(MutationUpdate, closeArgs.ID)
 
-	issue, _ := store.GetIssue(ctx, closeArgs.ID)
-	data, _ := json.Marshal(issue)
+	closedIssue, _ := store.GetIssue(ctx, closeArgs.ID)
+	data, _ := json.Marshal(closedIssue)
 	return Response{
 		Success: true,
 		Data:    data,
@@ -512,6 +550,12 @@ func (s *Server) handleDelete(req *Request) Response {
 			continue
 		}
 
+		// Check if issue is a template (beads-1ra): templates are read-only
+		if issue.IsTemplate {
+			errors = append(errors, fmt.Sprintf("%s: cannot delete template (templates are read-only)", issueID))
+			continue
+		}
+
 		// Create tombstone instead of hard delete (bd-rp4o fix)
 		// This preserves deletion history and prevents resurrection during sync
 		type tombstoner interface {
@@ -701,6 +745,12 @@ func (s *Server) handleList(req *Request) Response {
 	// Pinned filtering (bd-p8e)
 	filter.Pinned = listArgs.Pinned
 
+	// Template filtering (beads-1ra): exclude templates by default
+	if !listArgs.IncludeTemplates {
+		isTemplate := false
+		filter.IsTemplate = &isTemplate
+	}
+
 	// Guard against excessive ID lists to avoid SQLite parameter limits
 	const maxIDs = 1000
 	if len(filter.IDs) > maxIDs {