Move agent queries inline: {{nodes}} → {{tool: memory_query}}

Add "format": "full" option to memory_query that renders with
full content, graph metrics, and hub analysis (format_nodes_section).
Convert 6 agents (linker, challenger, connector, extractor, replay,
transfer) to inline their queries via {{tool: memory_query}} instead
of separate header query + {{nodes}} placeholder.

Co-Authored-By: Proof of Concept <poc@bcachefs.org>

src/agent/tools/memory.rs

@@ -238,11 +238,26 @@ async fn supersede(agent: &Option<std::sync::Arc<crate::agent::Agent>>, args: &s
 
 async fn query(args: &serde_json::Value) -> Result<String> {
     let query_str = get_str(args, "query")?;
+    let format = args.get("format").and_then(|v| v.as_str()).unwrap_or("compact");
     let arc = cached_store().await?;
     let store = arc.lock().await;
     let graph = store.build_graph();
-    crate::query_parser::query_to_string(&store, &graph, query_str)
-        .map_err(|e| anyhow::anyhow!("{}", e))
+
+    match format {
+        "full" => {
+            // Rich output with full content, graph metrics, hub analysis
+            let stages = crate::search::Stage::parse_pipeline(query_str)
+                .map_err(|e| anyhow::anyhow!("{}", e))?;
+            let results = crate::search::run_query(&stages, vec![], &graph, &store, false, 100);
+            let keys: Vec<String> = results.into_iter().map(|(k, _)| k).collect();
+            let items = crate::subconscious::defs::keys_to_replay_items(&store, &keys, &graph);
+            Ok(crate::subconscious::prompts::format_nodes_section(&store, &items, &graph))
+        }
+        _ => {
+            crate::query_parser::query_to_string(&store, &graph, query_str)
+                .map_err(|e| anyhow::anyhow!("{}", e))
+        }
+    }
 }
 
 // ── Journal tools ──────────────────────────────────────────────

src/subconscious/agents/challenger.agent

@@ -1,4 +1,4 @@
-{"agent": "challenger", "query": "all | type:semantic | not-visited:challenger,14d | sort:priority | limit:10", "schedule": "weekly"}
+{"agent": "challenger", "schedule": "weekly"}
 # Challenger Agent — Adversarial Truth-Testing
 
 
@@ -52,4 +52,4 @@ For each target node, one of:
 
 ## Target nodes to challenge
 
-{{NODES}}
+{{tool: memory_query {"query": "all | type:semantic | not-visited:challenger,14d | sort:priority | limit:10", "format": "full"}}}

src/subconscious/agents/connector.agent

@@ -1,4 +1,4 @@
-{"agent": "connector", "query": "all | type:semantic | not-visited:connector,7d | sort:priority | limit:20", "schedule": "daily"}
+{"agent": "connector", "schedule": "daily"}
 # Connector Agent — Cross-Domain Insight
 
 
@@ -83,4 +83,4 @@ you're exploring and you have context to judge them, reweight those too.
 
 ## Nodes to examine for cross-community connections
 
-{{NODES}}
+{{tool: memory_query {"query": "all | type:semantic | not-visited:connector,7d | sort:priority | limit:20", "format": "full"}}}

src/subconscious/agents/extractor.agent

@@ -1,4 +1,4 @@
-{"agent": "extractor", "query": "all | not-visited:extractor,7d | sort:priority | limit:3 | spread | not-visited:extractor,7d | limit:20", "schedule": "daily"}
+{"agent": "extractor", "schedule": "daily"}
 # Extractor Agent — Knowledge Organizer
 
 {{tool: memory_render core-personality}}
@@ -48,4 +48,4 @@ pattern you've found.
 
 ## Neighborhood nodes
 
-{{NODES}}
+{{tool: memory_query {"query": "all | not-visited:extractor,7d | sort:priority | limit:3 | spread | not-visited:extractor,7d | limit:20", "format": "full"}}}

src/subconscious/agents/linker.agent

@@ -1,4 +1,4 @@
-{"agent":"linker","query":"all | not-visited:linker,7d | sort:isolation*0.7+recency(linker)*0.3 | limit:5","schedule":"daily"}
+{"agent":"linker","schedule":"daily"}
 
 # Linker Agent — Relational Binding
 
@@ -8,7 +8,7 @@
 
 ## Seed nodes
 
-{{nodes}}
+{{tool: memory_query {"query": "all | not-visited:linker,7d | sort:isolation*0.7+recency(linker)*0.3 | limit:5", "format": "full"}}}
 
 {{tool: memory_render memory-instructions-core-subconscious}}
 

src/subconscious/agents/replay.agent

@@ -1,4 +1,4 @@
-{"agent": "replay", "query": "all | !type:daily | !type:weekly | !type:monthly | sort:priority | limit:15", "schedule": "daily"}
+{"agent": "replay", "schedule": "daily"}
 # Replay Agent — Hippocampal Replay + Schema Assimilation
 
 
@@ -44,4 +44,4 @@ clusters and determine how it fits.
 
 ## Nodes to review
 
-{{NODES}}
+{{tool: memory_query {"query": "all | !type:daily | !type:weekly | !type:monthly | sort:priority | limit:15", "format": "full"}}}

src/subconscious/agents/transfer.agent

@@ -1,4 +1,4 @@
-{"agent": "transfer", "query": "all | type:episodic | sort:timestamp | limit:15", "schedule": "daily"}
+{"agent": "transfer", "schedule": "daily"}
 # Transfer Agent — Complementary Learning Systems
 
 {{tool: memory_render core-personality}}
@@ -51,4 +51,4 @@ entries, and extract those patterns into semantic nodes.
 
 ## Episodes to process
 
-{{EPISODES}}
+{{tool: memory_query {"query": "all | type:episodic | sort:timestamp | limit:15", "format": "full"}}}

src/subconscious/defs.rs

@@ -845,7 +845,7 @@ pub fn run_agent(
 }
 
 /// Convert a list of keys to ReplayItems with priority and graph metrics.
-fn keys_to_replay_items(
+pub fn keys_to_replay_items(
     store: &Store,
     keys: &[String],
     graph: &Graph,

src/subconscious/prompts.rs

@@ -66,7 +66,7 @@ pub fn format_topology_header(graph: &Graph) -> String {
         n, e, graph.community_count(), sigma, alpha, gini, avg_cc, hub_list)
 }
 
-pub(super) fn format_nodes_section(store: &Store, items: &[ReplayItem], graph: &Graph) -> String {
+pub fn format_nodes_section(store: &Store, items: &[ReplayItem], graph: &Graph) -> String {
     let hub_thresh = graph.hub_threshold();
     let mut out = String::new();
     for item in items {