unify memory tracking: entries are the single source of truth

Memory tool results (memory_render) are now pushed as
ConversationEntry::Memory with the node key, instead of plain
Messages. Remove loaded_nodes from ContextState — the debug
screen reads memory info from Memory entries in the conversation.

Surfaced memories from surface-observe are pushed as separate
Memory entries, reflections as separate system-reminder messages.
User input is no longer polluted with hook output.

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

src/agent/runner.rs

@@ -102,7 +102,6 @@ impl Agent {
             personality,
             journal: Vec::new(),
             working_stack: Vec::new(),
-            loaded_nodes: Vec::new(),
             entries: Vec::new(),
         };
         let session_id = format!("poc-agent-{}", chrono::Utc::now().format("%Y%m%d-%H%M%S"));
@@ -144,8 +143,8 @@ impl Agent {
         msgs
     }
 
-    /// Run agent orchestration cycle and return formatted output to inject.
-    fn run_agent_cycle(&mut self) -> Option<String> {
+    /// Run agent orchestration cycle, returning structured output.
+    fn run_agent_cycle(&mut self) -> crate::subconscious::subconscious::AgentCycleOutput {
         let transcript_path = self.conversation_log.as_ref()
             .map(|l| l.path().to_string_lossy().to_string())
             .unwrap_or_default();
@@ -157,12 +156,7 @@ impl Agent {
         );
 
         self.agent_cycles.trigger(&session);
-        let text = crate::subconscious::subconscious::format_agent_output(&self.agent_cycles.last_output);
-        if text.trim().is_empty() {
-            None
-        } else {
-            Some(text)
-        }
+        std::mem::take(&mut self.agent_cycles.last_output)
     }
 
     /// Push a conversation message — stamped and logged.
@@ -201,13 +195,32 @@ impl Agent {
         target: StreamTarget,
     ) -> Result<TurnResult> {
         // Run agent orchestration cycle (surface-observe, reflect, journal)
-        if let Some(hook_output) = self.run_agent_cycle() {
-            let enriched = format!("{}\n\n<system-reminder>\n{}\n</system-reminder>",
-                user_input, hook_output);
-            self.push_message(Message::user(enriched));
-        } else {
-            self.push_message(Message::user(user_input));
+        let cycle = self.run_agent_cycle();
+
+        // Surfaced memories — each as a separate Memory entry
+        for key in &cycle.surfaced_keys {
+            if let Some(rendered) = crate::cli::node::render_node(
+                &crate::store::Store::load().unwrap_or_default(), key,
+            ) {
+                let mut msg = Message::user(format!(
+                    "<system-reminder>\n--- {} (surfaced) ---\n{}\n</system-reminder>",
+                    key, rendered,
+                ));
+                msg.stamp();
+                self.push_entry(ConversationEntry::Memory { key: key.clone(), message: msg });
             }
+        }
+
+        // Reflection — separate system reminder
+        if let Some(ref reflection) = cycle.reflection {
+            self.push_message(Message::user(format!(
+                "<system-reminder>\n--- subconscious reflection ---\n{}\n</system-reminder>",
+                reflection.trim(),
+            )));
+        }
+
+        // User input — clean, just what was typed
+        self.push_message(Message::user(user_input));
         let _ = ui_tx.send(UiMessage::AgentUpdate(self.agent_cycles.snapshots()));
 
         let mut overflow_retries: u32 = 0;
@@ -482,37 +495,16 @@ impl Agent {
                 Err(e) => format!("Error: {:#}", e),
             };
 
