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>

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