feat: wikilink pills in message bubbles, noteList context injection

- Render [[wikilink]] reference pills inside sent message bubbles
  with type-colored badges; clicking a pill opens the note
- Add noteList (filtered note list titles, max 100) and noteListFilter
  to the structured context snapshot sent to the AI
- Thread noteList/noteListFilter from App → Editor → EditorRightPanel → AiPanel
- Store references in AiAgentMessage for display in chat history
- Add tests for reference pill rendering and noteList context

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

design/mcp-autodetect-status-bar.pen

@@ -0,0 +1 @@
+{"children":[],"variables":{}}

mcp-server/index.js

@@ -23,29 +23,44 @@ import {
   CallToolRequestSchema,
   ListToolsRequestSchema,
 } from '@modelcontextprotocol/sdk/types.js'
+import WebSocket from 'ws'
 import {
   readNote, createNote, searchNotes, appendToNote,
   editNoteFrontmatter, deleteNote, linkNotes, listNotes, vaultContext,
 } from './vault.js'
-import { startUiBridge } from './ws-bridge.js'
 
 const VAULT_PATH = process.env.VAULT_PATH || process.env.HOME + '/Laputa'
 const WS_UI_PORT = parseInt(process.env.WS_UI_PORT || '9711', 10)
+const WS_UI_URL = `ws://localhost:${WS_UI_PORT}`
 
-// Start the UI bridge so stdio-based MCP tools can broadcast UI actions.
-// If the port is already in use (e.g. by the running Laputa app), continue
-// without the bridge — vault tools still work via stdio MCP.
-let uiBridge = null
-startUiBridge(WS_UI_PORT).then((bridge) => {
-  uiBridge = bridge
-})
+// Connect as a WebSocket CLIENT to the UI bridge (run by ws-bridge.js).
+// The bridge relays messages to all other clients (the React frontend).
+let uiSocket = null
+const RECONNECT_INTERVAL_MS = 3000
+
+function connectUiBridge() {
+  try {
+    const ws = new WebSocket(WS_UI_URL)
+    ws.on('open', () => {
+      uiSocket = ws
+      console.error(`[mcp] Connected to UI bridge at ${WS_UI_URL}`)
+    })
+    ws.on('close', () => {
+      uiSocket = null
+      setTimeout(connectUiBridge, RECONNECT_INTERVAL_MS)
+    })
+    ws.on('error', () => {
+      // Silent — bridge may not be running yet, will retry
+    })
+  } catch {
+    setTimeout(connectUiBridge, RECONNECT_INTERVAL_MS)
+  }
+}
+connectUiBridge()
 
 function broadcastUiAction(action, payload) {
-  if (!uiBridge) return
-  const msg = JSON.stringify({ type: 'ui_action', action, ...payload })
-  for (const client of uiBridge.clients) {
-    if (client.readyState === 1) client.send(msg)
-  }
+  if (!uiSocket || uiSocket.readyState !== WebSocket.OPEN) return
+  uiSocket.send(JSON.stringify({ type: 'ui_action', action, ...payload }))
 }
 
 const TOOLS = [
@@ -233,6 +248,7 @@ async function handleCreateNote(args) {
   const frontmatter = {}
   if (args.is_a) frontmatter.is_a = args.is_a
   const absPath = await createNote(VAULT_PATH, args.path, args.title, frontmatter)
+  broadcastUiAction('vault_changed', { path: args.path })
   return { content: [{ type: 'text', text: `Created note at ${absPath}` }] }
 }
 
@@ -246,21 +262,25 @@ async function handleSearchNotes(args) {
 
 async function handleAppendToNote(args) {
   await appendToNote(VAULT_PATH, args.path, args.text)
+  broadcastUiAction('vault_changed', { path: args.path })
   return { content: [{ type: 'text', text: `Appended text to ${args.path}` }] }
 }
 
 async function handleEditFrontmatter(args) {
   const updated = await editNoteFrontmatter(VAULT_PATH, args.path, args.patch)
+  broadcastUiAction('vault_changed', { path: args.path })
   return { content: [{ type: 'text', text: JSON.stringify(updated) }] }
 }
 
 async function handleDeleteNote(args) {
   await deleteNote(VAULT_PATH, args.path)
+  broadcastUiAction('vault_changed', { path: args.path })
   return { content: [{ type: 'text', text: `Deleted ${args.path}` }] }
 }
 
 async function handleLinkNotes(args) {
   const arr = await linkNotes(VAULT_PATH, args.source_path, args.property, args.target_title)
+  broadcastUiAction('vault_changed', { path: args.source_path })
   return { content: [{ type: 'text', text: `${args.property}: [${arr.join(', ')}]` }] }
 }
 
@@ -293,7 +313,7 @@ function handleUiHighlight(args) {
 }
 
 function handleUiSetFilter(args) {
-  broadcastUiAction('set_filter', { type: args.type })
+  broadcastUiAction('set_filter', { filterType: args.type })
   return { content: [{ type: 'text', text: `Filter set to ${args.type}` }] }
 }
 

mcp-server/ws-bridge.js

@@ -50,18 +50,18 @@ function buildFrontmatter(args) {
 const TOOL_HANDLERS = {
   open_note: (args) => readNote(VAULT_PATH, args.path).then(text => ({ content: text })),
   read_note: (args) => readNote(VAULT_PATH, args.path).then(text => ({ content: text })),
-  create_note: (args) => createNote(VAULT_PATH, args.path, args.title, buildFrontmatter(args)),
+  create_note: (args) => createNote(VAULT_PATH, args.path, args.title, buildFrontmatter(args)).then(r => { broadcastUiAction('vault_changed', { path: args.path }); return r }),
   search_notes: (args) => searchNotes(VAULT_PATH, args.query, args.limit),
-  append_to_note: (args) => appendToNote(VAULT_PATH, args.path, args.text).then(() => ({ ok: true })),
-  edit_note_frontmatter: (args) => editNoteFrontmatter(VAULT_PATH, args.path, args.patch),
-  delete_note: (args) => deleteNote(VAULT_PATH, args.path).then(() => ({ ok: true })),
-  link_notes: (args) => linkNotes(VAULT_PATH, args.source_path, args.property, args.target_title),
+  append_to_note: (args) => appendToNote(VAULT_PATH, args.path, args.text).then(() => { broadcastUiAction('vault_changed', { path: args.path }); return { ok: true } }),
+  edit_note_frontmatter: (args) => editNoteFrontmatter(VAULT_PATH, args.path, args.patch).then(r => { broadcastUiAction('vault_changed', { path: args.path }); return r }),
+  delete_note: (args) => deleteNote(VAULT_PATH, args.path).then(() => { broadcastUiAction('vault_changed', { path: args.path }); return { ok: true } }),
+  link_notes: (args) => linkNotes(VAULT_PATH, args.source_path, args.property, args.target_title).then(r => { broadcastUiAction('vault_changed', { path: args.source_path }); return r }),
   list_notes: (args) => listNotes(VAULT_PATH, args.type_filter, args.sort),
   vault_context: () => vaultContext(VAULT_PATH),
   ui_open_note: (args) => { broadcastUiAction('open_note', { path: args.path }); return { ok: true } },
   ui_open_tab: (args) => { broadcastUiAction('open_tab', { path: args.path }); return { ok: true } },
   ui_highlight: (args) => { broadcastUiAction('highlight', { element: args.element, path: args.path }); return { ok: true } },
-  ui_set_filter: (args) => { broadcastUiAction('set_filter', { type: args.type }); return { ok: true } },
+  ui_set_filter: (args) => { broadcastUiAction('set_filter', { filterType: args.type }); return { ok: true } },
 }
 
 async function handleMessage(data) {
@@ -101,8 +101,15 @@ export function startUiBridge(port = WS_UI_PORT) {
 
     httpServer.listen(port, () => {
       const wss = new WebSocketServer({ server: httpServer })
-      wss.on('connection', () => {
+      wss.on('connection', (ws) => {
         console.error(`[ws-bridge] UI client connected on port ${port}`)
+        // Relay: when a client sends a message, broadcast to all OTHER clients.
+        // This allows the MCP stdio server (connected as a client) to reach the frontend.
+        ws.on('message', (raw) => {
+          for (const client of wss.clients) {
+            if (client !== ws && client.readyState === 1) client.send(raw.toString())
+          }
+        })
       })
       uiBridge = wss
       console.error(`[ws-bridge] UI bridge listening on ws://localhost:${port}`)

src-tauri/src/claude_cli.rs

@@ -1,4 +1,5 @@
 use serde::{Deserialize, Serialize};
+use std::collections::HashMap;
 use std::io::BufRead;
 use std::path::PathBuf;
 use std::process::{Command, Stdio};
@@ -18,10 +19,21 @@ pub enum ClaudeStreamEvent {
     Init { session_id: String },
     /// Incremental text chunk.
     TextDelta { text: String },
+    /// Incremental thinking/reasoning chunk.
+    ThinkingDelta { text: String },
     /// A tool call started (agent mode only).
-    ToolStart { tool_name: String, tool_id: String },
+    ToolStart {
+        tool_name: String,
+        tool_id: String,
+        #[serde(skip_serializing_if = "Option::is_none")]
+        input: Option<String>,
+    },
     /// A tool call finished (agent mode only).
-    ToolDone { tool_id: String },
+    ToolDone {
+        tool_id: String,
+        #[serde(skip_serializing_if = "Option::is_none")]
+        output: Option<String>,
+    },
     /// Final result text + session ID.
     Result { text: String, session_id: String },
     /// Something went wrong.
@@ -207,6 +219,15 @@ fn build_mcp_config(vault_path: &str) -> Result<String, String> {
     serde_json::to_string(&config).map_err(|e| format!("Failed to serialise MCP config: {e}"))
 }
 
+/// Mutable state accumulated across the JSON stream for a single subprocess.
+struct StreamState {
+    session_id: String,
+    /// Accumulates `input_json_delta` chunks keyed by tool_use id.
+    tool_inputs: HashMap<String, String>,
+    /// The tool_use id of the block currently being streamed.
+    current_tool_id: Option<String>,
+}
+
 /// Core subprocess runner shared by chat and agent modes.
 fn run_claude_subprocess<F>(bin: &PathBuf, args: &[String], emit: &mut F) -> Result<String, String>
 where
@@ -223,7 +244,11 @@ where
     let stdout = child.stdout.take().ok_or("No stdout handle")?;
     let reader = std::io::BufReader::new(stdout);
 
-    let mut session_id = String::new();
+    let mut state = StreamState {
+        session_id: String::new(),
+        tool_inputs: HashMap::new(),
+        current_tool_id: None,
+    };
 
     for line in reader.lines() {
         let line = match line {
@@ -245,7 +270,7 @@ where
             Err(_) => continue, // skip non-JSON lines
         };
 
-        dispatch_event(&json, &mut session_id, emit);
+        dispatch_event(&json, &mut state, emit);
     }
 
     // Read stderr for potential error messages.
@@ -257,7 +282,7 @@ where
 
     let status = child.wait().map_err(|e| format!("Wait failed: {e}"))?;
 
-    if !status.success() && session_id.is_empty() {
+    if !status.success() && state.session_id.is_empty() {
         let msg = if stderr_output.contains("not logged in")
             || stderr_output.contains("authentication")
             || stderr_output.contains("auth")
@@ -273,11 +298,11 @@ where
 
     emit(ClaudeStreamEvent::Done);
 
-    Ok(session_id)
+    Ok(state.session_id)
 }
 
 /// Parse a single JSON line from the stream and emit the appropriate event.
-fn dispatch_event<F>(json: &serde_json::Value, session_id: &mut String, emit: &mut F)
+fn dispatch_event<F>(json: &serde_json::Value, state: &mut StreamState, emit: &mut F)
 where
     F: FnMut(ClaudeStreamEvent),
 {
@@ -287,7 +312,7 @@ where
         // --- System init → capture session_id ---
         "system" if json["subtype"].as_str() == Some("init") => {
             if let Some(sid) = json["session_id"].as_str() {
-                *session_id = sid.to_string();
+                state.session_id = sid.to_string();
                 emit(ClaudeStreamEvent::Init {
                     session_id: sid.to_string(),
                 });
@@ -296,7 +321,7 @@ where
 
         // --- Streaming partial events (text deltas, tool_use starts) ---
         "stream_event" => {
-            dispatch_stream_event(json, emit);
+            dispatch_stream_event(json, state, emit);
         }
 
         // --- Tool progress (agent mode) ---
@@ -307,6 +332,18 @@ where
                 emit(ClaudeStreamEvent::ToolStart {
                     tool_name: name.to_string(),
                     tool_id: id.to_string(),
+                    input: None,
+                });
+            }
+        }
+
+        // --- Tool result (agent mode) ---
+        "tool_result" => {
+            if let Some(id) = json["tool_use_id"].as_str() {
+                let output = extract_tool_result_text(json);
+                emit(ClaudeStreamEvent::ToolDone {
+                    tool_id: id.to_string(),
+                    output,
                 });
             }
         }
@@ -315,7 +352,7 @@ where
         "result" => {
             let sid = json["session_id"].as_str().unwrap_or("").to_string();
             if !sid.is_empty() {
-                *session_id = sid.clone();
+                state.session_id = sid.clone();
             }
             let text = json["result"].as_str().unwrap_or("").to_string();
             emit(ClaudeStreamEvent::Result {
@@ -332,9 +369,11 @@ where
                         if let (Some(id), Some(name)) =
                             (block["id"].as_str(), block["name"].as_str())
                         {
+                            let input = format_tool_input(&block["input"], state, id);
                             emit(ClaudeStreamEvent::ToolStart {
                                 tool_name: name.to_string(),
                                 tool_id: id.to_string(),
+                                input,
                             });
                         }
                     }
@@ -347,7 +386,7 @@ where
 }
 
 /// Handle a `stream_event` (partial assistant message).
-fn dispatch_stream_event<F>(json: &serde_json::Value, emit: &mut F)
+fn dispatch_stream_event<F>(json: &serde_json::Value, state: &mut StreamState, emit: &mut F)
 where
     F: FnMut(ClaudeStreamEvent),
 {
@@ -357,29 +396,91 @@ where
     match event_type {
         "content_block_delta" => {
             let delta = &event["delta"];
-            if delta["type"].as_str() == Some("text_delta") {
-                if let Some(text) = delta["text"].as_str() {
-                    emit(ClaudeStreamEvent::TextDelta {
-                        text: text.to_string(),
-                    });
+            match delta["type"].as_str() {
+                Some("text_delta") => {
+                    if let Some(text) = delta["text"].as_str() {
+                        emit(ClaudeStreamEvent::TextDelta {
+                            text: text.to_string(),
+                        });
+                    }
                 }
+                Some("thinking_delta") => {
+                    if let Some(text) = delta["thinking"].as_str() {
+                        emit(ClaudeStreamEvent::ThinkingDelta {
+                            text: text.to_string(),
+                        });
+                    }
+                }
+                Some("input_json_delta") => {
+                    if let (Some(partial), Some(ref tid)) =
+                        (delta["partial_json"].as_str(), &state.current_tool_id)
+                    {
+                        state
+                            .tool_inputs
+                            .entry(tid.clone())
+                            .or_default()
+                            .push_str(partial);
+                    }
+                }
+                _ => {}
             }
         }
         "content_block_start" => {
             let block = &event["content_block"];
             if block["type"].as_str() == Some("tool_use") {
                 if let (Some(id), Some(name)) = (block["id"].as_str(), block["name"].as_str()) {
+                    state.current_tool_id = Some(id.to_string());
+                    state.tool_inputs.entry(id.to_string()).or_default();
                     emit(ClaudeStreamEvent::ToolStart {
                         tool_name: name.to_string(),
                         tool_id: id.to_string(),
+                        input: None,
                     });
                 }
             }
         }
+        "content_block_stop" => {
+            state.current_tool_id = None;
+        }
         _ => {}
     }
 }
 
+/// Build the tool input string, preferring accumulated delta chunks over the
+/// block's `input` field (which may be empty at stream start).
+fn format_tool_input(
+    block_input: &serde_json::Value,
+    state: &StreamState,
+    tool_id: &str,
+) -> Option<String> {
+    if let Some(accumulated) = state.tool_inputs.get(tool_id) {
+        if !accumulated.is_empty() {
+            return Some(accumulated.clone());
+        }
+    }
+    if !block_input.is_null() && block_input.as_object().is_some_and(|o| !o.is_empty()) {
+        return Some(block_input.to_string());
+    }
+    None
+}
+
+/// Extract displayable text from a `tool_result` event.
+fn extract_tool_result_text(json: &serde_json::Value) -> Option<String> {
+    // String content field
+    if let Some(s) = json["content"].as_str() {
+        return Some(s.to_string());
+    }
+    // Array of content blocks (Claude format)
+    if let Some(arr) = json["content"].as_array() {
+        let texts: Vec<&str> = arr.iter().filter_map(|b| b["text"].as_str()).collect();
+        if !texts.is_empty() {
+            return Some(texts.join("\n"));
+        }
+    }
+    // Fallback: "output" field
+    json["output"].as_str().map(|s| s.to_string())
+}
+
 #[cfg(test)]
 mod tests {
     use super::*;
@@ -408,12 +509,20 @@ mod tests {
 
     // --- dispatch_event / dispatch_stream_event ---
 
+    fn new_state() -> StreamState {
+        StreamState {
+            session_id: String::new(),
+            tool_inputs: HashMap::new(),
+            current_tool_id: None,
+        }
+    }
+
     /// Run dispatch_event on the given JSON and return (session_id, events).
     fn run_dispatch(json: serde_json::Value) -> (String, Vec<ClaudeStreamEvent>) {
-        let mut sid = String::new();
+        let mut state = new_state();
         let mut events = vec![];
-        dispatch_event(&json, &mut sid, &mut |e| events.push(e));
-        (sid, events)
+        dispatch_event(&json, &mut state, &mut |e| events.push(e));
+        (state.session_id, events)
     }
 
     /// Run dispatch_event with a pre-set session_id.
@@ -421,10 +530,23 @@ mod tests {
         json: serde_json::Value,
         initial_sid: &str,
     ) -> (String, Vec<ClaudeStreamEvent>) {
-        let mut sid = initial_sid.to_string();
+        let mut state = new_state();
+        state.session_id = initial_sid.to_string();
         let mut events = vec![];
-        dispatch_event(&json, &mut sid, &mut |e| events.push(e));
-        (sid, events)
+        dispatch_event(&json, &mut state, &mut |e| events.push(e));
+        (state.session_id, events)
+    }
+
+    /// Run multiple dispatch_event calls sharing state (for multi-event sequences).
+    fn run_dispatch_sequence(
+        events_json: Vec<serde_json::Value>,
+    ) -> (StreamState, Vec<ClaudeStreamEvent>) {
+        let mut state = new_state();
+        let mut events = vec![];
+        for json in &events_json {
+            dispatch_event(json, &mut state, &mut |e| events.push(e));
+        }
+        (state, events)
     }
 
     #[test]
@@ -468,7 +590,7 @@ mod tests {
             "event": { "type": "content_block_start", "index": 1, "content_block": { "type": "tool_use", "id": "tool_abc", "name": "read_note", "input": {} } }
         }));
         assert!(
-            matches!(&events[0], ClaudeStreamEvent::ToolStart { tool_name, tool_id } if tool_name == "read_note" && tool_id == "tool_abc")
+            matches!(&events[0], ClaudeStreamEvent::ToolStart { tool_name, tool_id, .. } if tool_name == "read_note" && tool_id == "tool_abc")
         );
     }
 
@@ -501,7 +623,7 @@ mod tests {
             "type": "tool_progress", "tool_name": "search_notes", "tool_use_id": "tool_xyz"
         }));
         assert!(
-            matches!(&events[0], ClaudeStreamEvent::ToolStart { tool_name, tool_id } if tool_name == "search_notes" && tool_id == "tool_xyz")
+            matches!(&events[0], ClaudeStreamEvent::ToolStart { tool_name, tool_id, .. } if tool_name == "search_notes" && tool_id == "tool_xyz")
         );
     }
 
@@ -523,7 +645,7 @@ mod tests {
         }));
         assert_eq!(events.len(), 1);
         assert!(
-            matches!(&events[0], ClaudeStreamEvent::ToolStart { tool_name, tool_id } if tool_name == "search_notes" && tool_id == "tu_1")
+            matches!(&events[0], ClaudeStreamEvent::ToolStart { tool_name, tool_id, .. } if tool_name == "search_notes" && tool_id == "tu_1")
         );
     }
 
@@ -541,7 +663,8 @@ mod tests {
     }
 
     #[test]
-    fn dispatch_stream_event_non_text_delta_is_ignored() {
+    fn dispatch_stream_event_input_json_delta_accumulates_silently() {
+        // input_json_delta doesn't emit events directly — it accumulates in state
         let (_, events) = run_dispatch(serde_json::json!({
             "type": "stream_event",
             "event": { "type": "content_block_delta", "index": 0, "delta": { "type": "input_json_delta", "partial_json": "{}" } }
@@ -566,6 +689,112 @@ mod tests {
         assert!(events.is_empty());
     }
 