-            // Track loaded/updated nodes
-            if result.is_ok() {
+            // Disambiguate memory renders from other tool results
+            let memory_key = if result.is_ok() {
                 match call.function.name.as_str() {
-                    "memory_render" | "memory_links" => {
-                        if let Some(key) = args.get("key").and_then(|v| v.as_str()) {
-                            if let Some(node) = crate::hippocampus::memory::MemoryNode::load(key) {
-                                // Replace if already tracked, otherwise add
-                                if let Some(existing) = self.context.loaded_nodes.iter_mut()
-                                    .find(|n| n.key == node.key) {
-                                    *existing = node;
+                    "memory_render" =>
+                        args.get("key").and_then(|v| v.as_str()).map(String::from),
+                    _ => None,
+                }
             } else {
-                                    self.context.loaded_nodes.push(node);
-                                }
-                            }
-                        }
-                    }
-                    "memory_write" => {
-                        if let Some(key) = args.get("key").and_then(|v| v.as_str()) {
-                            if let Some(node) = crate::hippocampus::memory::MemoryNode::load(key) {
-                                // Refresh if already tracked
-                                if let Some(existing) = self.context.loaded_nodes.iter_mut()
-                                    .find(|n| n.key == node.key) {
-                                    *existing = node;
-                                }
-                                // Don't auto-add writes — only renders register nodes
-                            }
-                        }
-                    }
-                    _ => {}
-                }
-            }
+                None
+            };
 
             let output = tools::ToolOutput {
                 text,
@@ -526,7 +518,13 @@ impl Agent {
                 result: output.text.clone(),
             });
             let _ = ui_tx.send(UiMessage::ToolFinished { id: call.id.clone() });
-            self.push_message(Message::tool_result(&call.id, &output.text));
+            let mut msg = Message::tool_result(&call.id, &output.text);
+            msg.stamp();
+            if let Some(key) = memory_key {
+                self.push_entry(ConversationEntry::Memory { key, message: msg });
+            } else {
+                self.push_entry(ConversationEntry::Message(msg));
+            }
             ds.had_tool_calls = true;
             if output.text.starts_with("Error:") {
                 ds.tool_errors += 1;
@@ -654,23 +652,29 @@ impl Agent {
             children: stack_children,
         });
 
-        // Loaded memory nodes — tracked by memory tools
-        if !self.context.loaded_nodes.is_empty() {
-            let node_children: Vec<ContextSection> = self.context.loaded_nodes.iter()
-                .map(|node| {
-                    let rendered = node.render();
+        // Memory nodes — extracted from Memory entries in the conversation
+        let memory_entries: Vec<&ConversationEntry> = self.context.entries.iter()
+            .filter(|e| e.is_memory())
+            .collect();
+        if !memory_entries.is_empty() {
+            let node_children: Vec<ContextSection> = memory_entries.iter()
+                .map(|entry| {
+                    let key = match entry {
+                        ConversationEntry::Memory { key, .. } => key.as_str(),
+                        _ => unreachable!(),
+                    };
+                    let text = entry.message().content_text();
                     ContextSection {
-                        name: format!("{} (v{}, w={:.2}, {} links)",
-                            node.key, node.version, node.weight, node.links.len()),
-                        tokens: count(&rendered),
-                        content: String::new(), // don't duplicate in debug view
+                        name: key.to_string(),
+                        tokens: count(text),
+                        content: String::new(),
                         children: Vec::new(),
                     }
                 })
                 .collect();
             let node_tokens: usize = node_children.iter().map(|c| c.tokens).sum();
             sections.push(ContextSection {
-                name: format!("Memory nodes ({} loaded)", self.context.loaded_nodes.len()),
+                name: format!("Memory nodes ({} loaded)", memory_entries.len()),
                 tokens: node_tokens,
                 content: String::new(),
                 children: node_children,

src/agent/types.rs

@@ -402,10 +402,6 @@ pub struct ContextState {
     pub personality: Vec<(String, String)>,
     pub journal: Vec<crate::agent::journal::JournalEntry>,
     pub working_stack: Vec<String>,
-    /// Memory nodes currently loaded — for debug display and refresh.
-    /// Content is NOT duplicated here; the actual content is in entries
-    /// as ConversationEntry::Memory.
-    pub loaded_nodes: Vec<crate::hippocampus::memory::MemoryNode>,
     /// Conversation entries — messages and memory, interleaved in order.
     /// Does NOT include system prompt, personality, or journal.
     pub entries: Vec<ConversationEntry>,

src/subconscious/subconscious.rs

@@ -13,6 +13,7 @@ use std::time::{Duration, Instant, SystemTime};
 pub use crate::session::HookSession;
 
 /// Output from a single agent orchestration cycle.
+#[derive(Default)]
 pub struct AgentCycleOutput {
     /// Memory node keys surfaced by surface-observe.
     pub surfaced_keys: Vec<String>,