nano-brain 2026.7.2 → 2026.7.3

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "nano-brain",
-  "version": "2026.7.2",
+  "version": "2026.7.3",
   "description": "Persistent memory and code intelligence for AI coding agents. Local MCP server with self-learning hybrid search (BM25 + vector + knowledge graph + LLM reranking), automatic session ingestion, codebase indexing, and 22 tools. Learns your preferences over time. Works with OpenCode, Claude, Cursor, Windsurf, and any MCP client.",
   "type": "module",
   "bin": {

package/src/index.ts

@@ -10,7 +10,6 @@ import { findCycles } from './graph.js';
 import { handleBench } from './bench.js';
 import { resolveHostUrl } from './host.js';
 import { SymbolGraph } from './symbol-graph.js';
-import { installService, uninstallService } from './service-installer.js';
 import { isTreeSitterAvailable } from './treesitter.js';
 import { QdrantVecStore } from './providers/qdrant.js';
 import { createVectorStore } from './vector-store.js';
@@ -30,11 +29,12 @@ import { log, initLogger, cliOutput, cliError, setStdioMode } from './logger.js'
 
 const DEFAULT_HTTP_PORT = 3100;
 
-async function detectRunningServer(port: number = DEFAULT_HTTP_PORT): Promise<boolean> {
+async function detectRunningServer(port: number = getHttpPort()): Promise<boolean> {
+  const host = getHttpHost();
   try {
     const controller = new AbortController();
     const timeout = setTimeout(() => controller.abort(), 1000);
-    const resp = await fetch(`http://localhost:${port}/health`, { signal: controller.signal });
+    const resp = await fetch(`http://${host}:${port}/health`, { signal: controller.signal });
     clearTimeout(timeout);
     return resp.ok;
   } catch {
@@ -42,51 +42,16 @@ async function detectRunningServer(port: number = DEFAULT_HTTP_PORT): Promise<bo
   }
 }
 
-const UNSAFE_SERVE_STOP_PATTERNS = [
-  /docker/i,
-  /docker-proxy/i,
-  /com\.docker/i,
-  /vpnkit/i,
-  /containerd/i,
-];
-
-function getProcessCommand(pid: number): string {
-  if (!Number.isInteger(pid) || pid <= 0) return '';
-  try {
-    return execSync(`ps -p ${pid} -o command=`, { encoding: 'utf-8' }).trim();
-  } catch {
-    return '';
-  }
-}
-
-function isUnsafeServeStopTarget(command: string): boolean {
-  if (!command) return true;
-  return UNSAFE_SERVE_STOP_PATTERNS.some((pattern) => pattern.test(command));
-}
-
-function isLikelyNanoBrainServerCommand(command: string): boolean {
-  if (!command) return false;
-  const normalized = command.toLowerCase();
-  const hasNanoBrainMarker =
-    normalized.includes('nano-brain') ||
-    normalized.includes('/bin/cli.js') ||
-    normalized.includes('/src/index.ts');
-
-  const hasServerModeMarker =
-    normalized.includes(' mcp') ||
-    normalized.includes(' serve') ||
-    normalized.includes('--daemon');
-
-  return hasNanoBrainMarker && hasServerModeMarker;
-}
 
 async function proxyGet(port: number, path: string): Promise<any> {
-  const resp = await fetch(`http://localhost:${port}${path}`);
+  const host = getHttpHost();
+  const resp = await fetch(`http://${host}:${port}${path}`);
   return resp.json();
 }
 
 async function proxyPost(port: number, path: string, body: any): Promise<any> {
-  const resp = await fetch(`http://localhost:${port}${path}`, {
+  const host = getHttpHost();
+  const resp = await fetch(`http://${host}:${port}${path}`, {
     method: 'POST',
     headers: { 'Content-Type': 'application/json' },
     body: JSON.stringify(body),
@@ -103,10 +68,16 @@ function isRunningInContainer(): boolean {
 }
 
 function getHttpHost(): string {
+  if (process.env.NANO_BRAIN_HOST) return process.env.NANO_BRAIN_HOST;
   return isRunningInContainer() ? 'host.docker.internal' : 'localhost';
 }
 