+    #[test]
+    fn dispatch_event_handles_tool_result_string_content() {
+        let (_, events) = run_dispatch(serde_json::json!({
+            "type": "tool_result",
+            "tool_use_id": "tool_abc",
+            "content": "Found 3 notes matching query"
+        }));
+        assert_eq!(events.len(), 1);
+        assert!(
+            matches!(&events[0], ClaudeStreamEvent::ToolDone { tool_id, output }
+                if tool_id == "tool_abc" && output.as_deref() == Some("Found 3 notes matching query"))
+        );
+    }
+
+    #[test]
+    fn dispatch_event_handles_tool_result_array_content() {
+        let (_, events) = run_dispatch(serde_json::json!({
+            "type": "tool_result",
+            "tool_use_id": "tool_def",
+            "content": [{ "type": "text", "text": "Line 1" }, { "type": "text", "text": "Line 2" }]
+        }));
+        assert!(
+            matches!(&events[0], ClaudeStreamEvent::ToolDone { output, .. }
+                if output.as_deref() == Some("Line 1\nLine 2"))
+        );
+    }
+
+    #[test]
+    fn dispatch_event_tool_result_missing_tool_id_is_ignored() {
+        let (_, events) = run_dispatch(serde_json::json!({
+            "type": "tool_result", "content": "result text"
+        }));
+        assert!(events.is_empty());
+    }
+
+    #[test]
+    fn dispatch_accumulates_input_json_deltas() {
+        let (_, events) = run_dispatch_sequence(vec![
+            // Start tool_use block
+            serde_json::json!({
+                "type": "stream_event",
+                "event": { "type": "content_block_start", "content_block": { "type": "tool_use", "id": "t1", "name": "search_notes", "input": {} } }
+            }),
+            // Input delta chunks
+            serde_json::json!({
+                "type": "stream_event",
+                "event": { "type": "content_block_delta", "delta": { "type": "input_json_delta", "partial_json": "{\"query\":" } }
+            }),
+            serde_json::json!({
+                "type": "stream_event",
+                "event": { "type": "content_block_delta", "delta": { "type": "input_json_delta", "partial_json": "\"test\"}" } }
+            }),
+            // Stop block
+            serde_json::json!({
+                "type": "stream_event",
+                "event": { "type": "content_block_stop" }
+            }),
+            // Assistant message triggers ToolStart with accumulated input
+            serde_json::json!({
+                "type": "assistant",
+                "message": { "content": [
+                    { "type": "tool_use", "id": "t1", "name": "search_notes", "input": { "query": "test" } }
+                ] }
+            }),
+        ]);
+        // First event: ToolStart with no input (from content_block_start)
+        assert!(matches!(
+            &events[0],
+            ClaudeStreamEvent::ToolStart { input: None, .. }
+        ));
+        // Second event: ToolStart with accumulated input (from assistant)
+        assert!(
+            matches!(&events[1], ClaudeStreamEvent::ToolStart { input: Some(inp), .. }
+                if inp == "{\"query\":\"test\"}")
+        );
+    }
+
+    #[test]
+    fn dispatch_assistant_uses_block_input_when_no_deltas() {
+        let (_, events) = run_dispatch(serde_json::json!({
+            "type": "assistant",
+            "message": { "content": [
+                { "type": "tool_use", "id": "tu_x", "name": "create_note", "input": { "title": "Hello", "content": "world" } }
+            ] }
+        }));
+        assert!(
+            matches!(&events[0], ClaudeStreamEvent::ToolStart { input: Some(inp), .. }
+                if inp.contains("title") && inp.contains("Hello"))
+        );
+    }
+
+    #[test]
+    fn content_block_stop_clears_current_tool() {
+        let (state, _) = run_dispatch_sequence(vec![
+            serde_json::json!({
+                "type": "stream_event",
+                "event": { "type": "content_block_start", "content_block": { "type": "tool_use", "id": "t1", "name": "x", "input": {} } }
+            }),
+            serde_json::json!({
+                "type": "stream_event",
+                "event": { "type": "content_block_stop" }
+            }),
+        ]);
+        assert!(state.current_tool_id.is_none());
+    }
+
     // --- run_claude_subprocess with mock scripts ---
 
     #[cfg(unix)]

src-tauri/src/lib.rs

@@ -391,11 +391,11 @@ async fn start_indexing(app_handle: tauri::AppHandle, vault_path: String) -> Res
             match indexing::auto_install_qmd() {
                 Ok(_) => log::info!("qmd auto-installed successfully"),
                 Err(e) => {
-                    log::warn!("qmd auto-install failed: {e}");
+                    log::info!("qmd not available (search disabled): {e}");
                     let _ = app_handle.emit(
                         "indexing-progress",
                         IndexingProgress {
-                            phase: "error".to_string(),
+                            phase: "unavailable".to_string(),
                             current: 0,
                             total: 0,
                             done: true,
@@ -433,6 +433,13 @@ async fn register_mcp_tools(vault_path: String) -> Result<String, String> {
         .map_err(|e| format!("Registration task failed: {e}"))?
 }
 
+#[tauri::command]
+async fn check_mcp_status() -> Result<mcp::McpStatus, String> {
+    tokio::task::spawn_blocking(mcp::check_mcp_status)
+        .await
+        .map_err(|e| format!("MCP status check failed: {e}"))
+}
+
 #[tauri::command]
 fn list_themes(vault_path: String) -> Result<Vec<ThemeFile>, String> {
     let vault_path = expand_tilde(&vault_path);
@@ -475,6 +482,12 @@ fn create_vault_theme(vault_path: String, name: Option<String>) -> Result<String
     theme::create_vault_theme(&vault_path, name.as_deref())
 }
 
+#[tauri::command]
+fn ensure_vault_themes(vault_path: String) -> Result<(), String> {
+    let vault_path = expand_tilde(&vault_path);
+    theme::ensure_vault_themes(&vault_path)
+}
+
 fn log_startup_result(label: &str, result: Result<usize, String>) {
     match result {
         Ok(n) if n > 0 => log::info!("{}: {} files", label, n),
@@ -664,13 +677,15 @@ pub fn run() {
             check_vault_exists,
             get_default_vault_path,
             register_mcp_tools,
+            check_mcp_status,
             list_themes,
             get_theme,
             get_vault_settings,
             save_vault_settings,
             set_active_theme,
             create_theme,
-            create_vault_theme
+            create_vault_theme,
+            ensure_vault_themes
         ])
         .build(tauri::generate_context!())
         .expect("error while building tauri application")

src-tauri/src/mcp.rs

@@ -1,6 +1,19 @@
+use serde::Serialize;
 use std::path::{Path, PathBuf};
 use std::process::{Child, Command};
 
+/// Status of the MCP server installation.
+#[derive(Debug, Serialize, Clone, PartialEq)]
+#[serde(rename_all = "snake_case")]
+pub enum McpStatus {
+    /// MCP is registered in Claude config and server files exist.
+    Installed,
+    /// MCP server files or config are missing but can be installed.
+    NotInstalled,
+    /// Claude CLI is not installed — must install that first.
+    NoClaudeCli,
+}
+
 /// Find the `node` binary path at runtime.
 pub(crate) fn find_node() -> Result<PathBuf, String> {
     let output = Command::new("which")
@@ -144,6 +157,57 @@ fn upsert_mcp_config(config_path: &Path, entry: &serde_json::Value) -> Result<bo
     Ok(was_update)
 }
 
+/// Check whether the MCP server is properly installed and registered.
+///
+/// Returns `Installed` when the laputa entry exists in `~/.claude/mcp.json`
+/// and the referenced index.js file is present. Returns `NoClaudeCli` when
+/// the Claude CLI binary cannot be found. Otherwise returns `NotInstalled`.
+pub fn check_mcp_status() -> McpStatus {
+    // Check Claude CLI first — no point installing MCP if Claude isn't available
+    if crate::claude_cli::find_claude_binary().is_err() {
+        return McpStatus::NoClaudeCli;
+    }
+
+    let config_path = match dirs::home_dir() {
+        Some(h) => h.join(".claude").join("mcp.json"),
+        None => return McpStatus::NotInstalled,
+    };
+
+    if !config_path.exists() {
+        return McpStatus::NotInstalled;
+    }
+
+    let raw = match std::fs::read_to_string(&config_path) {
+        Ok(r) => r,
+        Err(_) => return McpStatus::NotInstalled,
+    };
+
+    let config: serde_json::Value = match serde_json::from_str(&raw) {
+        Ok(c) => c,
+        Err(_) => return McpStatus::NotInstalled,
+    };
+
+    let entry = &config["mcpServers"]["laputa"];
+    if entry.is_null() {
+        return McpStatus::NotInstalled;
+    }
+
+    // Verify the referenced index.js actually exists on disk
+    if let Some(index_js) = entry["args"]
+        .as_array()
+        .and_then(|a| a.first())
+        .and_then(|v| v.as_str())
+    {
+        if !Path::new(index_js).exists() {
+            return McpStatus::NotInstalled;
+        }
+    } else {
+        return McpStatus::NotInstalled;
+    }
+
+    McpStatus::Installed
+}
+
 #[cfg(test)]
 mod tests {
     use super::*;
@@ -314,4 +378,29 @@ mod tests {
         // With empty config list, there were no updates, so status should be "registered"
         assert_eq!(status, "registered");
     }
+
+    #[test]
+    fn check_mcp_status_returns_valid_variant() {
+        // On a dev machine with Claude CLI and MCP registered, this should be Installed.
+        // On CI without Claude it might be NoClaudeCli. Either way it must not panic.
+        let status = check_mcp_status();
+        assert!(
+            matches!(
+                status,
+                McpStatus::Installed | McpStatus::NotInstalled | McpStatus::NoClaudeCli
+            ),
+            "unexpected status: {:?}",
+            status
+        );
+    }
+
+    #[test]
+    fn mcp_status_serializes_to_snake_case() {
+        let json = serde_json::to_string(&McpStatus::Installed).unwrap();
+        assert_eq!(json, r#""installed""#);
+        let json = serde_json::to_string(&McpStatus::NotInstalled).unwrap();
+        assert_eq!(json, r#""not_installed""#);
+        let json = serde_json::to_string(&McpStatus::NoClaudeCli).unwrap();
+        assert_eq!(json, r#""no_claude_cli""#);
+    }
 }

src-tauri/src/theme.rs

@@ -145,17 +145,50 @@ pub fn seed_default_themes(vault_path: &str) {
 }
 
 /// Seed the vault `theme/` directory with built-in vault-based theme notes.
-/// Safe to call multiple times — only writes files that are missing.
+/// Per-file idempotent: creates the directory if missing, writes each default
+/// file only when it doesn't exist or is empty (corrupt). Never overwrites
+/// existing files that have content.
 pub fn seed_vault_themes(vault_path: &str) {
-    seed_dir_with_files(
-        &Path::new(vault_path).join("theme"),
-        &[
-            ("default.md", DEFAULT_VAULT_THEME),
-            ("dark.md", DARK_VAULT_THEME),
-            ("minimal.md", MINIMAL_VAULT_THEME),
-        ],
-        "Seeded theme/ with built-in vault themes",
-    );
+    let theme_dir = Path::new(vault_path).join("theme");
+    if fs::create_dir_all(&theme_dir).is_err() {
+        return;
+    }
+    let defaults: &[(&str, &str)] = &[
+        ("default.md", DEFAULT_VAULT_THEME),
+        ("dark.md", DARK_VAULT_THEME),
+        ("minimal.md", MINIMAL_VAULT_THEME),
+    ];
+    let mut seeded = false;
+    for (name, content) in defaults {
+        let path = theme_dir.join(name);
+        let needs_write = !path.exists() || fs::metadata(&path).map_or(true, |m| m.len() == 0);
+        if needs_write {
+            let _ = fs::write(&path, content);
+            seeded = true;
+        }
+    }
+    if seeded {
+        log::info!("Seeded theme/ with built-in vault themes");
+    }
+}
+
+/// Ensure vault theme files exist. Returns an error if the theme directory
+/// cannot be created (e.g. read-only filesystem).
+pub fn ensure_vault_themes(vault_path: &str) -> Result<(), String> {
+    let theme_dir = Path::new(vault_path).join("theme");
+    fs::create_dir_all(&theme_dir).map_err(|e| format!("Failed to create theme directory: {e}"))?;
+    let defaults: &[(&str, &str)] = &[
+        ("default.md", DEFAULT_VAULT_THEME),
+        ("dark.md", DARK_VAULT_THEME),
+    ];
+    for (name, content) in defaults {
+        let path = theme_dir.join(name);
+        let needs_write = !path.exists() || fs::metadata(&path).map_or(true, |m| m.len() == 0);
+        if needs_write {
+            fs::write(&path, content).map_err(|e| format!("Failed to write theme/{name}: {e}"))?;
+        }
+    }
+    Ok(())
 }
 
 /// Create a new vault theme note in `theme/` directory.
@@ -856,4 +889,94 @@ mod tests {
         assert!(content.contains("accent-blue:"));
         assert!(content.contains("editor-font-size:"));
     }
+
+    #[test]
+    fn test_seed_vault_themes_writes_missing_files_in_existing_dir() {
+        let dir = TempDir::new().unwrap();
+        let vault = dir.path().join("vault");
+        let theme_dir = vault.join("theme");
+        fs::create_dir_all(&theme_dir).unwrap();
+        // Only default exists — dark and minimal should be seeded
+        fs::write(theme_dir.join("default.md"), DEFAULT_VAULT_THEME).unwrap();
+        let vp = vault.to_str().unwrap();
+
+        seed_vault_themes(vp);
+        assert!(theme_dir.join("dark.md").exists());
+        assert!(theme_dir.join("minimal.md").exists());
+    }
+
+    #[test]
+    fn test_seed_vault_themes_reseeds_empty_files() {
+        let dir = TempDir::new().unwrap();
+        let vault = dir.path().join("vault");
+        let theme_dir = vault.join("theme");
+        fs::create_dir_all(&theme_dir).unwrap();
+        // Create empty file — should be re-seeded
+        fs::write(theme_dir.join("default.md"), "").unwrap();
+        let vp = vault.to_str().unwrap();
+
+        seed_vault_themes(vp);
+        let content = fs::read_to_string(theme_dir.join("default.md")).unwrap();
+        assert!(content.contains("Is A: Theme"));
+    }
+
+    #[test]
+    fn test_seed_vault_themes_preserves_existing_content() {
+        let dir = TempDir::new().unwrap();
+        let vault = dir.path().join("vault");
+        let theme_dir = vault.join("theme");
+        fs::create_dir_all(&theme_dir).unwrap();
+        let custom = "---\nIs A: Theme\nbackground: \"#FF0000\"\n---\n# Custom\n";
+        fs::write(theme_dir.join("default.md"), custom).unwrap();
+        let vp = vault.to_str().unwrap();
+
+        seed_vault_themes(vp);
+        let content = fs::read_to_string(theme_dir.join("default.md")).unwrap();
+        assert!(
+            content.contains("#FF0000"),
+            "existing content must be preserved"
+        );
+    }
+
+    #[test]
+    fn test_ensure_vault_themes_creates_dir_and_defaults() {
+        let dir = TempDir::new().unwrap();
+        let vault = dir.path().join("vault");
+        fs::create_dir_all(&vault).unwrap();
+        let vp = vault.to_str().unwrap();
+
+        ensure_vault_themes(vp).unwrap();
+        assert!(vault.join("theme").is_dir());
+        assert!(vault.join("theme").join("default.md").exists());
+        assert!(vault.join("theme").join("dark.md").exists());
+    }
+
+    #[test]
+    fn test_ensure_vault_themes_reseeds_empty_files() {
+        let dir = TempDir::new().unwrap();
+        let vault = dir.path().join("vault");
+        let theme_dir = vault.join("theme");
+        fs::create_dir_all(&theme_dir).unwrap();
+        fs::write(theme_dir.join("default.md"), "").unwrap();
+        let vp = vault.to_str().unwrap();
+
+        ensure_vault_themes(vp).unwrap();
+        let content = fs::read_to_string(theme_dir.join("default.md")).unwrap();
+        assert!(content.contains("Is A: Theme"));
+    }
+
+    #[test]
+    fn test_ensure_vault_themes_preserves_custom_themes() {
+        let dir = TempDir::new().unwrap();
+        let vault = dir.path().join("vault");
+        let theme_dir = vault.join("theme");
+        fs::create_dir_all(&theme_dir).unwrap();
+        let custom = "---\nIs A: Theme\nbackground: \"#123456\"\n---\n";
+        fs::write(theme_dir.join("default.md"), custom).unwrap();
+        let vp = vault.to_str().unwrap();
+
+        ensure_vault_themes(vp).unwrap();
+        let content = fs::read_to_string(theme_dir.join("default.md")).unwrap();
+        assert!(content.contains("#123456"));
+    }
 }

src/App.css

@@ -61,3 +61,14 @@
 .tab-status-pulse {
   animation: tab-status-pulse 1.2s ease-in-out infinite;
 }
+
+/* AI highlight animation — applied by useAiActivity when MCP calls ui_highlight */
+@keyframes ai-highlight-glow {
+  0% { box-shadow: inset 0 0 0 2px rgba(99, 102, 241, 0.8); }
+  50% { box-shadow: inset 0 0 8px 2px rgba(99, 102, 241, 0.4); }
+  100% { box-shadow: inset 0 0 0 2px rgba(99, 102, 241, 0); }
+}
+
+.ai-highlight {
+  animation: ai-highlight-glow 0.8s ease-out;
+}

src/App.tsx

@@ -1,4 +1,4 @@
-import { useCallback, useEffect, useRef, useState } from 'react'
+import { useCallback, useEffect, useMemo, useRef, useState } from 'react'
 import { Sidebar } from './components/Sidebar'
 import { NoteList } from './components/NoteList'
 import { Editor } from './components/Editor'
@@ -13,7 +13,7 @@ import { StatusBar } from './components/StatusBar'
 import { SettingsPanel } from './components/SettingsPanel'
 import { GitHubVaultModal } from './components/GitHubVaultModal'
 import { WelcomeScreen } from './components/WelcomeScreen'
-import { useMcpRegistration } from './hooks/useMcpRegistration'
+import { useMcpStatus } from './hooks/useMcpStatus'
 import { useVaultLoader } from './hooks/useVaultLoader'
 import { useSettings } from './hooks/useSettings'
 import { useNoteActions } from './hooks/useNoteActions'
@@ -35,11 +35,14 @@ import { useOnboarding } from './hooks/useOnboarding'
 import { useThemeManager } from './hooks/useThemeManager'
 import { useEditorSaveWithLinks } from './hooks/useEditorSaveWithLinks'
 import { useNavigationGestures } from './hooks/useNavigationGestures'
+import { useAiActivity } from './hooks/useAiActivity'
 import { ConflictResolverModal } from './components/ConflictResolverModal'
 import { UpdateBanner } from './components/UpdateBanner'
 import { invoke } from '@tauri-apps/api/core'
 import { isTauri, mockInvoke } from './mock-tauri'
 import type { SidebarSelection } from './types'
+import type { NoteListItem } from './utils/ai-context'
+import { filterEntries } from './utils/noteListHelpers'
 import './App.css'
 
 // Type declaration for mock content storage
@@ -102,7 +105,7 @@ function App() {
   const { settings, saveSettings } = useSettings()
   const themeManager = useThemeManager(resolvedPath, vault.entries, vault.allContent)
 
-  useMcpRegistration(resolvedPath, setToastMessage)
+  const { mcpStatus, installMcp } = useMcpStatus(resolvedPath, setToastMessage)
 
   const autoSync = useAutoSync({
     vaultPath: resolvedPath,
@@ -208,6 +211,22 @@ function App() {
 
   useNavigationGestures({ onGoBack: handleGoBack, onGoForward: handleGoForward })
 
+  // MCP UI bridge: react to AI-driven open/highlight/vault-change events
+  const aiActivity = useAiActivity({
+    onOpenNote: (path) => {
+      const entry = vault.entries.find(e => e.path === path || e.path === `${resolvedPath}/${path}`)
+      if (entry) notes.handleSelectNote(entry)
+    },
+    onOpenTab: (path) => {
+      const entry = vault.entries.find(e => e.path === path || e.path === `${resolvedPath}/${path}`)
+      if (entry) notes.handleSelectNote(entry)
+    },
+    onSetFilter: (filterType) => {
+      setSelection({ kind: 'sectionGroup', type: filterType })
+    },
+    onVaultChanged: () => { vault.reloadVault() },
+  })
+
   const { triggerIncrementalIndex } = indexing
   const onAfterSave = useCallback(() => {
     vault.loadModifiedFiles()
@@ -367,10 +386,25 @@ function App() {
     onRestoreGettingStarted: vaultSwitcher.restoreGettingStarted,
     isGettingStartedHidden: vaultSwitcher.isGettingStartedHidden,
     vaultCount: vaultSwitcher.allVaults.length,
+    mcpStatus,
+    onInstallMcp: installMcp,
   })
 
   const activeTab = notes.tabs.find((t) => t.entry.path === notes.activeTabPath) ?? null
 
+  const aiNoteList = useMemo<NoteListItem[]>(() => {
+    return filterEntries(vault.entries, selection).map(e => ({
+      path: e.path, title: e.title, type: e.isA ?? 'Note',
+    }))
+  }, [vault.entries, selection])
+
+  const aiNoteListFilter = useMemo(() => {
+    if (selection.kind === 'sectionGroup') return { type: selection.type, query: '' }
+    if (selection.kind === 'topic') return { type: null, query: selection.entry.title }
+    if (selection.kind === 'entity') return { type: null, query: selection.entry.title }
+    return { type: null, query: '' }
+  }, [selection])
+
   // Show welcome/onboarding screen when vault doesn't exist
   if (onboarding.state.status === 'welcome' || onboarding.state.status === 'vault-missing') {
     const defaultPath = onboarding.state.defaultPath
@@ -413,13 +447,13 @@ function App() {
         )}
         {noteListVisible && (
           <>
-            <div className="app__note-list" style={{ width: layout.noteListWidth }}>
+            <div className={`app__note-list${aiActivity.highlightElement === 'notelist' ? ' ai-highlight' : ''}`} style={{ width: layout.noteListWidth }}>
               <NoteList entries={vault.entries} selection={selection} selectedNote={activeTab?.entry ?? null} allContent={vault.allContent} modifiedFiles={vault.modifiedFiles} modifiedFilesError={vault.modifiedFilesError} getNoteStatus={vault.getNoteStatus} sidebarCollapsed={!sidebarVisible} onSelectNote={notes.handleSelectNote} onReplaceActiveTab={notes.handleReplaceActiveTab} onCreateNote={notes.handleCreateNoteImmediate} onBulkArchive={bulkActions.handleBulkArchive} onBulkTrash={bulkActions.handleBulkTrash} onUpdateTypeSort={notes.handleUpdateFrontmatter} updateEntry={vault.updateEntry} />
             </div>
             <ResizeHandle onResize={layout.handleNoteListResize} />
           </>
         )}
-        <div className="app__editor">
+        <div className={`app__editor${aiActivity.highlightElement === 'editor' || aiActivity.highlightElement === 'tab' ? ' ai-highlight' : ''}`}>
           <Editor
             tabs={notes.tabs}
             activeTabPath={notes.activeTabPath}
@@ -446,6 +480,8 @@ function App() {
             showAIChat={dialogs.showAIChat}
             onToggleAIChat={dialogs.toggleAIChat}
             vaultPath={resolvedPath}
+            noteList={aiNoteList}
+            noteListFilter={aiNoteListFilter}
             onTrashNote={entryActions.handleTrashNote}
             onRestoreNote={entryActions.handleRestoreNote}
             onDeleteNote={handleDeleteNote}
@@ -467,7 +503,7 @@ function App() {
         </div>
       </div>
       <UpdateBanner status={updateStatus} actions={updateActions} />
-      <StatusBar noteCount={vault.entries.length} modifiedCount={vault.modifiedFiles.length} vaultPath={vaultSwitcher.vaultPath} vaults={vaultSwitcher.allVaults} onSwitchVault={vaultSwitcher.switchVault} onOpenSettings={dialogs.openSettings} onOpenLocalFolder={vaultSwitcher.handleOpenLocalFolder} onConnectGitHub={dialogs.openGitHubVault} onClickPending={() => setSelection({ kind: 'filter', filter: 'changes' })} hasGitHub={!!settings.github_token} syncStatus={autoSync.syncStatus} lastSyncTime={autoSync.lastSyncTime} conflictCount={autoSync.conflictFiles.length} lastCommitInfo={autoSync.lastCommitInfo} onTriggerSync={autoSync.triggerSync} onOpenConflictResolver={handleOpenConflictResolver} zoomLevel={zoom.zoomLevel} onZoomReset={zoom.zoomReset} buildNumber={buildNumber} onCheckForUpdates={handleCheckForUpdates} indexingProgress={indexing.progress} onRemoveVault={vaultSwitcher.removeVault} />
+      <StatusBar noteCount={vault.entries.length} modifiedCount={vault.modifiedFiles.length} vaultPath={vaultSwitcher.vaultPath} vaults={vaultSwitcher.allVaults} onSwitchVault={vaultSwitcher.switchVault} onOpenSettings={dialogs.openSettings} onOpenLocalFolder={vaultSwitcher.handleOpenLocalFolder} onConnectGitHub={dialogs.openGitHubVault} onClickPending={() => setSelection({ kind: 'filter', filter: 'changes' })} hasGitHub={!!settings.github_token} syncStatus={autoSync.syncStatus} lastSyncTime={autoSync.lastSyncTime} conflictCount={autoSync.conflictFiles.length} lastCommitInfo={autoSync.lastCommitInfo} onTriggerSync={autoSync.triggerSync} onOpenConflictResolver={handleOpenConflictResolver} zoomLevel={zoom.zoomLevel} onZoomReset={zoom.zoomReset} buildNumber={buildNumber} onCheckForUpdates={handleCheckForUpdates} indexingProgress={indexing.progress} onRetryIndexing={indexing.retryIndexing} onRemoveVault={vaultSwitcher.removeVault} mcpStatus={mcpStatus} onInstallMcp={installMcp} />
       <Toast message={toastMessage} onDismiss={() => setToastMessage(null)} />
       <QuickOpenPalette open={dialogs.showQuickOpen} entries={vault.entries} onSelect={notes.handleSelectNote} onClose={dialogs.closeQuickOpen} />
       <CommandPalette open={dialogs.showCommandPalette} commands={commands} onClose={dialogs.closeCommandPalette} />

src/components/AiActionCard.test.tsx

@@ -2,61 +2,166 @@ import { describe, it, expect, vi } from 'vitest'
 import { render, screen, fireEvent } from '@testing-library/react'
 import { AiActionCard } from './AiActionCard'
 
