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/main.rs

@@ -274,13 +274,6 @@ enum GraphCmd {
 
 #[derive(Subcommand)]
 enum AgentCmd {
-    /// Parse and apply links from digest nodes
-    #[command(name = "digest-links")]
-    DigestLinks {
-        /// Apply the links (default: dry run)
-        #[arg(long)]
-        apply: bool,
-    },
     /// Run a single agent by name
     Run {
         /// Agent name (e.g. observation, linker, distill)
@@ -304,13 +297,6 @@ enum AgentCmd {
         #[arg(long)]
         state_dir: Option<String>,
     },
-    /// Show spaced repetition replay queue
-    #[command(name = "replay-queue")]
-    ReplayQueue {
-        /// Number of items to show
-        #[arg(long, default_value_t = 10)]
-        count: usize,
-    },
 }
 
 #[derive(Subcommand)]
@@ -319,6 +305,8 @@ enum AdminCmd {
     Init,
     /// Report graph metrics (CC, communities, small-world)
     Health,
+    /// Show graph topology with hub warnings
+    Topology,
     /// Run consistency checks and repair
     Fsck,
     /// Find and merge duplicate nodes (same key, multiple UUIDs)
@@ -327,17 +315,6 @@ enum AdminCmd {
         #[arg(long)]
         apply: bool,
     },
-    /// Bulk rename: replace a character in all keys
-    #[command(name = "bulk-rename")]
-    BulkRename {
-        /// Character to replace
-        from: String,
-        /// Replacement character
-        to: String,
-        /// Apply changes (default: dry run)
-        #[arg(long)]
-        apply: bool,
-    },
     /// Brief metrics check (for cron/notifications)
     #[command(name = "daily-check")]
     DailyCheck,
@@ -471,10 +448,8 @@ impl Run for GraphCmd {
 impl Run for AgentCmd {
     fn run(self) -> Result<(), String> {
         match self {
-            Self::DigestLinks { apply } => cli::agent::cmd_digest_links(apply),
             Self::Run { agent, count, target, query, dry_run, local, state_dir }
                 => cli::agent::cmd_run_agent(&agent, count, &target, query.as_deref(), dry_run, local, state_dir.as_deref()),
-            Self::ReplayQueue { count } => cli::agent::cmd_replay_queue(count),
         }
     }
 }
@@ -484,9 +459,9 @@ impl Run for AdminCmd {
         match self {
             Self::Init          => cli::admin::cmd_init(),
             Self::Health        => cli::admin::cmd_health(),
+            Self::Topology      => cli::admin::cmd_topology(),
             Self::Fsck          => cli::admin::cmd_fsck(),
             Self::Dedup { apply } => cli::admin::cmd_dedup(apply),
-            Self::BulkRename { from, to, apply } => cli::admin::cmd_bulk_rename(&from, &to, apply),
             Self::DailyCheck    => cli::admin::cmd_daily_check(),
             Self::Import { files } => cli::admin::cmd_import(&files),
             Self::Export { files, all } => cli::admin::cmd_export(&files, all),