CLI: more RPC conversions, delete obsolete commands

- cmd_health: use graph_health RPC
- cmd_topology: new command using graph_topology RPC
- cmd_status: use graph_topology RPC (type counts folded into topology)
- cmd_run_agent: query resolution via memory_query RPC
- Delete cmd_bulk_rename (one-time migration, obsolete)
- Delete cmd_replay_queue, cmd_digest_links (unconscious agents handle)
- format_topology_header: add type counts, takes &Store now

Co-Authored-By: Kent Overstreet <kent.overstreet@linux.dev>

src/agent/tools/memory.rs

@@ -568,7 +568,7 @@ async fn graph_topology() -> Result<String> {
     let arc = cached_store().await?;
     let store = arc.lock().await;
     let graph = store.build_graph();
-    Ok(crate::subconscious::prompts::format_topology_header(&graph))
+    Ok(crate::subconscious::prompts::format_topology_header(&store, &graph))
 }
 
 async fn graph_health() -> Result<String> {