+const defaults = {
+  tool: 'create_note',
+  label: 'Creating note... (abc123)',
+  status: 'done' as const,
+  expanded: false,
+  onToggle: vi.fn(),
+}
+
 describe('AiActionCard', () => {
   it('renders label text', () => {
-    render(<AiActionCard tool="create_note" label="Created test.md" status="done" />)
+    render(<AiActionCard {...defaults} label="Created test.md" />)
     expect(screen.getByText('Created test.md')).toBeTruthy()
   })
 
   it('shows pending spinner', () => {
-    render(<AiActionCard tool="search_notes" label="Searching..." status="pending" />)
+    render(<AiActionCard {...defaults} tool="search_notes" label="Searching..." status="pending" />)
     expect(screen.getByTestId('status-pending')).toBeTruthy()
   })
 
   it('shows done check', () => {
-    render(<AiActionCard tool="create_note" label="Created" status="done" />)
+    render(<AiActionCard {...defaults} status="done" />)
     expect(screen.getByTestId('status-done')).toBeTruthy()
   })
 
   it('shows error icon', () => {
-    render(<AiActionCard tool="delete_note" label="Failed" status="error" />)
+    render(<AiActionCard {...defaults} tool="delete_note" label="Failed" status="error" />)
     expect(screen.getByTestId('status-error')).toBeTruthy()
   })
 
-  it('is clickable when path and onOpenNote provided', () => {
+  it('navigates to note when no details and path+onOpenNote provided', () => {
     const onOpenNote = vi.fn()
-    render(<AiActionCard tool="create_note" label="Open note" path="/vault/test.md" status="done" onOpenNote={onOpenNote} />)
-    fireEvent.click(screen.getByTestId('ai-action-card'))
+    const toggle = vi.fn()
+    render(
+      <AiActionCard {...defaults} path="/vault/test.md" onOpenNote={onOpenNote} onToggle={toggle} />,
+    )
+    fireEvent.click(screen.getByTestId('action-card-header'))
     expect(onOpenNote).toHaveBeenCalledWith('/vault/test.md')
+    expect(toggle).not.toHaveBeenCalled()
   })
 
-  it('has button role when clickable', () => {
-    render(<AiActionCard tool="create_note" label="Open note" path="/vault/test.md" status="done" onOpenNote={vi.fn()} />)
-    expect(screen.getByRole('button')).toBeTruthy()
-  })
-
-  it('is not clickable without path', () => {
+  it('toggles expand instead of navigating when details exist', () => {
     const onOpenNote = vi.fn()
-    render(<AiActionCard tool="create_note" label="Created" status="done" onOpenNote={onOpenNote} />)
-    fireEvent.click(screen.getByTestId('ai-action-card'))
+    const toggle = vi.fn()
+    render(
+      <AiActionCard
+        {...defaults}
+        path="/vault/test.md"
+        onOpenNote={onOpenNote}
+        onToggle={toggle}
+        input='{"title":"test"}'
+      />,
+    )
+    fireEvent.click(screen.getByTestId('action-card-header'))
+    expect(toggle).toHaveBeenCalled()
     expect(onOpenNote).not.toHaveBeenCalled()
   })
 
-  it('is not clickable without onOpenNote', () => {
-    render(<AiActionCard tool="create_note" label="Created" path="/vault/test.md" status="done" />)
-    const card = screen.getByTestId('ai-action-card')
-    expect(card.getAttribute('role')).toBeNull()
+  it('header has button role and is focusable', () => {
+    render(<AiActionCard {...defaults} />)
+    const header = screen.getByTestId('action-card-header')
+    expect(header.getAttribute('role')).toBe('button')
+    expect(header.getAttribute('tabindex')).toBe('0')
   })
 
   it('uses lighter background for ui_ tools', () => {
-    render(<AiActionCard tool="ui_open_tab" label="Opened tab" status="done" />)
+    render(<AiActionCard {...defaults} tool="ui_open_tab" label="Opened tab" />)
     const card = screen.getByTestId('ai-action-card')
     expect(card.style.background).toContain('0.06')
   })
 
   it('uses standard background for vault tools', () => {
-    render(<AiActionCard tool="create_note" label="Created" status="done" />)
+    render(<AiActionCard {...defaults} />)
     const card = screen.getByTestId('ai-action-card')
     expect(card.style.background).toContain('0.1')
   })
+
+  // --- Expand / collapse ---
+
+  it('does not show details when collapsed', () => {
+    render(<AiActionCard {...defaults} input='{"q":"test"}' output="found 3" expanded={false} />)
+    expect(screen.queryByTestId('action-card-details')).toBeNull()
+  })
+
+  it('shows details when expanded with input and output', () => {
+    render(<AiActionCard {...defaults} input='{"q":"test"}' output="found 3" expanded />)
+    expect(screen.getByTestId('action-card-details')).toBeTruthy()
+    expect(screen.getByTestId('detail-input')).toBeTruthy()
+    expect(screen.getByTestId('detail-output')).toBeTruthy()
+  })
+
+  it('shows only input when no output', () => {
+    render(<AiActionCard {...defaults} input='{"q":"test"}' expanded />)
+    expect(screen.getByTestId('detail-input')).toBeTruthy()
+    expect(screen.queryByTestId('detail-output')).toBeNull()
+  })
+
+  it('shows only output when no input', () => {
+    render(<AiActionCard {...defaults} output="result text" expanded />)
+    expect(screen.queryByTestId('detail-input')).toBeNull()
+    expect(screen.getByTestId('detail-output')).toBeTruthy()
+  })
+
+  it('does not show details when expanded but no input or output', () => {
+    render(<AiActionCard {...defaults} expanded />)
+    expect(screen.queryByTestId('action-card-details')).toBeNull()
+  })
+
+  it('formats JSON input prettily', () => {
+    render(<AiActionCard {...defaults} input='{"title":"Hello","content":"world"}' expanded />)
+    const inputBlock = screen.getByTestId('detail-input')
+    expect(inputBlock.textContent).toContain('"title": "Hello"')
+  })
+
+  it('truncates very long output', () => {
+    const longOutput = 'x'.repeat(1000)
+    render(<AiActionCard {...defaults} output={longOutput} expanded />)
+    const outputBlock = screen.getByTestId('detail-output')
+    expect(outputBlock.textContent!.length).toBeLessThan(1000)
+  })
+
+  // --- Keyboard accessibility ---
+
+  it('expands on Enter key', () => {
+    const toggle = vi.fn()
+    render(<AiActionCard {...defaults} onToggle={toggle} input='{"a":1}' />)
+    fireEvent.keyDown(screen.getByTestId('action-card-header'), { key: 'Enter' })
+    expect(toggle).toHaveBeenCalled()
+  })
+
+  it('expands on Space key', () => {
+    const toggle = vi.fn()
+    render(<AiActionCard {...defaults} onToggle={toggle} input='{"a":1}' />)
+    fireEvent.keyDown(screen.getByTestId('action-card-header'), { key: ' ' })
+    expect(toggle).toHaveBeenCalled()
+  })
+
+  it('collapses on Escape key when expanded', () => {
+    const toggle = vi.fn()
+    render(<AiActionCard {...defaults} onToggle={toggle} expanded input='{"a":1}' />)
+    fireEvent.keyDown(screen.getByTestId('action-card-header'), { key: 'Escape' })
+    expect(toggle).toHaveBeenCalled()
+  })
+
+  it('does not collapse on Escape when already collapsed', () => {
+    const toggle = vi.fn()
+    render(<AiActionCard {...defaults} onToggle={toggle} expanded={false} input='{"a":1}' />)
+    fireEvent.keyDown(screen.getByTestId('action-card-header'), { key: 'Escape' })
+    expect(toggle).not.toHaveBeenCalled()
+  })
+
+  it('sets aria-expanded attribute', () => {
+    const { rerender } = render(<AiActionCard {...defaults} expanded={false} />)
+    expect(screen.getByTestId('action-card-header').getAttribute('aria-expanded')).toBe('false')
+    rerender(<AiActionCard {...defaults} expanded />)
+    expect(screen.getByTestId('action-card-header').getAttribute('aria-expanded')).toBe('true')
+  })
+
+  it('shows error output in red for error status', () => {
+    render(<AiActionCard {...defaults} status="error" output="Permission denied" expanded />)
+    const outputBlock = screen.getByTestId('detail-output')
+    expect(outputBlock.style.color).toContain('destructive')
+  })
 })

src/components/AiActionCard.tsx

@@ -1,7 +1,7 @@
-import type { ReactNode } from 'react'
+import { type KeyboardEvent, type ReactNode, useCallback } from 'react'
 import {
   PencilSimple, MagnifyingGlass, Link, Trash, ChartBar, Eye, Sparkle,
-  CircleNotch, CheckCircle, XCircle,
+  CircleNotch, CheckCircle, XCircle, CaretRight, CaretDown,
 } from '@phosphor-icons/react'
 
 export type AiActionStatus = 'pending' | 'done' | 'error'
@@ -11,9 +11,15 @@ export interface AiActionCardProps {
   label: string
   path?: string
   status: AiActionStatus
+  input?: string
+  output?: string
+  expanded: boolean
+  onToggle: () => void
   onOpenNote?: (path: string) => void
 }
 
+const MAX_DETAIL_LENGTH = 800
+
 type IconRenderer = (size: number) => ReactNode
 
 const TOOL_ICON_MAP: Record<string, IconRenderer> = {
@@ -43,27 +49,118 @@ function StatusIndicator({ status }: { status: AiActionStatus }) {
   return <XCircle size={14} weight="fill" style={{ color: 'var(--destructive)' }} data-testid="status-error" />
 }
 
-export function AiActionCard({ tool, label, path, status, onOpenNote }: AiActionCardProps) {
-  const renderIcon = TOOL_ICON_MAP[tool] ?? DEFAULT_ICON
-  const isClickable = !!path && !!onOpenNote
-  const isUiTool = tool.startsWith('ui_')
+function truncateText(text: string): { text: string; truncated: boolean } {
+  if (text.length <= MAX_DETAIL_LENGTH) return { text, truncated: false }
+  return { text: text.slice(0, MAX_DETAIL_LENGTH), truncated: true }
+}
 
+function formatInputForDisplay(raw: string): string {
+  try {
+    return JSON.stringify(JSON.parse(raw), null, 2)
+  } catch {
+    return raw
+  }
+}
+
+function DetailBlock({ label, content, isError }: {
+  label: string; content: string; isError?: boolean
+}) {
+  const { text, truncated } = truncateText(content)
   return (
-    <div
-      className="flex items-center gap-2 rounded"
-      style={{
-        padding: '6px 10px',
-        fontSize: 12,
-        background: isUiTool ? 'rgba(74, 158, 255, 0.06)' : 'rgba(74, 158, 255, 0.1)',
-        cursor: isClickable ? 'pointer' : 'default',
-      }}
-      onClick={isClickable ? () => onOpenNote(path) : undefined}
-      role={isClickable ? 'button' : undefined}
-      data-testid="ai-action-card"
-    >
-      <span className="shrink-0 text-muted-foreground">{renderIcon(14)}</span>
-      <span className="flex-1 truncate">{label}</span>
-      <StatusIndicator status={status} />
+    <div style={{ marginTop: 6 }}>
+      <div
+        className="text-muted-foreground"
+        style={{ fontSize: 10, fontWeight: 600, textTransform: 'uppercase', marginBottom: 2 }}
+      >
+        {label}
+      </div>
+      <pre
+        data-testid={`detail-${label.toLowerCase()}`}
+        style={{
+          fontSize: 11,
+          lineHeight: 1.4,
+          margin: 0,
+          padding: '4px 6px',
+          borderRadius: 4,
+          background: 'var(--muted)',
+          color: isError ? 'var(--destructive)' : 'var(--foreground)',
+          whiteSpace: 'pre-wrap',
+          wordBreak: 'break-word',
+          maxHeight: 200,
+          overflow: 'auto',
+        }}
+      >
+        {text}{truncated && <span className="text-muted-foreground">{'…'}</span>}
+      </pre>
+    </div>
+  )
+}
+
+export function AiActionCard({
+  tool, label, path, status, input, output, expanded, onToggle, onOpenNote,
+}: AiActionCardProps) {
+  const renderIcon = TOOL_ICON_MAP[tool] ?? DEFAULT_ICON
+  const isUiTool = tool.startsWith('ui_')
+  const hasDetails = !!(input || output)
+
+  const handleKeyDown = useCallback((e: KeyboardEvent) => {
+    if (e.key === 'Enter' || e.key === ' ') {
+      e.preventDefault()
+      onToggle()
+    } else if (e.key === 'Escape' && expanded) {
+      e.preventDefault()
+      onToggle()
+    }
+  }, [onToggle, expanded])
+
+  const handleClick = useCallback(() => {
+    if (path && onOpenNote && !hasDetails) {
+      onOpenNote(path)
+    } else {
+      onToggle()
+    }
+  }, [path, onOpenNote, hasDetails, onToggle])
+
+  const formattedInput = input ? formatInputForDisplay(input) : undefined
+
+  return (
+    <div
+      data-testid="ai-action-card"
+      className="rounded"
+      style={{
+        fontSize: 12,
+        background: isUiTool ? 'rgba(74, 158, 255, 0.06)' : 'rgba(74, 158, 255, 0.1)',
+      }}
+    >
+      <div
+        className="flex items-center gap-2"
+        style={{ padding: '6px 10px', cursor: 'pointer' }}
+        role="button"
+        tabIndex={0}
+        aria-expanded={expanded}
+        onClick={handleClick}
+        onKeyDown={handleKeyDown}
+        data-testid="action-card-header"
+      >
+        <span className="shrink-0 text-muted-foreground" style={{ width: 14, display: 'flex' }}>
+          {hasDetails
+            ? (expanded ? <CaretDown size={12} /> : <CaretRight size={12} />)
+            : renderIcon(14)}
+        </span>
+        <span className="flex-1 truncate">{label}</span>
+        <StatusIndicator status={status} />
+      </div>
+      {expanded && hasDetails && (
+        <div
+          data-testid="action-card-details"
+          style={{ padding: '0 10px 8px 10px' }}
+        >
+          {formattedInput && <DetailBlock label="Input" content={formattedInput} />}
+          {output && (
+            <DetailBlock label="Output" content={output} isError={status === 'error'} />
+          )}
+        </div>
+      )}
     </div>
   )
 }

src/components/AiMessage.test.tsx

@@ -2,15 +2,20 @@ import { describe, it, expect, vi } from 'vitest'
 import { render, screen, fireEvent } from '@testing-library/react'
 import { AiMessage } from './AiMessage'
 
+vi.mock('./MarkdownContent', () => ({
+  MarkdownContent: ({ content }: { content: string }) => <div data-testid="markdown-content">{content}</div>,
+}))
+
 describe('AiMessage', () => {
   it('renders user message', () => {
     render(<AiMessage userMessage="Hello AI" actions={[]} />)
     expect(screen.getByText('Hello AI')).toBeTruthy()
   })
 
-  it('renders response text', () => {
-    render(<AiMessage userMessage="Ask" actions={[]} response="Here is the answer" />)
-    expect(screen.getByText('Here is the answer')).toBeTruthy()
+  it('renders response as markdown', () => {
+    render(<AiMessage userMessage="Ask" actions={[]} response="Here is the **answer**" />)
+    expect(screen.getByTestId('markdown-content')).toBeTruthy()
+    expect(screen.getByText('Here is the **answer**')).toBeTruthy()
   })
 
   it('shows undo button with response', () => {
@@ -18,23 +23,31 @@ describe('AiMessage', () => {
     expect(screen.getByTestId('undo-button')).toBeTruthy()
   })
 
-  it('renders reasoning toggle collapsed by default', () => {
-    render(<AiMessage userMessage="Ask" reasoning="Thinking about it..." actions={[]} />)
+  it('shows reasoning expanded while streaming (reasoningDone=false)', () => {
+    render(<AiMessage userMessage="Ask" reasoning="Thinking about it..." reasoningDone={false} actions={[]} />)
     expect(screen.getByTestId('reasoning-toggle')).toBeTruthy()
-    expect(screen.queryByTestId('reasoning-content')).toBeNull()
-  })
-
-  it('expands reasoning on toggle click', () => {
-    render(<AiMessage userMessage="Ask" reasoning="Thinking about it..." actions={[]} />)
-    fireEvent.click(screen.getByTestId('reasoning-toggle'))
     expect(screen.getByTestId('reasoning-content')).toBeTruthy()
     expect(screen.getByText('Thinking about it...')).toBeTruthy()
   })
 
-  it('collapses reasoning on second click', () => {
-    render(<AiMessage userMessage="Ask" reasoning="Thinking..." actions={[]} />)
+  it('auto-collapses reasoning when reasoningDone=true', () => {
+    render(<AiMessage userMessage="Ask" reasoning="Thinking..." reasoningDone actions={[]} />)
+    expect(screen.getByTestId('reasoning-toggle')).toBeTruthy()
+    expect(screen.queryByTestId('reasoning-content')).toBeNull()
+  })
+
+  it('expands collapsed reasoning on toggle click', () => {
+    render(<AiMessage userMessage="Ask" reasoning="Thinking..." reasoningDone actions={[]} />)
+    // Starts collapsed (reasoningDone=true)
+    expect(screen.queryByTestId('reasoning-content')).toBeNull()
     fireEvent.click(screen.getByTestId('reasoning-toggle'))
     expect(screen.getByTestId('reasoning-content')).toBeTruthy()
+  })
+
+  it('collapses expanded reasoning on toggle click', () => {
+    render(<AiMessage userMessage="Ask" reasoning="Thinking..." reasoningDone={false} actions={[]} />)
+    // Starts expanded (reasoningDone=false)
+    expect(screen.getByTestId('reasoning-content')).toBeTruthy()
     fireEvent.click(screen.getByTestId('reasoning-toggle'))
     expect(screen.queryByTestId('reasoning-content')).toBeNull()
   })
@@ -44,8 +57,8 @@ describe('AiMessage', () => {
       <AiMessage
         userMessage="Do something"
         actions={[
-          { tool: 'create_note', label: 'Created test.md', status: 'done' },
-          { tool: 'search_notes', label: 'Searched', status: 'pending' },
+          { tool: 'create_note', toolId: 't1', label: 'Created test.md', status: 'done' },
+          { tool: 'search_notes', toolId: 't2', label: 'Searched', status: 'pending' },
         ]}
       />,
     )
@@ -57,11 +70,11 @@ describe('AiMessage', () => {
     render(
       <AiMessage
         userMessage="Do"
-        actions={[{ tool: 'create_note', label: 'Open', path: '/vault/note.md', status: 'done' }]}
+        actions={[{ tool: 'create_note', toolId: 't1', label: 'Open', path: '/vault/note.md', status: 'done' }]}
         onOpenNote={onOpenNote}
       />,
     )
-    fireEvent.click(screen.getByTestId('ai-action-card'))
+    fireEvent.click(screen.getByTestId('action-card-header'))
     expect(onOpenNote).toHaveBeenCalledWith('/vault/note.md')
   })
 
