feat(mol): add bd mol commands, deprecate bd template

Adds the mol command group for molecule workflows:
- bd mol catalog - list available molecules
- bd mol show <id> - show molecule structure and variables
- bd mol bond <id> --var k=v - instantiate a molecule

Molecules are templates with workflow semantics - they are the
orchestration primitive for Gas Town. This unifies the template
system under the mol command.

The template commands are deprecated but still work:
- bd template list -> use bd mol catalog
- bd template show -> use bd mol show
- bd template instantiate -> use bd mol bond

Closes: bd-ffjt

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

cmd/bd/template.go

@@ -39,9 +39,10 @@ type InstantiateResult struct {
 }
 
 var templateCmd = &cobra.Command{
-	Use:     "template",
-	GroupID: "setup",
-	Short:   "Manage issue templates",
+	Use:        "template",
+	GroupID:    "setup",
+	Short:      "Manage issue templates",
+	Deprecated: "use 'bd mol' instead (mol catalog, mol show, mol bond)",
 	Long: `Manage Beads templates for creating issue hierarchies.
 
 Templates are epics with the "template" label. They can have child issues
@@ -57,8 +58,9 @@ To use a template:
 }
 
 var templateListCmd = &cobra.Command{
-	Use:   "list",
-	Short: "List available templates",
+	Use:        "list",
+	Short:      "List available templates",
+	Deprecated: "use 'bd mol catalog' instead",
 	Run: func(cmd *cobra.Command, args []string) {
 		ctx := rootCtx
 		var beadsTemplates []*types.Issue
@@ -121,9 +123,10 @@ var templateListCmd = &cobra.Command{
 }
 
 var templateShowCmd = &cobra.Command{
-	Use:   "show <template-id>",
-	Short: "Show template details",
-	Args:  cobra.ExactArgs(1),
+	Use:        "show <template-id>",
+	Short:      "Show template details",
+	Deprecated: "use 'bd mol show' instead",
+	Args:       cobra.ExactArgs(1),
 	Run: func(cmd *cobra.Command, args []string) {
 		ctx := rootCtx
 		var templateID string
@@ -193,8 +196,9 @@ func showBeadsTemplate(subgraph *TemplateSubgraph) {
 }
 
 var templateInstantiateCmd = &cobra.Command{
-	Use:   "instantiate <template-id>",
-	Short: "Create issues from a Beads template",
+	Use:        "instantiate <template-id>",
+	Short:      "Create issues from a Beads template",
+	Deprecated: "use 'bd mol bond' instead",
 	Long: `Instantiate a Beads template by cloning its subgraph and substituting variables.
 
 Variables are specified with --var key=value flags. The template's {{key}}