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)
 }