@@ -88,4 +101,69 @@ describe('AiMessage', () => {
     render(<AiMessage userMessage="Ask" actions={[]} />)
     expect(screen.queryByTestId('ai-action-card')).toBeNull()
   })
+
+  it('renders reference pills in user bubble', () => {
+    render(
+      <AiMessage
+        userMessage="Tell me about this"
+        references={[
+          { title: 'Marco', path: 'person/marco.md', type: 'Person' },
+          { title: 'Project X', path: 'project/x.md', type: 'Project' },
+        ]}
+        actions={[]}
+      />,
+    )
+    const pills = screen.getAllByTestId('message-reference-pill')
+    expect(pills).toHaveLength(2)
+    expect(pills[0].textContent).toBe('Marco')
+    expect(pills[1].textContent).toBe('Project X')
+  })
+
+  it('does not render pills when no references', () => {
+    render(<AiMessage userMessage="Hello" actions={[]} />)
+    expect(screen.queryAllByTestId('message-reference-pill')).toHaveLength(0)
+  })
+
+  it('does not render pills when references array is empty', () => {
+    render(<AiMessage userMessage="Hello" references={[]} actions={[]} />)
+    expect(screen.queryAllByTestId('message-reference-pill')).toHaveLength(0)
+  })
+
+  it('calls onOpenNote when a reference pill is clicked', () => {
+    const onOpenNote = vi.fn()
+    render(
+      <AiMessage
+        userMessage="Check this"
+        references={[{ title: 'Alpha', path: 'note/alpha.md', type: 'Note' }]}
+        actions={[]}
+        onOpenNote={onOpenNote}
+      />,
+    )
+    fireEvent.click(screen.getByTestId('message-reference-pill'))
+    expect(onOpenNote).toHaveBeenCalledWith('note/alpha.md')
+  })
+
+  it('expands and collapses action cards independently', () => {
+    render(
+      <AiMessage
+        userMessage="Do"
+        actions={[
+          { tool: 'search_notes', toolId: 't1', label: 'Searched', status: 'done', input: '{"q":"test"}', output: 'Found 3' },
+          { tool: 'create_note', toolId: 't2', label: 'Created', status: 'done', input: '{"title":"x"}' },
+        ]}
+      />,
+    )
+    const headers = screen.getAllByTestId('action-card-header')
+    // Both collapsed initially
+    expect(screen.queryByTestId('action-card-details')).toBeNull()
+    // Expand first card
+    fireEvent.click(headers[0])
+    expect(screen.getAllByTestId('action-card-details')).toHaveLength(1)
+    // Expand second card too
+    fireEvent.click(headers[1])
+    expect(screen.getAllByTestId('action-card-details')).toHaveLength(2)
+    // Collapse first card
+    fireEvent.click(headers[0])
+    expect(screen.getAllByTestId('action-card-details')).toHaveLength(1)
+  })
 })

src/components/AiMessage.tsx

@@ -1,24 +1,63 @@
-import { useState } from 'react'
+import { useState, useCallback, useEffect, useRef } from 'react'
 import { CaretRight, CaretDown, Brain, ArrowCounterClockwise } from '@phosphor-icons/react'
 import { AiActionCard, type AiActionStatus } from './AiActionCard'
+import { MarkdownContent } from './MarkdownContent'
+import type { NoteReference } from '../utils/ai-context'
+import { getTypeColor, getTypeLightColor } from '../utils/typeColors'
 
 export interface AiAction {
   tool: string
+  toolId: string
   label: string
   path?: string
   status: AiActionStatus
+  input?: string
+  output?: string
 }
 
 export interface AiMessageProps {
   userMessage: string
+  references?: NoteReference[]
   reasoning?: string
+  reasoningDone?: boolean
   actions: AiAction[]
   response?: string
   isStreaming?: boolean
   onOpenNote?: (path: string) => void
 }
 
-function UserBubble({ content }: { content: string }) {
+function ReferencePill({ reference, onClick }: {
+  reference: NoteReference
+  onClick?: (path: string) => void
+}) {
+  const color = getTypeColor(reference.type)
+  const lightColor = getTypeLightColor(reference.type)
+  return (
+    <button
+      className="inline-flex items-center border-none cursor-pointer transition-opacity hover:opacity-80"
+      style={{
+        background: lightColor,
+        color,
+        borderRadius: 9999,
+        padding: '1px 8px',
+        fontSize: 11,
+        fontWeight: 500,
+        fontFamily: 'inherit',
+        lineHeight: 1.4,
+      }}
+      onClick={() => onClick?.(reference.path)}
+      data-testid="message-reference-pill"
+    >
+      {reference.title}
+    </button>
+  )
+}
+
+function UserBubble({ content, references, onOpenNote }: {
+  content: string
+  references?: NoteReference[]
+  onOpenNote?: (path: string) => void
+}) {
   return (
     <div className="flex justify-end" style={{ marginBottom: 8 }}>
       <div
@@ -32,6 +71,13 @@ function UserBubble({ content }: { content: string }) {
           lineHeight: 1.5,
         }}
       >
+        {references && references.length > 0 && (
+          <div className="flex flex-wrap gap-1" style={{ marginBottom: 4 }}>
+            {references.map(ref => (
+              <ReferencePill key={ref.path} reference={ref} onClick={onOpenNote} />
+            ))}
+          </div>
+        )}
         {content}
       </div>
     </div>
@@ -41,6 +87,14 @@ function UserBubble({ content }: { content: string }) {
 function ReasoningBlock({ text, expanded, onToggle }: {
   text: string; expanded: boolean; onToggle: () => void
 }) {
+  const contentRef = useRef<HTMLDivElement>(null)
+
+  useEffect(() => {
+    if (expanded && contentRef.current) {
+      contentRef.current.scrollTop = contentRef.current.scrollHeight
+    }
+  }, [expanded, text])
+
   return (
     <div style={{ marginBottom: 8 }}>
       <button
@@ -55,8 +109,9 @@ function ReasoningBlock({ text, expanded, onToggle }: {
       </button>
       {expanded && (
         <div
+          ref={contentRef}
           className="text-muted-foreground"
-          style={{ fontSize: 12, lineHeight: 1.5, padding: '4px 0 4px 20px' }}
+          style={{ fontSize: 12, lineHeight: 1.5, padding: '4px 0 4px 20px', maxHeight: 200, overflowY: 'auto' }}
           data-testid="reasoning-content"
         >
           {text}
@@ -66,18 +121,25 @@ function ReasoningBlock({ text, expanded, onToggle }: {
   )
 }
 
-function ActionCardsList({ actions, onOpenNote }: {
-  actions: AiAction[]; onOpenNote?: (path: string) => void
+function ActionCardsList({ actions, onOpenNote, expandedIds, onToggleExpand }: {
+  actions: AiAction[]
+  onOpenNote?: (path: string) => void
+  expandedIds: Set<string>
+  onToggleExpand: (toolId: string) => void
 }) {
   return (
     <div className="flex flex-col gap-1" style={{ marginBottom: 8 }}>
-      {actions.map((action, i) => (
+      {actions.map((action) => (
         <AiActionCard
-          key={`${action.tool}-${i}`}
+          key={action.toolId}
           tool={action.tool}
           label={action.label}
           path={action.path}
           status={action.status}
+          input={action.input}
+          output={action.output}
+          expanded={expandedIds.has(action.toolId)}
+          onToggle={() => onToggleExpand(action.toolId)}
           onOpenNote={onOpenNote}
         />
       ))}
@@ -88,7 +150,7 @@ function ActionCardsList({ actions, onOpenNote }: {
 function ResponseBlock({ text }: { text: string }) {
   return (
     <div style={{ marginBottom: 4 }}>
-      <div style={{ fontSize: 13, lineHeight: 1.6 }}>{text}</div>
+      <MarkdownContent content={text} />
       <button
         className="flex items-center gap-1 border-none bg-transparent p-0 text-muted-foreground cursor-pointer hover:text-foreground transition-colors"
         style={{ fontSize: 11, marginTop: 4 }}
@@ -113,20 +175,43 @@ function StreamingIndicator() {
   )
 }
 
-export function AiMessage({ userMessage, reasoning, actions, response, isStreaming, onOpenNote }: AiMessageProps) {
-  const [reasoningExpanded, setReasoningExpanded] = useState(false)
+export function AiMessage({ userMessage, references, reasoning, reasoningDone, actions, response, isStreaming, onOpenNote }: AiMessageProps) {
+  // Manual override: null = follow auto behavior, true/false = user forced
+  const [userOverride, setUserOverride] = useState(false)
+  const [expandedActions, setExpandedActions] = useState<Set<string>>(new Set())
+
+  // Auto: expanded while reasoning streams, collapsed once done
+  // User can manually toggle to override the auto state
+  const autoExpanded = !reasoningDone
+  const reasoningExpanded = userOverride ? !autoExpanded : autoExpanded
+
+  const toggleAction = useCallback((toolId: string) => {
+    setExpandedActions(prev => {
+      const next = new Set(prev)
+      if (next.has(toolId)) next.delete(toolId)
+      else next.add(toolId)
+      return next
+    })
+  }, [])
 
   return (
     <div data-testid="ai-message" style={{ marginBottom: 16 }}>
-      <UserBubble content={userMessage} />
+      <UserBubble content={userMessage} references={references} onOpenNote={onOpenNote} />
       {reasoning && (
         <ReasoningBlock
           text={reasoning}
           expanded={reasoningExpanded}
-          onToggle={() => setReasoningExpanded(!reasoningExpanded)}
+          onToggle={() => setUserOverride(prev => !prev)}
+        />
+      )}
+      {actions.length > 0 && (
+        <ActionCardsList
+          actions={actions}
+          onOpenNote={onOpenNote}
+          expandedIds={expandedActions}
+          onToggleExpand={toggleAction}
         />
       )}
-      {actions.length > 0 && <ActionCardsList actions={actions} onOpenNote={onOpenNote} />}
       {response && <ResponseBlock text={response} />}
       {isStreaming && !response && <StreamingIndicator />}
     </div>

src/components/AiPanel.tsx

@@ -1,8 +1,9 @@
 import { useState, useRef, useEffect, useCallback, useMemo } from 'react'
 import { Robot, X, PaperPlaneRight, Plus, Link } from '@phosphor-icons/react'
 import { AiMessage } from './AiMessage'
+import { WikilinkChatInput } from './WikilinkChatInput'
 import { useAiAgent, type AiAgentMessage } from '../hooks/useAiAgent'
-import { collectLinkedEntries, buildContextualPrompt } from '../utils/ai-context'
+import { collectLinkedEntries, buildContextSnapshot, type NoteReference, type NoteListItem } from '../utils/ai-context'
 import type { VaultEntry } from '../types'
 
 export type { AiAgentMessage } from '../hooks/useAiAgent'
@@ -14,6 +15,9 @@ interface AiPanelProps {
   activeEntry?: VaultEntry | null
   entries?: VaultEntry[]
   allContent?: Record<string, string>
+  openTabs?: VaultEntry[]
+  noteList?: NoteListItem[]
+  noteListFilter?: { type: string | null; query: string }
 }
 
 function PanelHeader({ onClose, onClear }: { onClose: () => void; onClear: () => void }) {
@@ -103,54 +107,9 @@ function MessageHistory({ messages, isActive, onOpenNote, hasContext }: {
   )
 }
 
-function InputBar({ input, onInputChange, onSend, onKeyDown, isActive, hasContext, inputRef }: {
-  input: string; onInputChange: (v: string) => void
-  onSend: () => void; onKeyDown: (e: React.KeyboardEvent) => void
-  isActive: boolean; hasContext: boolean; inputRef: React.RefObject<HTMLInputElement | null>
-}) {
-  const sendDisabled = isActive || !input.trim()
-  return (
-    <div
-      className="flex shrink-0 flex-col border-t border-border"
-      style={{ padding: '8px 12px' }}
-    >
-      <div className="flex items-end gap-2">
-        <input
-          ref={inputRef}
-          value={input}
-          onChange={e => onInputChange(e.target.value)}
-          onKeyDown={onKeyDown}
-          className="flex-1 border border-border bg-transparent text-foreground"
-          style={{
-            fontSize: 13, borderRadius: 8, padding: '8px 10px',
-            outline: 'none', fontFamily: 'inherit',
-          }}
-          placeholder={hasContext ? 'Ask about this note...' : 'Ask the AI agent...'}
-          disabled={isActive}
-          data-testid="agent-input"
-        />
-        <button
-          className="shrink-0 flex items-center justify-center border-none cursor-pointer transition-colors"
-          style={{
-            background: sendDisabled ? 'var(--muted)' : 'var(--primary)',
-            color: sendDisabled ? 'var(--muted-foreground)' : 'white',
-            borderRadius: 8, width: 32, height: 34,
-            cursor: sendDisabled ? 'not-allowed' : 'pointer',
-          }}
-          onClick={onSend}
-          disabled={sendDisabled}
-          title="Send message"
-          data-testid="agent-send"
-        >
-          <PaperPlaneRight size={16} />
-        </button>
-      </div>
-    </div>
-  )
-}
-
-export function AiPanel({ onClose, onOpenNote, vaultPath, activeEntry, entries, allContent }: AiPanelProps) {
+export function AiPanel({ onClose, onOpenNote, vaultPath, activeEntry, entries, allContent, openTabs, noteList, noteListFilter }: AiPanelProps) {
   const [input, setInput] = useState('')
+  const [pendingRefs, setPendingRefs] = useState<NoteReference[]>([])
   const inputRef = useRef<HTMLInputElement>(null)
   const panelRef = useRef<HTMLElement>(null)
 
@@ -160,9 +119,17 @@ export function AiPanel({ onClose, onOpenNote, vaultPath, activeEntry, entries,
   }, [activeEntry, entries])
 
   const contextPrompt = useMemo(() => {
-    if (!activeEntry || !allContent) return undefined
-    return buildContextualPrompt(activeEntry, linkedEntries, allContent)
-  }, [activeEntry, linkedEntries, allContent])
+    if (!activeEntry || !allContent || !entries) return undefined
+    return buildContextSnapshot({
+      activeEntry,
+      allContent,
+      openTabs,
+      noteList,
+      noteListFilter,
+      entries,
+      references: pendingRefs.length > 0 ? pendingRefs : undefined,
+    })
+  }, [activeEntry, allContent, openTabs, noteList, noteListFilter, entries, pendingRefs])
 
   const agent = useAiAgent(vaultPath, contextPrompt)
   const hasContext = !!activeEntry
@@ -193,26 +160,28 @@ export function AiPanel({ onClose, onOpenNote, vaultPath, activeEntry, entries,
     return () => window.removeEventListener('keydown', handleEscape)
   }, [handleEscape])
 
-  const handleSend = () => {
-    if (!input.trim() || isActive) return
-    agent.sendMessage(input)
+  const handleSend = useCallback((text: string, references: NoteReference[]) => {
+    if (!text.trim() || isActive) return
+    setPendingRefs(references)
+    agent.sendMessage(text, references)
     setInput('')
-  }
-
-  const handleKeyDown = (e: React.KeyboardEvent) => {
-    if (e.key === 'Enter' && !e.shiftKey) {
-      e.preventDefault()
-      handleSend()
-    }
-  }
+  }, [isActive, agent])
 
   return (
     <aside
       ref={panelRef}
       tabIndex={-1}
-      className="flex flex-1 flex-col overflow-hidden border-l border-border bg-background text-foreground"
-      style={{ outline: 'none' }}
+      className="flex flex-1 flex-col overflow-hidden bg-background text-foreground"
+      style={{
+        outline: 'none',
+        borderLeft: isActive
+          ? '2px solid var(--accent-blue, #3b82f6)'
+          : '1px solid var(--border)',
+        animation: isActive ? 'ai-border-pulse 2s ease-in-out infinite' : undefined,
+        transition: 'border-color 0.3s ease',
+      }}
       data-testid="ai-panel"
+      data-ai-active={isActive || undefined}
     >
       <PanelHeader onClose={onClose} onClear={agent.clearConversation} />
       {activeEntry && (
@@ -224,15 +193,39 @@ export function AiPanel({ onClose, onOpenNote, vaultPath, activeEntry, entries,
         onOpenNote={onOpenNote}
         hasContext={hasContext}
       />
-      <InputBar
-        input={input}
-        onInputChange={setInput}
-        onSend={handleSend}
-        onKeyDown={handleKeyDown}
-        isActive={isActive}
-        hasContext={hasContext}
-        inputRef={inputRef}
-      />
+      <div
+        className="flex shrink-0 flex-col border-t border-border"
+        style={{ padding: '8px 12px' }}
+      >
+        <div className="flex items-end gap-2">
+          <div className="flex-1">
+            <WikilinkChatInput
+              entries={entries ?? []}
+              value={input}
+              onChange={setInput}
+              onSend={handleSend}
+              disabled={isActive}
+              placeholder={hasContext ? 'Ask about this note...' : 'Ask the AI agent...'}
+              inputRef={inputRef}
+            />
+          </div>
+          <button
+            className="shrink-0 flex items-center justify-center border-none cursor-pointer transition-colors"
+            style={{
+              background: (isActive || !input.trim()) ? 'var(--muted)' : 'var(--primary)',
+              color: (isActive || !input.trim()) ? 'var(--muted-foreground)' : 'white',
+              borderRadius: 8, width: 32, height: 34,
+              cursor: (isActive || !input.trim()) ? 'not-allowed' : 'pointer',
+            }}
+            onClick={() => handleSend(input, pendingRefs)}
+            disabled={isActive || !input.trim()}
+            title="Send message"
+            data-testid="agent-send"
+          >
+            <PaperPlaneRight size={16} />
+          </button>
+        </div>
+      </div>
     </aside>
   )
 }

src/components/Editor.tsx

@@ -5,6 +5,7 @@ import { useCreateBlockNote } from '@blocknote/react'
 import '@blocknote/mantine/style.css'
 import { uploadImageFile } from '../hooks/useImageDrop'
 import type { VaultEntry, GitCommit, NoteStatus } from '../types'
+import type { NoteListItem } from '../utils/ai-context'
 import type { FrontmatterValue } from './Inspector'
 import { ResizeHandle } from './ResizeHandle'
 import { TabBar } from './TabBar'
@@ -48,6 +49,8 @@ interface EditorProps {
   showAIChat?: boolean
   onToggleAIChat?: () => void
   vaultPath?: string
+  noteList?: NoteListItem[]
+  noteListFilter?: { type: string | null; query: string }
   onTrashNote?: (path: string) => void
   onRestoreNote?: (path: string) => void
   onDeleteNote?: (path: string) => void
@@ -117,7 +120,7 @@ export const Editor = memo(function Editor({
   inspectorEntry, inspectorContent, allContent, gitHistory,
   onUpdateFrontmatter, onDeleteProperty, onAddProperty,
   showAIChat, onToggleAIChat,
-  vaultPath,
+  vaultPath, noteList, noteListFilter,
   onTrashNote, onRestoreNote, onDeleteNote, onArchiveNote, onUnarchiveNote,
   onRenameTab, onContentChange, onSave, onTitleSync,
   canGoBack, canGoForward, onGoBack, onGoForward, leftPanelsCollapsed,
@@ -228,6 +231,9 @@ export const Editor = memo(function Editor({
           allContent={allContent}
           gitHistory={gitHistory}
           vaultPath={vaultPath ?? ''}
+          openTabs={tabs.map(t => t.entry)}
+          noteList={noteList}
+          noteListFilter={noteListFilter}
           onToggleInspector={onToggleInspector}
           onToggleAIChat={onToggleAIChat}
           onNavigateWikilink={onNavigateWikilink}

src/components/EditorRightPanel.tsx

@@ -1,4 +1,5 @@
 import type { VaultEntry, GitCommit } from '../types'
+import type { NoteListItem } from '../utils/ai-context'
 import { Inspector, type FrontmatterValue } from './Inspector'
 import { AiPanel } from './AiPanel'
 
@@ -12,6 +13,9 @@ interface EditorRightPanelProps {
   allContent: Record<string, string>
   gitHistory: GitCommit[]
   vaultPath: string
+  openTabs?: VaultEntry[]
+  noteList?: NoteListItem[]
+  noteListFilter?: { type: string | null; query: string }
   onToggleInspector: () => void
   onToggleAIChat?: () => void
   onNavigateWikilink: (target: string) => void
@@ -24,7 +28,8 @@ interface EditorRightPanelProps {
 
 export function EditorRightPanel({
   showAIChat, inspectorCollapsed, inspectorWidth,
-  inspectorEntry, inspectorContent, entries, allContent, gitHistory, vaultPath,
+  inspectorEntry, inspectorContent, entries, allContent, gitHistory, vaultPath, openTabs,
+  noteList, noteListFilter,
   onToggleInspector, onToggleAIChat, onNavigateWikilink, onViewCommitDiff,
   onUpdateFrontmatter, onDeleteProperty, onAddProperty, onOpenNote,
 }: EditorRightPanelProps) {
@@ -41,6 +46,9 @@ export function EditorRightPanel({
           activeEntry={inspectorEntry}
           entries={entries}
           allContent={allContent}
+          openTabs={openTabs}
+          noteList={noteList}
+          noteListFilter={noteListFilter}
         />
       </div>
     )

src/components/Sidebar.tsx

@@ -165,7 +165,7 @@ function SortableSection({ group, sectionProps }: {
   sectionProps: Omit<SectionContentProps, 'group' | 'items' | 'isCollapsed' | 'onToggle' | 'isRenaming' | 'renameInitialValue'>
     & { entries: VaultEntry[]; collapsed: Record<string, boolean>; onToggle: (type: string) => void; renamingType: string | null; renameInitialValue: string }
 }) {
-  const { attributes, setNodeRef, transform, transition, isDragging } = useSortable({ id: group.type })
+  const { attributes, listeners, setNodeRef, transform, transition, isDragging } = useSortable({ id: group.type })
   const items = sectionProps.entries.filter((e) => e.isA === group.type && !e.archived && !e.trashed)
   const isCollapsed = sectionProps.collapsed[group.type] ?? true
   const isRenaming = sectionProps.renamingType === group.type
@@ -178,6 +178,7 @@ function SortableSection({ group, sectionProps }: {
         onSelectNote={sectionProps.onSelectNote} onCreateType={sectionProps.onCreateType}
         onCreateNewType={sectionProps.onCreateNewType} onContextMenu={sectionProps.onContextMenu}
         onToggle={() => sectionProps.onToggle(group.type)}
+        dragHandleProps={listeners}
         isRenaming={isRenaming}
         renameInitialValue={isRenaming ? sectionProps.renameInitialValue : undefined}
         onRenameSubmit={sectionProps.onRenameSubmit}

src/components/SidebarParts.tsx

@@ -75,6 +75,7 @@ export interface SectionContentProps {
   onCreateNewType?: () => void
   onContextMenu: (e: React.MouseEvent, type: string) => void
   onToggle: () => void
+  dragHandleProps?: Record<string, unknown>
   isRenaming?: boolean
   renameInitialValue?: string
   onRenameSubmit?: (value: string) => void
@@ -93,7 +94,7 @@ function resolveCreateHandler(type: string, onCreateType?: (type: string) => voi
 
 export function SectionContent({
   group, items, isCollapsed, selection, onSelect, onSelectNote,
-  onCreateType, onCreateNewType, onContextMenu, onToggle,
+  onCreateType, onCreateNewType, onContextMenu, onToggle, dragHandleProps,
   isRenaming, renameInitialValue, onRenameSubmit, onRenameCancel,
 }: SectionContentProps) {
   const { label, type, Icon, customColor } = group
@@ -113,6 +114,7 @@ export function SectionContent({
         onContextMenu={(e) => onContextMenu(e, type)}
         onToggle={onToggle}
         onCreate={(e) => { e.stopPropagation(); onCreate?.() }}
+        dragHandleProps={dragHandleProps}
         isRenaming={isRenaming}
         renameInitialValue={renameInitialValue}
         onRenameSubmit={onRenameSubmit}
@@ -182,11 +184,12 @@ function InlineRenameInput({ initialValue, onSubmit, onCancel }: {
   )
 }
 
-function SectionHeader({ label, type, Icon, sectionColor, isCollapsed, isActive, showCreate, onSelect, onContextMenu, onToggle, onCreate, isRenaming, renameInitialValue, onRenameSubmit, onRenameCancel }: {
+function SectionHeader({ label, type, Icon, sectionColor, isCollapsed, isActive, showCreate, onSelect, onContextMenu, onToggle, onCreate, dragHandleProps, isRenaming, renameInitialValue, onRenameSubmit, onRenameCancel }: {
   label: string; type: string; Icon: ComponentType<IconProps>
   sectionColor: string; isCollapsed: boolean; isActive: boolean; showCreate: boolean
   onSelect: () => void; onContextMenu: (e: React.MouseEvent) => void
   onToggle: () => void; onCreate: (e: React.MouseEvent) => void
+  dragHandleProps?: Record<string, unknown>
   isRenaming?: boolean; renameInitialValue?: string
   onRenameSubmit?: (value: string) => void; onRenameCancel?: () => void
 }) {
@@ -194,6 +197,7 @@ function SectionHeader({ label, type, Icon, sectionColor, isCollapsed, isActive,
     <div
       className={cn("group/section flex cursor-pointer select-none items-center justify-between rounded transition-colors", isActive ? "bg-secondary" : "hover:bg-accent")}
       style={{ padding: '6px 8px 6px 16px', borderRadius: 4, gap: 4 }}
+      {...dragHandleProps}
       onClick={() => {
         if (isRenaming) return
         if (isCollapsed) { onToggle(); onSelect() }

src/components/StatusBar.test.tsx

@@ -265,17 +265,46 @@ describe('StatusBar', () => {
     expect(screen.getByText('Index ready')).toBeInTheDocument()
   })
 
-  it('shows error state in indexing badge', () => {
+  it('shows error state in indexing badge with retry label', () => {
     render(
       <StatusBar
         noteCount={100}
         vaultPath="/Users/luca/Laputa"
         vaults={vaults}
         onSwitchVault={vi.fn()}
-        indexingProgress={{ phase: 'error', current: 0, total: 0, done: true, error: 'qmd not available' }}
+        indexingProgress={{ phase: 'error', current: 0, total: 0, done: true, error: 'qmd update failed' }}
       />
     )
-    expect(screen.getByText('Index error')).toBeInTheDocument()
+    expect(screen.getByText('Index failed — retry')).toBeInTheDocument()
+  })
+
+  it('hides indexing badge when phase is unavailable', () => {
+    render(
+      <StatusBar
+        noteCount={100}
+        vaultPath="/Users/luca/Laputa"
+        vaults={vaults}
+        onSwitchVault={vi.fn()}
+        indexingProgress={{ phase: 'unavailable', current: 0, total: 0, done: true, error: 'qmd not available' }}
+      />
+    )
+    expect(screen.queryByTestId('status-indexing')).not.toBeInTheDocument()
+  })
+
+  it('calls onRetryIndexing when clicking error badge', () => {
+    const onRetryIndexing = vi.fn()
+    render(
+      <StatusBar
+        noteCount={100}
+        vaultPath="/Users/luca/Laputa"
+        vaults={vaults}
+        onSwitchVault={vi.fn()}
+        indexingProgress={{ phase: 'error', current: 0, total: 0, done: true, error: 'qmd update failed' }}
+        onRetryIndexing={onRetryIndexing}
+      />
+    )
+    fireEvent.click(screen.getByTestId('status-indexing'))
+    expect(onRetryIndexing).toHaveBeenCalledOnce()
   })
 
   it('hides indexing badge when phase is idle', () => {
@@ -310,4 +339,59 @@ describe('StatusBar', () => {
     )
     expect(screen.getByText('Installing search…')).toBeInTheDocument()
   })
+
+  it('shows MCP warning badge when status is not_installed', () => {
+    render(
+      <StatusBar noteCount={100} vaultPath="/Users/luca/Laputa" vaults={vaults} onSwitchVault={vi.fn()} mcpStatus="not_installed" />
+    )
+    expect(screen.getByTestId('status-mcp')).toBeInTheDocument()
+    expect(screen.getByTitle('MCP server not installed — click to install')).toBeInTheDocument()
+  })
+
+  it('shows MCP warning badge when status is no_claude_cli', () => {
+    render(
+      <StatusBar noteCount={100} vaultPath="/Users/luca/Laputa" vaults={vaults} onSwitchVault={vi.fn()} mcpStatus="no_claude_cli" />
+    )
+    expect(screen.getByTestId('status-mcp')).toBeInTheDocument()
+    expect(screen.getByTitle('Claude CLI not found — install it first')).toBeInTheDocument()
+  })
+
+  it('hides MCP badge when status is installed', () => {
+    render(
+      <StatusBar noteCount={100} vaultPath="/Users/luca/Laputa" vaults={vaults} onSwitchVault={vi.fn()} mcpStatus="installed" />
+    )
+    expect(screen.queryByTestId('status-mcp')).not.toBeInTheDocument()
+  })
+
+  it('hides MCP badge when status is checking', () => {
+    render(
+      <StatusBar noteCount={100} vaultPath="/Users/luca/Laputa" vaults={vaults} onSwitchVault={vi.fn()} mcpStatus="checking" />
+    )
+    expect(screen.queryByTestId('status-mcp')).not.toBeInTheDocument()
+  })
+
+  it('hides MCP badge when no mcpStatus prop provided', () => {
+    render(
+      <StatusBar noteCount={100} vaultPath="/Users/luca/Laputa" vaults={vaults} onSwitchVault={vi.fn()} />
+    )
+    expect(screen.queryByTestId('status-mcp')).not.toBeInTheDocument()
+  })
+
+  it('calls onInstallMcp when clicking MCP badge with not_installed status', () => {
+    const onInstallMcp = vi.fn()
+    render(
+      <StatusBar noteCount={100} vaultPath="/Users/luca/Laputa" vaults={vaults} onSwitchVault={vi.fn()} mcpStatus="not_installed" onInstallMcp={onInstallMcp} />
+    )
+    fireEvent.click(screen.getByTestId('status-mcp'))
+    expect(onInstallMcp).toHaveBeenCalledOnce()
+  })
+
+  it('does not call onInstallMcp when clicking MCP badge with no_claude_cli status', () => {
+    const onInstallMcp = vi.fn()
+    render(
+      <StatusBar noteCount={100} vaultPath="/Users/luca/Laputa" vaults={vaults} onSwitchVault={vi.fn()} mcpStatus="no_claude_cli" onInstallMcp={onInstallMcp} />
+    )
+    fireEvent.click(screen.getByTestId('status-mcp'))
+    expect(onInstallMcp).not.toHaveBeenCalled()
+  })
 })

src/components/StatusBar.tsx

@@ -1,7 +1,8 @@
 import { useState, useRef, useEffect } from 'react'
-import { Package, RefreshCw, FileText, Bell, Settings, FolderOpen, Check, Github, CircleDot, AlertTriangle, Loader2, GitCommitHorizontal, Search, X } from 'lucide-react'
+import { Package, RefreshCw, FileText, Bell, Settings, FolderOpen, Check, Github, CircleDot, AlertTriangle, Loader2, GitCommitHorizontal, Search, X, Cpu } from 'lucide-react'
 import type { LastCommitInfo, SyncStatus } from '../types'
 import type { IndexingProgress } from '../hooks/useIndexing'
+import type { McpStatus } from '../hooks/useMcpStatus'
 import { openExternalUrl } from '../utils/url'
 
 export interface VaultOption {
@@ -32,7 +33,10 @@ interface StatusBarProps {
   buildNumber?: string
   onCheckForUpdates?: () => void
   indexingProgress?: IndexingProgress
+  onRetryIndexing?: () => void
   onRemoveVault?: (path: string) => void
+  mcpStatus?: McpStatus
+  onInstallMcp?: () => void
 }
 
 function VaultMenuIcon({ isActive, unavailable }: { isActive: boolean; unavailable: boolean }) {
@@ -237,23 +241,31 @@ const INDEXING_LABELS: Record<string, string> = {
   scanning: 'Indexing…',
   embedding: 'Embedding…',
   complete: 'Index ready',
-  error: 'Index error',
+  error: 'Index failed — retry',
+  unavailable: 'Search unavailable',
 }
 
-function IndexingBadge({ progress }: { progress: IndexingProgress }) {
-  if (progress.phase === 'idle') return null
+function IndexingBadge({ progress, onRetry }: { progress: IndexingProgress; onRetry?: () => void }) {
+  if (progress.phase === 'idle' || progress.phase === 'unavailable') return null
   const label = INDEXING_LABELS[progress.phase] ?? progress.phase
   const isActive = !progress.done
+  const isError = progress.phase === 'error'
   const showCount = progress.total > 0 && isActive
   const displayText = showCount
     ? `${label} ${progress.current.toLocaleString()}/${progress.total.toLocaleString()}`
     : label
-  const color = progress.phase === 'error' ? 'var(--accent-orange)' : 'var(--accent-blue, #3b82f6)'
+  const color = isError ? 'var(--accent-orange)' : 'var(--accent-blue, #3b82f6)'
 
   return (
     <>
       <span style={SEP_STYLE}>|</span>
-      <span style={{ ...ICON_STYLE, color }} data-testid="status-indexing">
+      <span
+        role={isError && onRetry ? 'button' : undefined}
+        onClick={isError && onRetry ? onRetry : undefined}
+        style={{ ...ICON_STYLE, color, cursor: isError && onRetry ? 'pointer' : 'default' }}
+        title={isError ? 'Click to retry indexing' : undefined}
+        data-testid="status-indexing"
+      >
         {isActive
           ? <Loader2 size={13} className="animate-spin" />
           : <Search size={13} />
@@ -282,7 +294,42 @@ function PendingBadge({ count, onClick }: { count: number; onClick?: () => void
   )
 }
 
-export function StatusBar({ noteCount, modifiedCount = 0, vaultPath, vaults, onSwitchVault, onOpenSettings, onOpenLocalFolder, onConnectGitHub, onClickPending, hasGitHub, syncStatus = 'idle', lastSyncTime = null, conflictCount = 0, lastCommitInfo, onTriggerSync, onOpenConflictResolver, zoomLevel = 100, onZoomReset, buildNumber, onCheckForUpdates, indexingProgress, onRemoveVault }: StatusBarProps) {
+const MCP_TOOLTIPS: Record<string, string> = {
+  not_installed: 'MCP server not installed — click to install',
+  no_claude_cli: 'Claude CLI not found — install it first',
+}
+
+function McpBadge({ status, onInstall }: { status: McpStatus; onInstall?: () => void }) {
+  if (status === 'installed' || status === 'checking') return null
+  const tooltip = MCP_TOOLTIPS[status] ?? 'MCP status unknown'
+  const clickable = status === 'not_installed' && !!onInstall
+  return (
+    <>
+      <span style={SEP_STYLE}>|</span>
+      <span
+        role={clickable ? 'button' : undefined}
+        onClick={clickable ? onInstall : undefined}
+        style={{
+          ...ICON_STYLE,
+          color: 'var(--accent-orange)',
+          cursor: clickable ? 'pointer' : 'default',
+          padding: '2px 4px',
+          borderRadius: 3,
+          background: 'transparent',
+        }}
+        title={tooltip}
+        data-testid="status-mcp"
+        onMouseEnter={clickable ? (e) => { e.currentTarget.style.background = 'var(--hover)' } : undefined}
+        onMouseLeave={clickable ? (e) => { e.currentTarget.style.background = 'transparent' } : undefined}
+      >
+        <Cpu size={13} />MCP
+        <AlertTriangle size={10} style={{ marginLeft: 2 }} />
+      </span>
+    </>
+  )
+}
+
+export function StatusBar({ noteCount, modifiedCount = 0, vaultPath, vaults, onSwitchVault, onOpenSettings, onOpenLocalFolder, onConnectGitHub, onClickPending, hasGitHub, syncStatus = 'idle', lastSyncTime = null, conflictCount = 0, lastCommitInfo, onTriggerSync, onOpenConflictResolver, zoomLevel = 100, onZoomReset, buildNumber, onCheckForUpdates, indexingProgress, onRetryIndexing, onRemoveVault, mcpStatus, onInstallMcp }: StatusBarProps) {
   const [, setTick] = useState(0)
   useEffect(() => {
     const id = setInterval(() => setTick((t) => t + 1), 30_000)
@@ -308,7 +355,8 @@ export function StatusBar({ noteCount, modifiedCount = 0, vaultPath, vaults, onS
         {lastCommitInfo && <CommitBadge info={lastCommitInfo} />}
         <ConflictBadge count={conflictCount} onClick={onOpenConflictResolver} />
         <PendingBadge count={modifiedCount} onClick={onClickPending} />
-        {indexingProgress && <IndexingBadge progress={indexingProgress} />}
+        {indexingProgress && <IndexingBadge progress={indexingProgress} onRetry={onRetryIndexing} />}
+        {mcpStatus && <McpBadge status={mcpStatus} onInstall={onInstallMcp} />}
       </div>
       <div style={{ display: 'flex', alignItems: 'center', gap: 12 }}>
         <span style={ICON_STYLE}><FileText size={13} />{noteCount.toLocaleString()} notes</span>

src/components/WikilinkChatInput.test.tsx

@@ -0,0 +1,283 @@
+import { useState } from 'react'
+import { describe, it, expect, vi } from 'vitest'
+import { render, screen, fireEvent, act } from '@testing-library/react'
+import { WikilinkChatInput } from './WikilinkChatInput'
+import type { VaultEntry } from '../types'
+
+const makeEntry = (overrides: Partial<VaultEntry> = {}): VaultEntry => ({
+  path: '/vault/note/test.md',
+  filename: 'test.md',
+  title: 'Test Note',
+  isA: 'Note',
+  aliases: [],
+  belongsTo: [],
+  relatedTo: [],
+  status: null,
+  owner: null,
+  cadence: null,
+  archived: false,
+  trashed: false,
+  trashedAt: null,
+  modifiedAt: 1700000000,
+  createdAt: 1700000000,
+  fileSize: 100,
+  snippet: '',
+  wordCount: 0,
+  relationships: {},
+  icon: null,
+  color: null,
+  order: null,
+  outgoingLinks: [],
+  ...overrides,
+})
+
+const entries: VaultEntry[] = [
+  makeEntry({ path: '/vault/alpha.md', title: 'Alpha', filename: 'alpha.md', isA: 'Project' }),
+  makeEntry({ path: '/vault/beta.md', title: 'Beta', filename: 'beta.md', isA: 'Person' }),
+  makeEntry({ path: '/vault/gamma.md', title: 'Gamma', filename: 'gamma.md' }),
+  makeEntry({ path: '/vault/trashed.md', title: 'Trashed', filename: 'trashed.md', trashed: true }),
+  makeEntry({ path: '/vault/archived.md', title: 'Archived', filename: 'archived.md', archived: true }),
+]
+
+/** Wrapper that manages controlled value state so onChange/selectSuggestion work correctly. */
+function Controlled({ onSend, ...props }: {
+  entries: VaultEntry[]
+  onSend?: (text: string, refs: Array<{ title: string; path: string; type: string | null }>) => void
+  disabled?: boolean
+  placeholder?: string
+}) {
+  const [value, setValue] = useState('')
+  return (
+    <WikilinkChatInput
+      entries={props.entries}
+      value={value}
+      onChange={setValue}
+      onSend={onSend ?? vi.fn()}
+      disabled={props.disabled}
+      placeholder={props.placeholder}
+    />
+  )
+}
+
+/** Helper: type in the input and wait for debounce to flush. */
+async function typeAndWait(text: string) {
+  fireEvent.change(screen.getByTestId('agent-input'), {
+    target: { value: text, selectionStart: text.length },
+  })
+  await act(() => { vi.advanceTimersByTime(150) })
+}
+
+describe('WikilinkChatInput', () => {
+  it('renders input with placeholder', () => {
+    render(<Controlled entries={entries} placeholder="Ask something..." />)
+    const input = screen.getByTestId('agent-input') as HTMLInputElement
+    expect(input.placeholder).toBe('Ask something...')
+  })
+
+  it('calls onChange when typing', () => {
+    const onChange = vi.fn()
+    render(
+      <WikilinkChatInput entries={entries} value="" onChange={onChange} onSend={vi.fn()} />,
+    )
+    fireEvent.change(screen.getByTestId('agent-input'), { target: { value: 'hello' } })
+    expect(onChange).toHaveBeenCalledWith('hello')
+  })
+
+  it('shows wikilink menu when [[ is typed', async () => {
+    vi.useFakeTimers()
+    render(<Controlled entries={entries} />)
+    await typeAndWait('[[a')
+    expect(screen.getByTestId('wikilink-menu')).toBeTruthy()
+    vi.useRealTimers()
+  })
+
+  it('filters suggestions matching query', async () => {
+    vi.useFakeTimers()
+    render(<Controlled entries={entries} />)
+    await typeAndWait('[[alp')
+    const menu = screen.getByTestId('wikilink-menu')
+    expect(menu.textContent).toContain('Alpha')
+    expect(menu.textContent).not.toContain('Beta')
+    vi.useRealTimers()
+  })
+
+  it('excludes trashed and archived entries from suggestions', async () => {
+    vi.useFakeTimers()
+    render(<Controlled entries={entries} />)
+    await typeAndWait('[[t')
+    const menu = screen.queryByTestId('wikilink-menu')
+    if (menu) {
+      expect(menu.textContent).not.toContain('Trashed')
+      expect(menu.textContent).not.toContain('Archived')
+    }
+    vi.useRealTimers()
+  })
+
+  it('selects suggestion on click and creates pill', async () => {
+    vi.useFakeTimers()
+    render(<Controlled entries={entries} />)
+    await typeAndWait('[[a')
+
+    const menu = screen.getByTestId('wikilink-menu')
+    const items = menu.querySelectorAll('[class*="cursor-pointer"]')
+    expect(items.length).toBeGreaterThan(0)
+    fireEvent.click(items[0])
+
+    const pills = screen.queryAllByTestId('reference-pill')
+    expect(pills.length).toBe(1)
+    vi.useRealTimers()
+  })
+
+  it('does not duplicate pills for same note', async () => {
+    vi.useFakeTimers()
+    render(<Controlled entries={entries} />)
+
+    // First selection
+    await typeAndWait('[[alp')
+    fireEvent.click(screen.getByTestId('wikilink-menu').querySelectorAll('[class*="cursor-pointer"]')[0])
+    expect(screen.queryAllByTestId('reference-pill').length).toBe(1)
+
+    // Second selection of same note
+    await typeAndWait('[[alp')
+    fireEvent.click(screen.getByTestId('wikilink-menu').querySelectorAll('[class*="cursor-pointer"]')[0])
+    expect(screen.queryAllByTestId('reference-pill').length).toBe(1) // No duplicate
+    vi.useRealTimers()
+  })
+
+  it('removes pill when x button is clicked', async () => {
+    vi.useFakeTimers()
+    render(<Controlled entries={entries} />)
+
+    await typeAndWait('[[alp')
+    fireEvent.click(screen.getByTestId('wikilink-menu').querySelectorAll('[class*="cursor-pointer"]')[0])
+    expect(screen.queryAllByTestId('reference-pill').length).toBe(1)
+
+    const pill = screen.getByTestId('reference-pill')
+    fireEvent.click(pill.querySelector('button')!)
+    expect(screen.queryAllByTestId('reference-pill').length).toBe(0)
+    vi.useRealTimers()
+  })
+
+  it('navigates suggestions with keyboard', async () => {
+    vi.useFakeTimers()
+    render(<Controlled entries={entries} />)
+    await typeAndWait('[[a')
+
+    const input = screen.getByTestId('agent-input')
+    fireEvent.keyDown(input, { key: 'ArrowDown' })
+    fireEvent.keyDown(input, { key: 'ArrowUp' })
+    // Escape closes menu
+    fireEvent.keyDown(input, { key: 'Escape' })
+    expect(screen.queryByTestId('wikilink-menu')).toBeNull()
+    vi.useRealTimers()
+  })
+
+  it('selects suggestion with Enter key', async () => {
+    vi.useFakeTimers()
+    render(<Controlled entries={entries} />)
+    await typeAndWait('[[alp')
+    expect(screen.getByTestId('wikilink-menu')).toBeTruthy()
+
+    fireEvent.keyDown(screen.getByTestId('agent-input'), { key: 'Enter' })
+    expect(screen.queryAllByTestId('reference-pill').length).toBe(1)
+    vi.useRealTimers()
+  })
+
+  it('calls onSend with text and references on Enter without menu', async () => {
+    vi.useFakeTimers()
+    const onSend = vi.fn()
+    render(<Controlled entries={entries} onSend={onSend} />)
+
+    // Type non-wikilink text
+    fireEvent.change(screen.getByTestId('agent-input'), {
+      target: { value: 'hello', selectionStart: 5 },
+    })
+    fireEvent.keyDown(screen.getByTestId('agent-input'), { key: 'Enter' })
+    expect(onSend).toHaveBeenCalledWith('hello', [])
+    vi.useRealTimers()
+  })
+
+  it('does not send on Enter+Shift', () => {
+    const onSend = vi.fn()
+    render(
+      <WikilinkChatInput entries={entries} value="hello" onChange={vi.fn()} onSend={onSend} />,
+    )
+    fireEvent.keyDown(screen.getByTestId('agent-input'), { key: 'Enter', shiftKey: true })
+    expect(onSend).not.toHaveBeenCalled()
+  })
+
+  it('does not send on Enter when input is empty', () => {
+    const onSend = vi.fn()
+    render(
+      <WikilinkChatInput entries={entries} value="" onChange={vi.fn()} onSend={onSend} />,
+    )
+    fireEvent.keyDown(screen.getByTestId('agent-input'), { key: 'Enter' })
+    expect(onSend).not.toHaveBeenCalled()
+  })
+
+  it('disables input when disabled prop is true', () => {
+    render(<Controlled entries={entries} disabled />)
+    expect((screen.getByTestId('agent-input') as HTMLInputElement).disabled).toBe(true)
+  })
+
+  it('closes menu when ]] is typed', async () => {
+    vi.useFakeTimers()
+    render(<Controlled entries={entries} />)
+    await typeAndWait('[[alp')
+    expect(screen.getByTestId('wikilink-menu')).toBeTruthy()
+
+    // Type ]] to close
+    fireEvent.change(screen.getByTestId('agent-input'), {
+      target: { value: '[[alp]]', selectionStart: 7 },
+    })
+    expect(screen.queryByTestId('wikilink-menu')).toBeNull()
+    vi.useRealTimers()
+  })
+
+  it('shows type badge for non-Note types in suggestions', async () => {
+    vi.useFakeTimers()
+    render(<Controlled entries={entries} />)
+    await typeAndWait('[[alp')
+    const menu = screen.getByTestId('wikilink-menu')
+    expect(menu.textContent).toContain('Project')
+    vi.useRealTimers()
+  })
+
+  it('matches by alias', async () => {
+    vi.useFakeTimers()
+    const entriesWithAlias = [
+      ...entries,
+      makeEntry({ path: '/vault/delta.md', title: 'Delta', filename: 'delta.md', aliases: ['DLT'] }),
+    ]
+    render(<Controlled entries={entriesWithAlias} />)
+    await typeAndWait('[[DLT')
+    const menu = screen.getByTestId('wikilink-menu')
+    expect(menu.textContent).toContain('Delta')
+    vi.useRealTimers()
+  })
+
+  it('sends references with onSend after selecting pills', async () => {
+    vi.useFakeTimers()
+    const onSend = vi.fn()
+    render(<Controlled entries={entries} onSend={onSend} />)
+
+    // Select a pill first
+    await typeAndWait('[[alp')
+    fireEvent.click(screen.getByTestId('wikilink-menu').querySelectorAll('[class*="cursor-pointer"]')[0])
+    expect(screen.queryAllByTestId('reference-pill').length).toBe(1)
+
+    // Type a message and send
+    fireEvent.change(screen.getByTestId('agent-input'), {
+      target: { value: 'tell me about it', selectionStart: 16 },
+    })
+    fireEvent.keyDown(screen.getByTestId('agent-input'), { key: 'Enter' })
+
+    expect(onSend).toHaveBeenCalledOnce()
+    const [text, refs] = onSend.mock.calls[0]
+    expect(text).toBe('tell me about it')
+    expect(refs).toHaveLength(1)
+    expect(refs[0].title).toBe('Alpha')
+    expect(refs[0].path).toBe('/vault/alpha.md')
+    vi.useRealTimers()
+  })
+})

src/components/WikilinkChatInput.tsx

@@ -0,0 +1,264 @@
+/**
+ * Chat input with [[wikilink]] autocomplete.
+ *
+ * When the user types `[[`, a dropdown appears with vault note suggestions.
+ * Selecting a note inserts a colored pill in the input and records a reference.
+ */
+import { useState, useRef, useMemo, useEffect } from 'react'
+import type { VaultEntry } from '../types'
+import type { NoteReference } from '../utils/ai-context'
+import { getTypeColor, getTypeLightColor, buildTypeEntryMap } from '../utils/typeColors'
+
+const MAX_SUGGESTIONS = 20
+const MIN_QUERY_LENGTH = 1
+const DEBOUNCE_MS = 100
+
+interface WikilinkChatInputProps {
+  entries: VaultEntry[]
+  value: string
+  onChange: (value: string) => void
+  onSend: (text: string, references: NoteReference[]) => void
+  disabled?: boolean
+  placeholder?: string
+  inputRef?: React.RefObject<HTMLInputElement | null>
+}
+
+interface Pill {
+  title: string
+  path: string
+  type: string | null
+  color?: string
+  lightColor?: string
+}
+
+interface SuggestionEntry {
+  title: string
+  path: string
+  isA: string | null
+  color?: string
+  lightColor?: string
+}
+
+function matchEntries(
+  entries: VaultEntry[],
+  query: string,
+  typeEntryMap: Record<string, VaultEntry>,
+): SuggestionEntry[] {
+  if (query.length < MIN_QUERY_LENGTH) return []
+  const lower = query.toLowerCase()
+  const matches = entries.filter(e =>
+    !e.trashed && !e.archived && (
+      e.title.toLowerCase().includes(lower) ||
+      e.aliases.some(a => a.toLowerCase().includes(lower))
+    ),
+  )
+  return matches.slice(0, MAX_SUGGESTIONS).map(e => {
+    const te = typeEntryMap[e.isA ?? '']
+    return {
+      title: e.title,
+      path: e.path,
+      isA: e.isA,
+      color: e.isA ? getTypeColor(e.isA, te?.color) : undefined,
+      lightColor: e.isA ? getTypeLightColor(e.isA, te?.color) : undefined,
+    }
+  })
+}
+
+export function WikilinkChatInput({
+  entries, value, onChange, onSend, disabled, placeholder, inputRef: externalRef,
+}: WikilinkChatInputProps) {
+  const [pills, setPills] = useState<Pill[]>([])
+  const [showMenu, setShowMenu] = useState(false)
+  const [selectedIndex, setSelectedIndex] = useState(0)
+  const [debouncedQuery, setDebouncedQuery] = useState('')
+  const internalRef = useRef<HTMLInputElement>(null)
+  const inputRefToUse = externalRef ?? internalRef
+  const menuRef = useRef<HTMLDivElement>(null)
+  const debounceTimer = useRef<ReturnType<typeof setTimeout>>(undefined)
+
+  const typeEntryMap = useMemo(() => buildTypeEntryMap(entries), [entries])
+
+  const suggestions = useMemo(
+    () => showMenu ? matchEntries(entries, debouncedQuery, typeEntryMap) : [],
+    [entries, debouncedQuery, typeEntryMap, showMenu],
+  )
+
+  // Clamp selection to valid range
+  const clampedIndex = suggestions.length > 0
+    ? Math.min(selectedIndex, suggestions.length - 1)
+    : 0
+
+  useEffect(() => {
+    if (!menuRef.current || clampedIndex < 0) return
+    const el = menuRef.current.children[clampedIndex] as HTMLElement | undefined
+    el?.scrollIntoView?.({ block: 'nearest' })
+  }, [clampedIndex])
+
+  function selectSuggestion(suggestion: SuggestionEntry) {
+    const cursor = inputRefToUse.current?.selectionStart ?? value.length
+    const textBefore = value.slice(0, cursor)
+    const bracketIdx = textBefore.lastIndexOf('[[')
+    if (bracketIdx < 0) return
+
+    const textAfter = value.slice(cursor)
+    const newValue = textBefore.slice(0, bracketIdx) + textAfter
+
+    onChange(newValue)
+    setPills(prev => {
+      if (prev.some(p => p.path === suggestion.path)) return prev
+      return [...prev, {
+        title: suggestion.title,
+        path: suggestion.path,
+        type: suggestion.isA,
+        color: suggestion.color,
+        lightColor: suggestion.lightColor,
+      }]
+    })
+    setShowMenu(false)
+    setTimeout(() => inputRefToUse.current?.focus(), 0)
+  }
+
+  function handleChange(e: React.ChangeEvent<HTMLInputElement>) {
+    const newValue = e.target.value
+    onChange(newValue)
+
+    const cursor = e.target.selectionStart ?? newValue.length
+    const textBefore = newValue.slice(0, cursor)
+    const bracketIdx = textBefore.lastIndexOf('[[')
+
+    if (bracketIdx >= 0 && !textBefore.slice(bracketIdx).includes(']]')) {
+      const query = textBefore.slice(bracketIdx + 2)
+      setShowMenu(true)
+      setSelectedIndex(0)
+      clearTimeout(debounceTimer.current)
+      debounceTimer.current = setTimeout(() => setDebouncedQuery(query), DEBOUNCE_MS)
+    } else {
+      setShowMenu(false)
+    }
+  }
+
+  function handleKeyDown(e: React.KeyboardEvent) {
+    if (showMenu && suggestions.length > 0) {
+      if (e.key === 'ArrowDown') {
+        e.preventDefault()
+        setSelectedIndex(i => (i + 1) % suggestions.length)
+        return
+      }
+      if (e.key === 'ArrowUp') {
+        e.preventDefault()
+        setSelectedIndex(i => (i <= 0 ? suggestions.length - 1 : i - 1))
+        return
+      }
+      if (e.key === 'Enter') {
+        e.preventDefault()
+        selectSuggestion(suggestions[clampedIndex])
+        return
+      }
+      if (e.key === 'Escape') {
+        e.preventDefault()
+        setShowMenu(false)
+        return
+      }
+    }
+
+    if (e.key === 'Enter' && !e.shiftKey) {
+      e.preventDefault()
+      if (!value.trim() && pills.length === 0) return
+      const references: NoteReference[] = pills.map(p => ({
+        title: p.title,
+        path: p.path,
+        type: p.type,
+      }))
+      onSend(value, references)
+      setPills([])
+    }
+  }
+
+  return (
+    <div style={{ position: 'relative' }}>
+      {pills.length > 0 && (
+        <div className="flex flex-wrap gap-1" style={{ marginBottom: 4 }}>
+          {pills.map(pill => (
+            <span
+              key={pill.path}
+              className="inline-flex items-center gap-1 text-xs"
+              style={{
+                background: pill.lightColor ?? 'var(--muted)',
+                color: pill.color ?? 'var(--foreground)',
+                borderRadius: 9999,
+                padding: '1px 8px 1px 6px',
+                fontWeight: 500,
+              }}
+              data-testid="reference-pill"
+            >
+              {pill.title}
+              <button
+                className="border-none bg-transparent p-0 cursor-pointer"
+                style={{ color: 'inherit', opacity: 0.6, fontSize: 10, lineHeight: 1 }}
+                onClick={() => setPills(prev => prev.filter(p => p.path !== pill.path))}
+                tabIndex={-1}
+              >
+                ×
+              </button>
+            </span>
+          ))}
+        </div>
+      )}
+      <input
+        ref={inputRefToUse}
+        value={value}
+        onChange={handleChange}
+        onKeyDown={handleKeyDown}
+        className="flex-1 border border-border bg-transparent text-foreground"
+        style={{
+          fontSize: 13, borderRadius: 8, padding: '8px 10px',
+          outline: 'none', fontFamily: 'inherit', width: '100%', boxSizing: 'border-box',
+        }}
+        placeholder={placeholder}
+        disabled={disabled}
+        data-testid="agent-input"
+      />
+      {showMenu && suggestions.length > 0 && (
+        <div
+          ref={menuRef}
+          className="wikilink-menu"
+          style={{
+            position: 'absolute', bottom: '100%', left: 0, right: 0,
+            marginBottom: 4, maxHeight: 260, overflowY: 'auto',
+          }}
+          data-testid="wikilink-menu"
+        >
+          {suggestions.map((s, i) => (
+            <div
+              key={s.path}
+              className="flex items-center justify-between gap-2 cursor-pointer transition-colors"
+              style={{
+                padding: '6px 10px',
+                fontSize: 13,
+                background: i === clampedIndex ? 'var(--accent)' : undefined,
+              }}
+              onMouseDown={e => e.preventDefault()}
+              onClick={() => selectSuggestion(s)}
+              onMouseEnter={() => setSelectedIndex(i)}
+            >
+              <span className="truncate">{s.title}</span>
+              {s.isA && s.isA !== 'Note' && (
+                <span
+                  className="shrink-0 text-xs"
+                  style={{
+                    color: s.color,
+                    backgroundColor: s.lightColor,
+                    borderRadius: 9999,
+                    padding: '1px 8px',
+                  }}
+                >
+                  {s.isA}
+                </span>
+              )}
+            </div>
+          ))}
+        </div>
+      )}
+    </div>
+  )
+}

src/hooks/useAiActivity.test.ts

@@ -7,6 +7,7 @@ let lastWsInstance: MockWebSocket | null = null
 class MockWebSocket {
   onmessage: ((event: MessageEvent) => void) | null = null
   onerror: (() => void) | null = null
+  onclose: (() => void) | null = null
   close = vi.fn()
   url: string
 
@@ -82,10 +83,10 @@ describe('useAiActivity', () => {
     expect(result.current.highlightElement).toBeNull()
   })
 
-  it('ignores non-highlight messages', () => {
+  it('ignores non-ui_action messages', () => {
     const { result } = renderHook(() => useAiActivity())
     act(() => {
-      sendWsMessage({ type: 'ui_action', action: 'other_action' })
+      sendWsMessage({ type: 'other', action: 'highlight', element: 'editor' })
     })
     expect(result.current.highlightElement).toBeNull()
   })
@@ -112,4 +113,57 @@ describe('useAiActivity', () => {
     expect(result.current.highlightElement).toBe('properties')
     expect(result.current.highlightPath).toBeNull()
   })
+
+  it('calls onOpenNote callback on open_note action', () => {
+    const onOpenNote = vi.fn()
+    renderHook(() => useAiActivity({ onOpenNote }))
+    act(() => {
+      sendWsMessage({ type: 'ui_action', action: 'open_note', path: 'project/foo.md' })
+    })
+    expect(onOpenNote).toHaveBeenCalledWith('project/foo.md')
+  })
+
+  it('calls onOpenTab callback on open_tab action', () => {
+    const onOpenTab = vi.fn()
+    renderHook(() => useAiActivity({ onOpenTab }))
+    act(() => {
+      sendWsMessage({ type: 'ui_action', action: 'open_tab', path: 'note/bar.md' })
+    })
+    expect(onOpenTab).toHaveBeenCalledWith('note/bar.md')
+  })
+
+  it('calls onSetFilter callback on set_filter action', () => {
+    const onSetFilter = vi.fn()
+    renderHook(() => useAiActivity({ onSetFilter }))
+    act(() => {
+      sendWsMessage({ type: 'ui_action', action: 'set_filter', filterType: 'Project' })
+    })
+    expect(onSetFilter).toHaveBeenCalledWith('Project')
+  })
+
+  it('calls onVaultChanged callback on vault_changed action', () => {
+    const onVaultChanged = vi.fn()
+    renderHook(() => useAiActivity({ onVaultChanged }))
+    act(() => {
+      sendWsMessage({ type: 'ui_action', action: 'vault_changed', path: 'note/new.md' })
+    })
+    expect(onVaultChanged).toHaveBeenCalledWith('note/new.md')
+  })
+
+  it('does not call onOpenNote when path is missing', () => {
+    const onOpenNote = vi.fn()
+    renderHook(() => useAiActivity({ onOpenNote }))
+    act(() => {
+      sendWsMessage({ type: 'ui_action', action: 'open_note' })
+    })
+    expect(onOpenNote).not.toHaveBeenCalled()
+  })
+
+  it('reconnects on close after delay', () => {
+    renderHook(() => useAiActivity())
+    const firstWs = lastWsInstance
+    act(() => { firstWs?.onclose?.() })
+    act(() => { vi.advanceTimersByTime(3000) })
+    expect(lastWsInstance).not.toBe(firstWs)
+  })
 })

src/hooks/useAiActivity.ts

@@ -1,4 +1,4 @@
-import { useState, useEffect, useRef } from 'react'
+import { useState, useEffect, useRef, useCallback } from 'react'
 
 export type HighlightElement = 'editor' | 'tab' | 'properties' | 'notelist' | null
 
@@ -7,58 +7,89 @@ export interface AiActivity {
   highlightPath: string | null
 }
 
+export interface AiActivityCallbacks {
+  onOpenNote?: (path: string) => void
+  onOpenTab?: (path: string) => void
+  onSetFilter?: (type: string) => void
+  onVaultChanged?: (path?: string) => void
+}
+
 const WS_UI_URL = 'ws://localhost:9711'
 const HIGHLIGHT_DURATION_MS = 800
+const RECONNECT_DELAY_MS = 3000
 
 /**
- * Listens on the UI WebSocket bridge (port 9711) for highlight events
- * from the AI agent. Sets highlightElement for 800ms then auto-clears.
+ * Listens on the UI WebSocket bridge (port 9711) for UI action events
+ * from the MCP server. Handles highlight, open_note, open_tab, set_filter,
+ * and vault_changed actions.
  */
-export function useAiActivity(): AiActivity {
+export function useAiActivity(callbacks?: AiActivityCallbacks): AiActivity {
   const [highlightElement, setHighlightElement] = useState<HighlightElement>(null)
   const [highlightPath, setHighlightPath] = useState<string | null>(null)
   const timerRef = useRef<ReturnType<typeof setTimeout> | null>(null)
+  const callbacksRef = useRef(callbacks)
+  useEffect(() => { callbacksRef.current = callbacks })
+
+  const handleMessage = useCallback((event: MessageEvent) => {
+    try {
+      const data = JSON.parse(event.data as string)
+      if (data.type !== 'ui_action') return
+      switch (data.action) {
+        case 'highlight':
+          setHighlightElement(data.element ?? null)
+          setHighlightPath(data.path ?? null)
+          if (timerRef.current) clearTimeout(timerRef.current)
+          timerRef.current = setTimeout(() => {
+            setHighlightElement(null)
+            setHighlightPath(null)
+          }, HIGHLIGHT_DURATION_MS)
+          break
+        case 'open_note':
+          if (data.path) callbacksRef.current?.onOpenNote?.(data.path)
+          break
+        case 'open_tab':
+          if (data.path) callbacksRef.current?.onOpenTab?.(data.path)
+          break
+        case 'set_filter':
+          if (data.filterType) callbacksRef.current?.onSetFilter?.(data.filterType)
+          break
+        case 'vault_changed':
+          callbacksRef.current?.onVaultChanged?.(data.path)
+          break
+      }
+    } catch {
+      // Ignore parse errors from malformed messages
+    }
+  }, [])
 
   useEffect(() => {
     let ws: WebSocket | null = null
     let mounted = true
+    let reconnectTimer: ReturnType<typeof setTimeout> | null = null
 
-    try {
-      ws = new WebSocket(WS_UI_URL)
-
-      ws.onmessage = (event) => {
-        if (!mounted) return
-        try {
-          const data = JSON.parse(event.data as string)
-          if (data.type === 'ui_action' && data.action === 'highlight') {
-            setHighlightElement(data.element ?? null)
-            setHighlightPath(data.path ?? null)
-            if (timerRef.current) clearTimeout(timerRef.current)
-            timerRef.current = setTimeout(() => {
-              if (mounted) {
-                setHighlightElement(null)
-                setHighlightPath(null)
-              }
-            }, HIGHLIGHT_DURATION_MS)
-          }
-        } catch {
-          // Ignore parse errors from malformed messages
+    function connect() {
+      if (!mounted) return
+      try {
+        ws = new WebSocket(WS_UI_URL)
+        ws.onmessage = handleMessage
+        ws.onclose = () => {
+          if (mounted) reconnectTimer = setTimeout(connect, RECONNECT_DELAY_MS)
         }
+        ws.onerror = () => { /* Silent — bridge may not be running */ }
+      } catch {
+        if (mounted) reconnectTimer = setTimeout(connect, RECONNECT_DELAY_MS)
       }
-
-      ws.onerror = () => {
-        // Silent — UI bridge may not be running
-      }
-    } catch {
-      // WebSocket connection failed — bridge not available
     }
 
+    connect()
+
     return () => {
       mounted = false
       ws?.close()
       if (timerRef.current) clearTimeout(timerRef.current)
+      if (reconnectTimer) clearTimeout(reconnectTimer)
     }
-  }, [])
+  }, [handleMessage])
 
   return { highlightElement, highlightPath }
 }

src/hooks/useAiAgent.ts

@@ -3,9 +3,13 @@
  * Uses Claude CLI subprocess with MCP tools via Tauri.
  *
  * States: idle -> thinking -> tool-executing -> done/error
+ *
+ * Reasoning streams live while Claude thinks, then auto-collapses.
+ * Response text accumulates internally and is revealed as a complete block on done.
  */
 import { useState, useCallback, useRef, useEffect } from 'react'
 import type { AiAction } from '../components/AiMessage'
+import type { NoteReference } from '../utils/ai-context'
 import { streamClaudeAgent, buildAgentSystemPrompt } from '../utils/ai-agent'
 import { nextMessageId } from '../utils/ai-chat'
 
@@ -13,7 +17,9 @@ export type AgentStatus = 'idle' | 'thinking' | 'tool-executing' | 'done' | 'err
 
 export interface AiAgentMessage {
   userMessage: string
+  references?: NoteReference[]
   reasoning?: string
+  reasoningDone?: boolean
   actions: AiAction[]
   response?: string
   isStreaming?: boolean
@@ -25,16 +31,19 @@ export function useAiAgent(vaultPath: string, contextPrompt?: string) {
   const [status, setStatus] = useState<AgentStatus>('idle')
   const abortRef = useRef({ aborted: false })
   const contextRef = useRef(contextPrompt)
+  const responseAccRef = useRef('')
   useEffect(() => {
     contextRef.current = contextPrompt
   }, [contextPrompt])
 
-  const sendMessage = useCallback(async (text: string) => {
+  const sendMessage = useCallback(async (text: string, references?: NoteReference[]) => {
     if (!text.trim() || status === 'thinking' || status === 'tool-executing') return
 
+    const refs = references && references.length > 0 ? references : undefined
+
     if (!vaultPath) {
       setMessages(prev => [...prev, {
-        userMessage: text.trim(), actions: [],
+        userMessage: text.trim(), references: refs, actions: [],
         response: 'No vault loaded. Open a vault first.',
         id: nextMessageId(),
       }])
@@ -42,10 +51,11 @@ export function useAiAgent(vaultPath: string, contextPrompt?: string) {
     }
 
     abortRef.current = { aborted: false }
+    responseAccRef.current = ''
 
     const messageId = nextMessageId()
     setMessages(prev => [...prev, {
-      userMessage: text.trim(), actions: [], isStreaming: true, id: messageId,
+      userMessage: text.trim(), references: refs, actions: [], isStreaming: true, id: messageId,
     }])
     setStatus('thinking')
 
@@ -53,41 +63,85 @@ export function useAiAgent(vaultPath: string, contextPrompt?: string) {
       setMessages(prev => prev.map(m => m.id === messageId ? fn(m) : m))
     }
 
-    // When a contextual prompt is provided (from buildContextualPrompt),
-    // use it directly — it already includes the system preamble.
+    const markReasoningDone = () => {
+      update(m => m.reasoningDone ? m : { ...m, reasoningDone: true })
+    }
+
     const systemPrompt = contextRef.current ?? buildAgentSystemPrompt()
 
     await streamClaudeAgent(text.trim(), systemPrompt, vaultPath, {
-      onText: (text) => {
+      onThinking: (chunk) => {
         if (abortRef.current.aborted) return
-        update(m => ({ ...m, response: (m.response ?? '') + text }))
+        update(m => ({ ...m, reasoning: (m.reasoning ?? '') + chunk }))
       },
 
-      onToolStart: (toolName, toolId) => {
+      onText: (chunk) => {
         if (abortRef.current.aborted) return
+        markReasoningDone()
+        responseAccRef.current += chunk
+      },
+
+      onToolStart: (toolName, toolId, input) => {
+        if (abortRef.current.aborted) return
+        markReasoningDone()
         setStatus('tool-executing')
+        update(m => {
+          const existing = m.actions.find(a => a.toolId === toolId)
+          if (existing) {
+            return {
+              ...m,
+              actions: m.actions.map(a =>
+                a.toolId === toolId ? { ...a, input: input ?? a.input } : a,
+              ),
+            }
+          }
+          return {
+            ...m,
+            actions: [...m.actions, {
+              tool: toolName,
+              toolId,
+              label: formatToolLabel(toolName, toolId),
+              status: 'pending' as const,
+              input,
+            }],
+          }
+        })
+      },
+
+      onToolDone: (toolId, output) => {
+        if (abortRef.current.aborted) return
         update(m => ({
           ...m,
-          actions: [...m.actions, {
-            tool: toolName,
-            label: formatToolLabel(toolName, toolId),
-            status: 'pending' as const,
-          }],
+          actions: m.actions.map(a =>
+            a.toolId === toolId ? { ...a, status: 'done' as const, output } : a,
+          ),
         }))
       },
 
       onError: (error) => {
         if (abortRef.current.aborted) return
         setStatus('error')
-        update(m => ({ ...m, isStreaming: false, response: (m.response ?? '') + `\nError: ${error}` }))
+        const partial = responseAccRef.current
+        update(m => ({
+          ...m,
+          isStreaming: false,
+          reasoningDone: true,
+          response: partial ? `${partial}\n\nError: ${error}` : `Error: ${error}`,
+          actions: m.actions.map(a =>
+            a.status === 'pending' ? { ...a, status: 'error' as const } : a,
+          ),
+        }))
       },
 
       onDone: () => {
         if (abortRef.current.aborted) return
         setStatus('done')
+        const finalResponse = responseAccRef.current || undefined
         update(m => ({
           ...m,
           isStreaming: false,
+          reasoningDone: true,
+          response: finalResponse,
           actions: m.actions.map(a => a.status === 'pending' ? { ...a, status: 'done' as const } : a),
         }))
       },
@@ -96,6 +150,7 @@ export function useAiAgent(vaultPath: string, contextPrompt?: string) {
 
   const clearConversation = useCallback(() => {
     abortRef.current.aborted = true
+    responseAccRef.current = ''
     setMessages([])
     setStatus('idle')
   }, [])

src/hooks/useAppCommands.ts

@@ -64,6 +64,8 @@ interface AppCommandsConfig {
   onRestoreGettingStarted?: () => void
   isGettingStartedHidden?: boolean
   vaultCount?: number
+  mcpStatus?: string
+  onInstallMcp?: () => void
 }
 
 /** Sets up keyboard shortcuts, command registry, menu events, and keyboard navigation. */
@@ -172,6 +174,8 @@ export function useAppCommands(config: AppCommandsConfig): CommandAction[] {
     onRestoreGettingStarted: config.onRestoreGettingStarted,
     isGettingStartedHidden: config.isGettingStartedHidden,
     vaultCount: config.vaultCount,
+    mcpStatus: config.mcpStatus,
+    onInstallMcp: config.onInstallMcp,
   })
 
   useKeyboardNavigation({

src/hooks/useCommandRegistry.ts

@@ -19,6 +19,8 @@ interface CommandRegistryConfig {
   entries: VaultEntry[]
   modifiedCount: number
   conflictCount?: number
+  mcpStatus?: string
+  onInstallMcp?: () => void
 
   onQuickOpen: () => void
   onCreateNote: () => void
@@ -193,6 +195,7 @@ export function useCommandRegistry(config: CommandRegistryConfig): CommandAction
     onCheckForUpdates,
     onCreateType,
     onRemoveActiveVault, onRestoreGettingStarted, isGettingStartedHidden, vaultCount,
+    mcpStatus, onInstallMcp,
   } = config
 
   const hasActiveNote = activeTabPath !== null
@@ -252,6 +255,7 @@ export function useCommandRegistry(config: CommandRegistryConfig): CommandAction
       { id: 'remove-vault', label: 'Remove Vault from List', group: 'Settings', keywords: ['vault', 'remove', 'disconnect', 'hide'], enabled: (vaultCount ?? 0) > 1 && !!onRemoveActiveVault, execute: () => onRemoveActiveVault?.() },
       { id: 'restore-getting-started', label: 'Restore Getting Started Vault', group: 'Settings', keywords: ['vault', 'restore', 'demo', 'getting started', 'reset'], enabled: !!isGettingStartedHidden && !!onRestoreGettingStarted, execute: () => onRestoreGettingStarted?.() },
       { id: 'check-updates', label: 'Check for Updates', group: 'Settings', keywords: ['update', 'version', 'upgrade', 'release'], enabled: true, execute: () => onCheckForUpdates?.() },
+      { id: 'install-mcp', label: 'Install MCP Server', group: 'Settings', keywords: ['mcp', 'claude', 'ai', 'tools', 'install'], enabled: mcpStatus === 'not_installed' && !!onInstallMcp, execute: () => onInstallMcp?.() },
 
       // Type-aware: "New [Type]" and "List [Type]"
       ...buildTypeCommands(vaultTypes, onCreateNoteOfType, onSelect),
@@ -269,5 +273,6 @@ export function useCommandRegistry(config: CommandRegistryConfig): CommandAction
     onGoBack, onGoForward, canGoBack, canGoForward,
     vaultTypes, themes, activeThemeId, onSwitchTheme, onCreateTheme, onOpenTheme,
     onRemoveActiveVault, onRestoreGettingStarted, isGettingStartedHidden, vaultCount,
+    mcpStatus, onInstallMcp,
   ])
 }

src/hooks/useIndexing.test.ts

@@ -1,23 +1,18 @@
-import { describe, it, expect, vi, beforeEach } from 'vitest'
-import { renderHook, act, waitFor } from '@testing-library/react'
+import { describe, it, expect, vi, beforeEach, afterEach } from 'vitest'
+import { renderHook, act } from '@testing-library/react'
 import { useIndexing } from './useIndexing'
 
+vi.mock('@tauri-apps/api/core', () => ({ invoke: vi.fn() }))
+vi.mock('@tauri-apps/api/event', () => ({ listen: vi.fn().mockResolvedValue(vi.fn()) }))
 vi.mock('../mock-tauri', () => ({
   isTauri: () => false,
-  mockInvoke: vi.fn().mockImplementation((cmd: string) => {
-    if (cmd === 'get_index_status') {
-      return Promise.resolve({
-        available: true,
-        qmd_installed: true,
-        collection_exists: true,
-        indexed_count: 100,
-        embedded_count: 80,
-        pending_embed: 0,
-      })
-    }
-    if (cmd === 'start_indexing') return Promise.resolve(null)
-    if (cmd === 'trigger_incremental_index') return Promise.resolve(null)
-    return Promise.resolve(null)
+  mockInvoke: vi.fn().mockResolvedValue({
+    available: true,
+    qmd_installed: true,
+    collection_exists: true,
+    indexed_count: 100,
+    embedded_count: 80,
+    pending_embed: 0,
   }),
 }))
 
@@ -25,135 +20,60 @@ const { mockInvoke } = await import('../mock-tauri') as { mockInvoke: ReturnType
 
 describe('useIndexing', () => {
   beforeEach(() => {
+    vi.useFakeTimers()
     vi.clearAllMocks()
+    mockInvoke.mockResolvedValue({
+      available: true,
+      qmd_installed: true,
+      collection_exists: true,
+      indexed_count: 100,
+      embedded_count: 80,
+      pending_embed: 0,
+    })
   })
 
-  it('starts with idle progress', () => {
-    const { result } = renderHook(() => useIndexing('/vault'))
+  afterEach(() => {
+    vi.useRealTimers()
+  })
+
+  it('starts with idle phase', () => {
+    const { result } = renderHook(() => useIndexing('/test/vault'))
     expect(result.current.progress.phase).toBe('idle')
-    expect(result.current.progress.done).toBe(false)
   })
 
-  it('checks index status on mount', async () => {
-    renderHook(() => useIndexing('/vault'))
-    await waitFor(() => {
-      expect(mockInvoke).toHaveBeenCalledWith('get_index_status', { vaultPath: '/vault' })
-    })
+  it('auto-dismisses error phase after 15 seconds', async () => {
+    const { result } = renderHook(() => useIndexing('/test/vault'))
+
+    // Simulate setting error state via retryIndexing
+    mockInvoke.mockRejectedValueOnce(new Error('qmd update failed'))
+    await act(async () => { await result.current.retryIndexing() })
+    expect(result.current.progress.phase).toBe('error')
+
+    act(() => { vi.advanceTimersByTime(15000) })
+    expect(result.current.progress.phase).toBe('idle')
   })
 
-  it('does not start indexing when collection exists and no pending embeds', async () => {
-    renderHook(() => useIndexing('/vault'))
-    await waitFor(() => {
-      expect(mockInvoke).toHaveBeenCalledWith('get_index_status', { vaultPath: '/vault' })
-    })
-    expect(mockInvoke).not.toHaveBeenCalledWith('start_indexing', expect.anything())
+  it('sets unavailable phase for missing qmd errors', async () => {
+    const { result } = renderHook(() => useIndexing('/test/vault'))
+
+    mockInvoke.mockRejectedValueOnce(new Error('bun not installed'))
+    await act(async () => { await result.current.retryIndexing() })
+    expect(result.current.progress.phase).toBe('unavailable')
   })
 
-  it('starts indexing when collection is missing', async () => {
-    mockInvoke.mockImplementation((cmd: string) => {
-      if (cmd === 'get_index_status') {
-        return Promise.resolve({
-          available: true,
-          qmd_installed: true,
-          collection_exists: false,
-          indexed_count: 0,
-          embedded_count: 0,
-          pending_embed: 0,
-        })
-      }
-      return Promise.resolve(null)
-    })
+  it('auto-dismisses unavailable phase after 8 seconds', async () => {
+    const { result } = renderHook(() => useIndexing('/test/vault'))
 
-    const { result } = renderHook(() => useIndexing('/vault'))
-    await waitFor(() => {
-      expect(mockInvoke).toHaveBeenCalledWith('start_indexing', { vaultPath: '/vault' })
-    })
-    expect(result.current.progress.phase).not.toBe('idle')
+    mockInvoke.mockRejectedValueOnce(new Error('bun not installed'))
+    await act(async () => { await result.current.retryIndexing() })
+    expect(result.current.progress.phase).toBe('unavailable')
+
+    act(() => { vi.advanceTimersByTime(8000) })
+    expect(result.current.progress.phase).toBe('idle')
   })
 
-  it('starts indexing when qmd is not installed', async () => {
-    mockInvoke.mockImplementation((cmd: string) => {
-      if (cmd === 'get_index_status') {
-        return Promise.resolve({
-          available: false,
-          qmd_installed: false,
-          collection_exists: false,
-          indexed_count: 0,
-          embedded_count: 0,
-          pending_embed: 0,
-        })
-      }
-      return Promise.resolve(null)
-    })
-
-    renderHook(() => useIndexing('/vault'))
-    await waitFor(() => {
-      expect(mockInvoke).toHaveBeenCalledWith('start_indexing', { vaultPath: '/vault' })
-    })
-  })
-
-  it('starts indexing when pending embeds exist', async () => {
-    mockInvoke.mockImplementation((cmd: string) => {
-      if (cmd === 'get_index_status') {
-        return Promise.resolve({
-          available: true,
-          qmd_installed: true,
-          collection_exists: true,
-          indexed_count: 100,
-          embedded_count: 80,
-          pending_embed: 20,
-        })
-      }
-      return Promise.resolve(null)
-    })
-
-    renderHook(() => useIndexing('/vault'))
-    await waitFor(() => {
-      expect(mockInvoke).toHaveBeenCalledWith('start_indexing', { vaultPath: '/vault' })
-    })
-  })
-
-  it('triggerIncrementalIndex calls the command', async () => {
-    const { result } = renderHook(() => useIndexing('/vault'))
-    await act(async () => {
-      await result.current.triggerIncrementalIndex()
-    })
-    expect(mockInvoke).toHaveBeenCalledWith('trigger_incremental_index', { vaultPath: '/vault' })
-  })
-
-  it('handles index status check failure gracefully', async () => {
-    mockInvoke.mockImplementation((cmd: string) => {
-      if (cmd === 'get_index_status') return Promise.reject(new Error('network error'))
-      return Promise.resolve(null)
-    })
-
-    const { result } = renderHook(() => useIndexing('/vault'))
-    // Should remain idle — not crash
-    await waitFor(() => {
-      expect(result.current.progress.phase).toBe('idle')
-    })
-  })
-
-  it('sets error phase when start_indexing fails', async () => {
-    mockInvoke.mockImplementation((cmd: string) => {
-      if (cmd === 'get_index_status') {
-        return Promise.resolve({
-          available: false,
-          qmd_installed: false,
-          collection_exists: false,
-          indexed_count: 0,
-          embedded_count: 0,
-          pending_embed: 0,
-        })
-      }
-      if (cmd === 'start_indexing') return Promise.reject(new Error('install failed'))
-      return Promise.resolve(null)
-    })
-
-    const { result } = renderHook(() => useIndexing('/vault'))
-    await waitFor(() => {
-      expect(result.current.progress.phase).toBe('error')
-    })
-    expect(result.current.progress.error).toContain('install failed')
+  it('exposes retryIndexing function', () => {
+    const { result } = renderHook(() => useIndexing('/test/vault'))
+    expect(typeof result.current.retryIndexing).toBe('function')
   })
 })

src/hooks/useIndexing.ts

@@ -3,7 +3,7 @@ import { invoke } from '@tauri-apps/api/core'
 import { isTauri, mockInvoke } from '../mock-tauri'
 
 export interface IndexingProgress {
-  phase: 'idle' | 'installing' | 'scanning' | 'embedding' | 'complete' | 'error'
+  phase: 'idle' | 'installing' | 'scanning' | 'embedding' | 'complete' | 'error' | 'unavailable'
   current: number
   total: number
   done: boolean
@@ -66,7 +66,7 @@ export function useIndexing(vaultPath: string) {
         if (needsIndexing && !indexingRef.current) {
           indexingRef.current = true
           setProgress({
-            phase: 'scanning',
+            phase: status.qmd_installed ? 'scanning' : 'installing',
             current: 0,
             total: status.indexed_count,
             done: false,
@@ -74,16 +74,17 @@ export function useIndexing(vaultPath: string) {
           })
           // Fire and forget — progress updates come via events
           invokeCmd('start_indexing', { vaultPath }).catch((err) => {
-            if (!cancelled) {
-              setProgress({
-                phase: 'error',
-                current: 0,
-                total: 0,
-                done: true,
-                error: String(err),
-              })
-              indexingRef.current = false
-            }
+            if (cancelled) return
+            const msg = String(err)
+            const isUnavailable = msg.includes('not installed') || msg.includes('not available')
+            setProgress({
+              phase: isUnavailable ? 'unavailable' : 'error',
+              current: 0,
+              total: 0,
+              done: true,
+              error: msg,
+            })
+            indexingRef.current = false
           })
         }
       } catch {
@@ -95,12 +96,20 @@ export function useIndexing(vaultPath: string) {
     return () => { cancelled = true }
   }, [vaultPath])
 
-  // Auto-dismiss the "complete" status after 5 seconds
+  // Auto-dismiss transient statuses after a delay
   useEffect(() => {
     if (progress.phase === 'complete') {
       const timer = setTimeout(() => setProgress(IDLE), 5000)
       return () => clearTimeout(timer)
     }
+    if (progress.phase === 'unavailable') {
+      const timer = setTimeout(() => setProgress(IDLE), 8000)
+      return () => clearTimeout(timer)
+    }
+    if (progress.phase === 'error') {
+      const timer = setTimeout(() => setProgress(IDLE), 15000)
+      return () => clearTimeout(timer)
+    }
   }, [progress.phase])
 
   const triggerIncrementalIndex = useCallback(async () => {
@@ -112,5 +121,20 @@ export function useIndexing(vaultPath: string) {
     }
   }, [])
 
-  return { progress, triggerIncrementalIndex }
+  const retryIndexing = useCallback(async () => {
+    if (indexingRef.current || !vaultPathRef.current) return
+    indexingRef.current = true
+    setProgress({ phase: 'scanning', current: 0, total: 0, done: false, error: null })
+    try {
+      await invokeCmd('start_indexing', { vaultPath: vaultPathRef.current })
+    } catch (err) {
+      const msg = String(err)
+      const isUnavailable = msg.includes('not installed') || msg.includes('not available')
+      setProgress({ phase: isUnavailable ? 'unavailable' : 'error', current: 0, total: 0, done: true, error: msg })
+    } finally {
+      indexingRef.current = false
+    }
+  }, [])
+
+  return { progress, triggerIncrementalIndex, retryIndexing }
 }

src/hooks/useMcpRegistration.ts

@@ -1,33 +0,0 @@
-import { useEffect, useRef } from 'react'
-import { invoke } from '@tauri-apps/api/core'
-import { isTauri, mockInvoke } from '../mock-tauri'
-
-function tauriCall<T>(command: string, args: Record<string, unknown>): Promise<T> {
-  return isTauri() ? invoke<T>(command, args) : mockInvoke<T>(command, args)
-}
-
-/**
- * Registers Laputa as an MCP server in Claude Code and Cursor config files.
- * Fires once per vault path (skips duplicates).
- */
-export function useMcpRegistration(
-  vaultPath: string,
-  onToast: (msg: string) => void,
-) {
-  const registeredRef = useRef<string | null>(null)
-
-  useEffect(() => {
-    if (registeredRef.current === vaultPath) return
-    registeredRef.current = vaultPath
-
-    tauriCall<string>('register_mcp_tools', { vaultPath })
-      .then((status) => {
-        if (status === 'registered') {
-          onToast('Laputa registered as MCP tool for Claude Code')
-        }
-      })
-      .catch(() => {
-        // Silently ignore — not critical for app operation
-      })
-  }, [vaultPath]) // eslint-disable-line react-hooks/exhaustive-deps -- onToast is stable via ref
-}

src/hooks/useMcpStatus.test.ts

@@ -0,0 +1,151 @@
+import { describe, it, expect, vi, beforeEach } from 'vitest'
+import { renderHook, act, waitFor } from '@testing-library/react'
+import { useMcpStatus } from './useMcpStatus'
+
+vi.mock('@tauri-apps/api/core', () => ({
+  invoke: vi.fn(),
+}))
+
+vi.mock('../mock-tauri', () => ({
+  isTauri: () => false,
+  mockInvoke: vi.fn(),
+}))
+
+const { mockInvoke } = await import('../mock-tauri') as { mockInvoke: ReturnType<typeof vi.fn> }
+
+describe('useMcpStatus', () => {
+  beforeEach(() => {
+    vi.clearAllMocks()
+  })
+
+  it('starts in checking state and resolves to installed', async () => {
+    mockInvoke.mockImplementation((cmd: string) => {
+      if (cmd === 'check_mcp_status') return Promise.resolve('installed')
+      if (cmd === 'register_mcp_tools') return Promise.resolve('updated')
+      return Promise.resolve(null)
+    })
+
+    const onToast = vi.fn()
+    const { result } = renderHook(() => useMcpStatus('/vault', onToast))
+
+    expect(result.current.mcpStatus).toBe('checking')
+
+    await waitFor(() => {
+      expect(result.current.mcpStatus).toBe('installed')
+    })
+  })
+
+  it('resolves to not_installed when check returns not_installed', async () => {
+    mockInvoke.mockImplementation((cmd: string) => {
+      if (cmd === 'check_mcp_status') return Promise.resolve('not_installed')
+      if (cmd === 'register_mcp_tools') return Promise.reject(new Error('fail'))
+      return Promise.resolve(null)
+    })
+
+    const onToast = vi.fn()
+    const { result } = renderHook(() => useMcpStatus('/vault', onToast))
+
+    await waitFor(() => {
+      expect(result.current.mcpStatus).toBe('not_installed')
+    })
+  })
+
+  it('resolves to no_claude_cli when check returns no_claude_cli', async () => {
+    mockInvoke.mockImplementation((cmd: string) => {
+      if (cmd === 'check_mcp_status') return Promise.resolve('no_claude_cli')
+      if (cmd === 'register_mcp_tools') return Promise.reject(new Error('no cli'))
+      return Promise.resolve(null)
+    })
+
+    const onToast = vi.fn()
+    const { result } = renderHook(() => useMcpStatus('/vault', onToast))
+
+    await waitFor(() => {
+      expect(result.current.mcpStatus).toBe('no_claude_cli')
+    })
+  })
+
+  it('install action calls register_mcp_tools and updates status', async () => {
+    mockInvoke.mockImplementation((cmd: string) => {
+      if (cmd === 'check_mcp_status') return Promise.resolve('not_installed')
+      if (cmd === 'register_mcp_tools') return Promise.resolve('registered')
+      return Promise.resolve(null)
+    })
+
+    const onToast = vi.fn()
+    const { result } = renderHook(() => useMcpStatus('/vault', onToast))
+
+    await waitFor(() => {
+      expect(result.current.mcpStatus).toBe('installed')
+    })
+
+    // Reset to test install action directly
+    mockInvoke.mockImplementation((cmd: string) => {
+      if (cmd === 'check_mcp_status') return Promise.resolve('not_installed')
+      if (cmd === 'register_mcp_tools') return Promise.resolve('registered')
+      return Promise.resolve(null)
+    })
+
+    await act(async () => {
+      await result.current.installMcp()
+    })
+
+    expect(result.current.mcpStatus).toBe('installed')
+    expect(onToast).toHaveBeenCalledWith('MCP server installed successfully')
+  })
+
+  it('install action shows error toast on failure', async () => {
+    mockInvoke.mockImplementation((cmd: string) => {
+      if (cmd === 'check_mcp_status') return Promise.resolve('not_installed')
+      if (cmd === 'register_mcp_tools') return Promise.reject(new Error('disk full'))
+      return Promise.resolve(null)
+    })
+
+    const onToast = vi.fn()
+    const { result } = renderHook(() => useMcpStatus('/vault', onToast))
+
+    await waitFor(() => {
+      expect(result.current.mcpStatus).toBe('not_installed')
+    })
+
+    await act(async () => {
+      await result.current.installMcp()
+    })
+
+    expect(result.current.mcpStatus).toBe('not_installed')
+    expect(onToast).toHaveBeenCalledWith(expect.stringContaining('MCP install failed'))
+  })
+
+  it('shows toast when registered for the first time', async () => {
+    mockInvoke.mockImplementation((cmd: string) => {
+      if (cmd === 'check_mcp_status') return Promise.resolve('installed')
+      if (cmd === 'register_mcp_tools') return Promise.resolve('registered')
+      return Promise.resolve(null)
+    })
+
+    const onToast = vi.fn()
+    renderHook(() => useMcpStatus('/vault', onToast))
+
+    await waitFor(() => {
+      expect(onToast).toHaveBeenCalledWith('Laputa registered as MCP tool for Claude Code')
+    })
+  })
+
+  it('does not show toast when already registered', async () => {
+    mockInvoke.mockImplementation((cmd: string) => {
+      if (cmd === 'check_mcp_status') return Promise.resolve('installed')
+      if (cmd === 'register_mcp_tools') return Promise.resolve('updated')
+      return Promise.resolve(null)
+    })
+
+    const onToast = vi.fn()
+    renderHook(() => useMcpStatus('/vault', onToast))
+
+    await waitFor(() => {
+      expect(mockInvoke).toHaveBeenCalledWith('register_mcp_tools', { vaultPath: '/vault' })
+    })
+
+    // 'updated' should not trigger a toast
+    expect(onToast).not.toHaveBeenCalledWith('Laputa registered as MCP tool for Claude Code')
+  })
+})

src/hooks/useMcpStatus.ts

@@ -0,0 +1,72 @@
+import { useCallback, useEffect, useRef, useState } from 'react'
+import { invoke } from '@tauri-apps/api/core'
+import { isTauri, mockInvoke } from '../mock-tauri'
+
+export type McpStatus = 'checking' | 'installed' | 'not_installed' | 'no_claude_cli'
+
+function tauriCall<T>(command: string, args?: Record<string, unknown>): Promise<T> {
+  return isTauri() ? invoke<T>(command, args) : mockInvoke<T>(command, args)
+}
+
+/**
+ * Detects MCP server status on vault open and provides an install action.
+ *
+ * Combines the old `useMcpRegistration` functionality (auto-register on vault
+ * switch) with new status detection for the status bar indicator.
+ */
+export function useMcpStatus(
+  vaultPath: string,
+  onToast: (msg: string) => void,
+) {
+  const [status, setStatus] = useState<McpStatus>('checking')
+  const registeredRef = useRef<string | null>(null)
+  const onToastRef = useRef(onToast)
+  useEffect(() => { onToastRef.current = onToast })
+
+  // Check MCP status on vault open / vault switch
+  useEffect(() => {
+    let cancelled = false
+    setStatus('checking') // eslint-disable-line react-hooks/set-state-in-effect -- reset to checking on vault switch
+
+    tauriCall<string>('check_mcp_status')
+      .then((result) => {
+        if (!cancelled) setStatus(result as McpStatus)
+      })
+      .catch(() => {
+        if (!cancelled) setStatus('not_installed')
+      })
+
+    return () => { cancelled = true }
+  }, [vaultPath])
+
+  // Auto-register on vault switch (preserves old useMcpRegistration behavior)
+  useEffect(() => {
+    if (registeredRef.current === vaultPath) return
+    registeredRef.current = vaultPath
+
+    tauriCall<string>('register_mcp_tools', { vaultPath })
+      .then((result) => {
+        if (result === 'registered') {
+          onToastRef.current('Laputa registered as MCP tool for Claude Code')
+        }
+        setStatus('installed')
+      })
+      .catch(() => {
+        // Non-critical — status check will show the right state
+      })
+  }, [vaultPath])
+
+  const install = useCallback(async () => {
+    setStatus('checking')
+    try {
+      await tauriCall<string>('register_mcp_tools', { vaultPath })
+      setStatus('installed')
+      onToastRef.current('MCP server installed successfully')
+    } catch (e) {
+      setStatus('not_installed')
+      onToastRef.current(`MCP install failed: ${e}`)
+    }
+  }, [vaultPath])
+
+  return { mcpStatus: status, installMcp: install }
+}

src/hooks/useThemeManager.test.ts

@@ -478,4 +478,17 @@ describe('useThemeManager', () => {
     // Light theme isDark should be false (default state is false, so this is stable)
     expect(result.current.isDark).toBe(false)
   })
+
+  it('calls ensure_vault_themes on mount with vaultPath', async () => {
+    renderHook(() => useThemeManager('/vault', entries, allContent))
+    await waitFor(() => {
+      expect(mockInvokeFn).toHaveBeenCalledWith('ensure_vault_themes', { vaultPath: '/vault' })
+    })
+  })
+
+  it('does not call ensure_vault_themes when vaultPath is null', async () => {
+    renderHook(() => useThemeManager(null, entries, allContent))
+    await new Promise(r => setTimeout(r, 50))
+    expect(mockInvokeFn).not.toHaveBeenCalledWith('ensure_vault_themes', expect.anything())
+  })
 })

src/hooks/useThemeManager.ts

@@ -196,6 +196,11 @@ export function useThemeManager(
   entries: VaultEntry[],
   allContent: Record<string, string>,
 ): ThemeManager {
+  // Ensure default theme files exist on vault open (creates theme/ dir + defaults if missing)
+  useEffect(() => {
+    if (vaultPath) tauriCall('ensure_vault_themes', { vaultPath }).catch(() => {})
+  }, [vaultPath])
+
   const { activeThemeId, setActiveThemeId, reload } = useThemeSetting(vaultPath)
   const cachedThemeContent = activeThemeId ? allContent[activeThemeId] : undefined
   const { clearDom: clearTheme, isDark } = useThemeApplier(activeThemeId, cachedThemeContent)

src/index.css

@@ -289,3 +289,26 @@
 .ai-markdown .hljs-attribute { color: #005cc5; }
 .ai-markdown .hljs-deletion { color: #b31d28; background: #ffeef0; }
 .ai-markdown .hljs-meta { color: #6a737d; }
+
+/* --- AI panel working border animation --- */
+
+@keyframes ai-border-pulse {
+  0%, 100% { border-color: var(--accent-blue, #3b82f6); opacity: 1; }
+  50% { border-color: var(--accent-blue, #93c5fd); opacity: 0.6; }
+}
+
+/* --- Typing indicator dots --- */
+
+.typing-dot {
+  display: inline-block;
+  width: 6px;
+  height: 6px;
+  border-radius: 50%;
+  background: var(--muted-foreground);
+  animation: typing-bounce 1.2s ease-in-out infinite;
+}
+
+@keyframes typing-bounce {
+  0%, 60%, 100% { opacity: 0.3; transform: translateY(0); }
+  30% { opacity: 1; transform: translateY(-3px); }
+}

src/mock-tauri/mock-handlers.ts

@@ -264,6 +264,7 @@ export const mockHandlers: Record<string, (args: any) => any> = {
   },
   create_getting_started_vault: () => '/Users/mock/Documents/Getting Started',
   register_mcp_tools: () => 'registered',
+  check_mcp_status: () => 'installed',
   get_index_status: () => ({ available: true, qmd_installed: true, collection_exists: true, indexed_count: 100, embedded_count: 80, pending_embed: 0 }),
   start_indexing: () => null,
   trigger_incremental_index: () => null,
@@ -309,6 +310,7 @@ line-height-base: 1.6
     syncWindowContent()
     return path
   },
+  ensure_vault_themes: (): null => null,
 }
 
 export function addMockEntry(_entry: VaultEntry, content: string): void {

src/test/setup.ts

@@ -2,6 +2,13 @@ import '@testing-library/jest-dom/vitest'
 import { vi } from 'vitest'
 import { createElement, type ReactNode, type ComponentType } from 'react'
 
+// Suppress undici WebSocket ERR_INVALID_ARG_TYPE in jsdom (jsdom Event ≠ Node Event)
+// eslint-disable-next-line @typescript-eslint/no-explicit-any
+;(globalThis as any).process?.on?.('uncaughtException', (err: Error & { code?: string }) => {
+  if (err.code === 'ERR_INVALID_ARG_TYPE' && err.message?.includes('Event')) return
+  throw err
+})
+
 // Mock scrollIntoView for jsdom (not implemented)
 Element.prototype.scrollIntoView = vi.fn()
 

src/utils/ai-agent.ts

@@ -24,15 +24,18 @@ export function buildAgentSystemPrompt(vaultContext?: string): string {
 type ClaudeAgentStreamEvent =
   | { kind: 'Init'; session_id: string }
   | { kind: 'TextDelta'; text: string }
-  | { kind: 'ToolStart'; tool_name: string; tool_id: string }
-  | { kind: 'ToolDone'; tool_id: string }
+  | { kind: 'ThinkingDelta'; text: string }
+  | { kind: 'ToolStart'; tool_name: string; tool_id: string; input?: string }
+  | { kind: 'ToolDone'; tool_id: string; output?: string }
   | { kind: 'Result'; text: string; session_id: string }
   | { kind: 'Error'; message: string }
   | { kind: 'Done' }
 
 export interface AgentStreamCallbacks {
   onText: (text: string) => void
-  onToolStart: (toolName: string, toolId: string) => void
+  onThinking: (text: string) => void
+  onToolStart: (toolName: string, toolId: string, input?: string) => void
+  onToolDone: (toolId: string, output?: string) => void
   onError: (message: string) => void
   onDone: () => void
 }
@@ -64,8 +67,14 @@ export async function streamClaudeAgent(
       case 'TextDelta':
         callbacks.onText(data.text)
         break
+      case 'ThinkingDelta':
+        callbacks.onThinking(data.text)
+        break
       case 'ToolStart':
-        callbacks.onToolStart(data.tool_name, data.tool_id)
+        callbacks.onToolStart(data.tool_name, data.tool_id, data.input)
+        break
+      case 'ToolDone':
+        callbacks.onToolDone(data.tool_id, data.output)
         break
       case 'Error':
         callbacks.onError(data.message)

src/utils/ai-context.test.ts

@@ -1,5 +1,5 @@
 import { describe, it, expect } from 'vitest'
-import { resolveTarget, collectLinkedEntries, buildContextualPrompt } from './ai-context'
+import { resolveTarget, collectLinkedEntries, buildContextualPrompt, buildContextSnapshot } from './ai-context'
 import type { VaultEntry } from '../types'
 
 const makeEntry = (overrides: Partial<VaultEntry> = {}): VaultEntry => ({
@@ -183,3 +183,165 @@ describe('buildContextualPrompt', () => {
     expect(prompt).toContain('AI assistant integrated into Laputa')
   })
 })
+
+describe('buildContextSnapshot', () => {
+  const active = makeEntry({ path: '/vault/a.md', title: 'Alpha', isA: 'Project', status: 'active', owner: 'Alice' })
+  const entries = [
+    active,
+    makeEntry({ path: '/vault/b.md', title: 'Beta', isA: 'Person' }),
+    makeEntry({ path: '/vault/c.md', title: 'Gamma', isA: 'Note' }),
+  ]
+  const allContent: Record<string, string> = {
+    '/vault/a.md': '# Alpha\nProject content.',
+    '/vault/b.md': '# Beta\nPerson content.',
+    '/vault/c.md': '# Gamma\nNote content.',
+  }
+
+  it('includes activeNote with body and frontmatter', () => {
+    const result = buildContextSnapshot({ activeEntry: active, allContent, entries })
+    expect(result).toContain('Alpha')
+    expect(result).toContain('Project content.')
+    expect(result).toContain('"type": "Project"')
+    expect(result).toContain('"status": "active"')
+    expect(result).toContain('"owner": "Alice"')
+  })
+
+  it('includes system preamble', () => {
+    const result = buildContextSnapshot({ activeEntry: active, allContent, entries })
+    expect(result).toContain('AI assistant integrated into Laputa')
+    expect(result).toContain('Context Snapshot')
+  })
+
+  it('includes vault summary with types and totalNotes', () => {
+    const result = buildContextSnapshot({ activeEntry: active, allContent, entries })
+    const json = JSON.parse(result.split('```json\n')[1].split('\n```')[0])
+    expect(json.vault.totalNotes).toBe(3)
+    expect(json.vault.types).toContain('Project')
+    expect(json.vault.types).toContain('Person')
+    expect(json.vault.types).toContain('Note')
+  })
+
+  it('includes openTabs excluding active note', () => {
+    const tab = makeEntry({ path: '/vault/b.md', title: 'Beta', isA: 'Person' })
+    const result = buildContextSnapshot({
+      activeEntry: active, allContent, entries,
+      openTabs: [active, tab],
+    })
+    const json = JSON.parse(result.split('```json\n')[1].split('\n```')[0])
+    expect(json.openTabs).toHaveLength(1)
+    expect(json.openTabs[0].title).toBe('Beta')
+  })
+
+  it('omits openTabs when none besides active', () => {
+    const result = buildContextSnapshot({
+      activeEntry: active, allContent, entries,
+      openTabs: [active],
+    })
+    const json = JSON.parse(result.split('```json\n')[1].split('\n```')[0])
+    expect(json.openTabs).toBeUndefined()
+  })
+
+  it('includes noteListFilter when present', () => {
+    const result = buildContextSnapshot({
+      activeEntry: active, allContent, entries,
+      noteListFilter: { type: 'Project', query: 'search' },
+    })
+    const json = JSON.parse(result.split('```json\n')[1].split('\n```')[0])
+    expect(json.noteListFilter.type).toBe('Project')
+    expect(json.noteListFilter.query).toBe('search')
+  })
+
+  it('omits noteListFilter when empty', () => {
+    const result = buildContextSnapshot({
+      activeEntry: active, allContent, entries,
+      noteListFilter: { type: null, query: '' },
+    })
+    const json = JSON.parse(result.split('```json\n')[1].split('\n```')[0])
+    expect(json.noteListFilter).toBeUndefined()
+  })
+
+  it('includes referencedNotes with bodies', () => {
+    const result = buildContextSnapshot({
+      activeEntry: active, allContent, entries,
+      references: [
+        { title: 'Beta', path: '/vault/b.md', type: 'Person' },
+        { title: 'Gamma', path: '/vault/c.md', type: null },
+      ],
+    })
+    const json = JSON.parse(result.split('```json\n')[1].split('\n```')[0])
+    expect(json.referencedNotes).toHaveLength(2)
+    expect(json.referencedNotes[0].title).toBe('Beta')
+    expect(json.referencedNotes[0].body).toContain('Person content.')
+    expect(json.referencedNotes[1].type).toBe('Note') // null fallback
+  })
+
+  it('filters out references with no content', () => {
+    const result = buildContextSnapshot({
+      activeEntry: active, allContent, entries,
+      references: [
+        { title: 'Beta', path: '/vault/b.md', type: 'Person' },
+        { title: 'Missing', path: '/vault/missing.md', type: null },
+      ],
+    })
+    const json = JSON.parse(result.split('```json\n')[1].split('\n```')[0])
+    expect(json.referencedNotes).toHaveLength(1)
+    expect(json.referencedNotes[0].title).toBe('Beta')
+  })
+
+  it('omits referencedNotes when no references provided', () => {
+    const result = buildContextSnapshot({ activeEntry: active, allContent, entries })
+    const json = JSON.parse(result.split('```json\n')[1].split('\n```')[0])
+    expect(json.referencedNotes).toBeUndefined()
+  })
+
+  it('includes noteList when provided', () => {
+    const noteList = [
+      { path: '/vault/a.md', title: 'Alpha', type: 'Project' },
+      { path: '/vault/b.md', title: 'Beta', type: 'Person' },
+    ]
+    const result = buildContextSnapshot({
+      activeEntry: active, allContent, entries,
+      noteList,
+    })
+    const json = JSON.parse(result.split('```json\n')[1].split('\n```')[0])
+    expect(json.noteList).toHaveLength(2)
+    expect(json.noteList[0].title).toBe('Alpha')
+    expect(json.noteList[1].type).toBe('Person')
+  })
+
+  it('truncates noteList at 100 items', () => {
+    const noteList = Array.from({ length: 150 }, (_, i) => ({
+      path: `/vault/note-${i}.md`, title: `Note ${i}`, type: 'Note',
+    }))
+    const result = buildContextSnapshot({
+      activeEntry: active, allContent, entries,
+      noteList,
+    })
+    const json = JSON.parse(result.split('```json\n')[1].split('\n```')[0])
+    expect(json.noteList).toHaveLength(100)
+    expect(json.noteListTruncated).toEqual({ shown: 100, total: 150 })
+  })
+
+  it('omits noteList when empty', () => {
+    const result = buildContextSnapshot({
+      activeEntry: active, allContent, entries,
+      noteList: [],
+    })
+    const json = JSON.parse(result.split('```json\n')[1].split('\n```')[0])
+    expect(json.noteList).toBeUndefined()
+  })
+
+  it('includes belongsTo and relatedTo in frontmatter', () => {
+    const entryWithRels = makeEntry({
+      path: '/vault/a.md', title: 'Alpha',
+      belongsTo: ['[[Parent]]'],
+      relatedTo: ['[[Sibling]]'],
+      relationships: { people: ['[[Alice]]'] },
+    })
+    const result = buildContextSnapshot({ activeEntry: entryWithRels, allContent, entries })
+    const json = JSON.parse(result.split('```json\n')[1].split('\n```')[0])
+    expect(json.activeNote.frontmatter.belongsTo).toEqual(['[[Parent]]'])
+    expect(json.activeNote.frontmatter.relatedTo).toEqual(['[[Sibling]]'])
+    expect(json.activeNote.frontmatter.relationships).toEqual({ people: ['[[Alice]]'] })
+  })
+})

src/utils/ai-context.ts

@@ -1,6 +1,6 @@
 /**
- * AI contextual chat — builds the context note list from the active note
- * and its first-degree linked notes (outgoingLinks + relationships).
+ * AI contextual chat — builds a structured context snapshot from the active note,
+ * open tabs, vault metadata, and optional explicit note references.
  */
 
 import type { VaultEntry } from '../types'
@@ -34,19 +34,16 @@ export function collectLinkedEntries(
     }
   }
 
-  // outgoingLinks are raw targets (no [[ ]] wrapper)
   for (const target of active.outgoingLinks) {
     addTarget(target)
   }
 
-  // relationships values are wikilink references like [[target]]
   for (const refs of Object.values(active.relationships)) {
     for (const ref of refs) {
       addTarget(wikilinkTarget(ref))
     }
   }
 
-  // belongsTo and relatedTo are also wikilink references
   for (const ref of active.belongsTo) {
     addTarget(wikilinkTarget(ref))
   }
@@ -57,7 +54,110 @@ export function collectLinkedEntries(
   return linked
 }
 
-/** Build a contextual system prompt from the active note and its linked notes. */
+/** A note reference from the user's [[wikilink]] selection in the chat input. */
+export interface NoteReference {
+  title: string
+  path: string
+  type: string | null
+}
+
+/** Lightweight note summary for the context snapshot. */
+export interface NoteListItem {
+  path: string
+  title: string
+  type: string
+}
+
+/** Parameters for building the structured context snapshot. */
+export interface ContextSnapshotParams {
+  activeEntry: VaultEntry
+  allContent: Record<string, string>
+  openTabs?: VaultEntry[]
+  noteList?: NoteListItem[]
+  noteListFilter?: { type: string | null; query: string }
+  entries: VaultEntry[]
+  references?: NoteReference[]
+}
+
+function entryFrontmatter(e: VaultEntry): Record<string, unknown> {
+  const fm: Record<string, unknown> = {}
+  if (e.isA) fm.type = e.isA
+  if (e.status) fm.status = e.status
+  if (e.owner) fm.owner = e.owner
+  if (e.belongsTo.length > 0) fm.belongsTo = e.belongsTo
+  if (e.relatedTo.length > 0) fm.relatedTo = e.relatedTo
+  if (Object.keys(e.relationships).length > 0) fm.relationships = e.relationships
+  return fm
+}
+
+const MAX_NOTE_LIST_ITEMS = 100
+
+/** Build a structured context snapshot as a system prompt for Claude. */
+export function buildContextSnapshot(params: ContextSnapshotParams): string {
+  const { activeEntry, allContent, openTabs, noteList, noteListFilter, entries, references } = params
+
+  const snapshot: Record<string, unknown> = {
+    activeNote: {
+      path: activeEntry.path,
+      title: activeEntry.title,
+      type: activeEntry.isA ?? 'Note',
+      frontmatter: entryFrontmatter(activeEntry),
+      body: allContent[activeEntry.path] ?? '',
+    },
+  }
+
+  const otherTabs = openTabs?.filter(t => t.path !== activeEntry.path)
+  if (otherTabs && otherTabs.length > 0) {
+    snapshot.openTabs = otherTabs.map(t => ({
+      path: t.path,
+      title: t.title,
+      type: t.isA ?? 'Note',
+      frontmatter: entryFrontmatter(t),
+    }))
+  }
+
+  if (noteList && noteList.length > 0) {
+    const items = noteList.slice(0, MAX_NOTE_LIST_ITEMS)
+    snapshot.noteList = items
+    if (noteList.length > MAX_NOTE_LIST_ITEMS) {
+      snapshot.noteListTruncated = { shown: MAX_NOTE_LIST_ITEMS, total: noteList.length }
+    }
+  }
+
+  if (noteListFilter && (noteListFilter.type || noteListFilter.query)) {
+    snapshot.noteListFilter = noteListFilter
+  }
+
+  const types = new Set<string>()
+  for (const e of entries) {
+    if (e.isA) types.add(e.isA)
+  }
+  snapshot.vault = {
+    types: [...types].sort(),
+    totalNotes: entries.length,
+  }
+
+  if (references && references.length > 0) {
+    snapshot.referencedNotes = references
+      .filter(ref => allContent[ref.path] !== undefined)
+      .map(ref => ({
+        path: ref.path,
+        title: ref.title,
+        type: ref.type ?? 'Note',
+        body: allContent[ref.path] ?? '',
+      }))
+  }
+
+  const preamble = [
+    'You are an AI assistant integrated into Laputa, a personal knowledge management app.',
+    'The user is viewing a specific note. Use the structured context below to answer questions accurately.',
+    'You can also use MCP tools to search, read, create, or edit notes in the vault.',
+  ].join('\n')
+
+  return `${preamble}\n\n## Context Snapshot\n\`\`\`json\n${JSON.stringify(snapshot, null, 2)}\n\`\`\``
+}
+
+/** Legacy: Build a contextual system prompt (text-based). */
 export function buildContextualPrompt(
   active: VaultEntry,
   linkedEntries: VaultEntry[],