-async function detectRunningServerContainer(port: number = DEFAULT_HTTP_PORT): Promise<boolean> {
+function getHttpPort(): number {
+  if (process.env.NANO_BRAIN_PORT) return parseInt(process.env.NANO_BRAIN_PORT, 10);
+  return DEFAULT_HTTP_PORT;
+}
+
+async function detectRunningServerContainer(port: number = getHttpPort()): Promise<boolean> {
   const host = getHttpHost();
   try {
     const controller = new AbortController();
@@ -220,14 +191,6 @@ nano-brain - Memory system with hybrid search
     --host=<addr>   Bind address (default: 127.0.0.1)
     --daemon        Run as background daemon
     stop            Stop running daemon
-  serve             Start SSE server as background daemon (shortcut)
-    --port=<n>      HTTP port (default: 3100)
-    --foreground    Run in foreground instead of detaching
-    stop [--force]  Stop running server (safe PID checks)
-    status          Show server status
-    install         Install as system service (launchd on macOS, systemd on Linux)
-      --force       Overwrite existing service file
-    uninstall       Remove system service
   status            Show index health, embedding server status, and stats
     --all           Show status for all workspaces
   collection        Manage collections
@@ -431,264 +394,6 @@ async function handleMcp(globalOpts: GlobalOptions, commandArgs: string[]): Prom
   });
 }
 
-async function handleServe(globalOpts: GlobalOptions, commandArgs: string[]): Promise<void> {
-  const SERVE_PID_FILE = path.join(NANO_BRAIN_HOME, 'serve.pid');
-  const SERVE_LOG_FILE = path.join(NANO_BRAIN_HOME, 'logs', 'server.log');
-
-  let port = 3100;
-  let foreground = false;
-  let subcommand: string | undefined;
-  let root: string | undefined;
-  let force = false;
-
-  for (const arg of commandArgs) {
-    if (arg.startsWith('--port=')) {
-      port = parseInt(arg.substring(7), 10);
-    } else if (arg.startsWith('--root=')) {
-      root = arg.substring(7);
-    } else if (arg === '--foreground' || arg === '-f') {
-      foreground = true;
-    } else if (arg === '--force') {
-      force = true;
-    } else if (arg === 'stop' || arg === 'status' || arg === 'install' || arg === 'uninstall') {
-      subcommand = arg;
-    }
-  }
-
-  // serve stop
-  if (subcommand === 'stop') {
-    let stopped = false;
-    const skippedUnsafe: Array<{ pid: number; command: string; source: string }> = [];
-
-    const tryStopPid = (pid: number, source: string): boolean => {
-      if (!Number.isInteger(pid) || pid <= 0) return false;
-
-      const command = getProcessCommand(pid);
-      if (!force && (isUnsafeServeStopTarget(command) || !isLikelyNanoBrainServerCommand(command))) {
-        skippedUnsafe.push({ pid, command, source });
-        return false;
-      }
-
-      try {
-        process.kill(pid, 'SIGTERM');
-        cliOutput(`Stopped nano-brain server (${source}, PID: ${pid})`);
-        return true;
-      } catch {
-        return false;
-      }
-    };
-
-    // Try stopping via PID file
-    try {
-      if (fs.existsSync(SERVE_PID_FILE)) {
-        const pidText = fs.readFileSync(SERVE_PID_FILE, 'utf-8').trim();
-        const pid = parseInt(pidText, 10);
-        if (tryStopPid(pid, 'PID file')) {
-          stopped = true;
-          fs.unlinkSync(SERVE_PID_FILE);
-        } else if (fs.existsSync(SERVE_PID_FILE)) {
-          // Remove stale/invalid PID file and continue with safe fallback
-          fs.unlinkSync(SERVE_PID_FILE);
-        }
-      }
-    } catch {
-      // Process might already be dead
-      if (fs.existsSync(SERVE_PID_FILE)) fs.unlinkSync(SERVE_PID_FILE);
-    }
-
-    // Secondary stop: try to find process by port if PID file failed or was missing
-    if (!stopped) {
-      try {
-        const isPortActive = await detectRunningServer(port);
-        if (isPortActive) {
-          const platform = process.platform;
-          if (platform === 'darwin' || platform === 'linux') {
-            try {
-              const cmd = platform === 'darwin'
-                ? `lsof -ti tcp:${port}`
-                : `lsof -ti tcp:${port} 2>/dev/null || fuser ${port}/tcp 2>/dev/null`;
-              const raw = execSync(cmd, { encoding: 'utf-8' }).trim();
-              const candidatePids = Array.from(
-                new Set(
-                  (raw.match(/\d+/g) || [])
-                    .map((value) => parseInt(value, 10))
-                    .filter((value) => Number.isInteger(value) && value > 0 && value !== port)
-                )
-              );
-
-              const stoppedPids: number[] = [];
-              for (const pid of candidatePids) {
-                if (tryStopPid(pid, `port ${port}`)) {
-                  stoppedPids.push(pid);
-                }
-              }
-
-              if (stoppedPids.length > 0) {
-                cliOutput(`Stopped nano-brain server on port ${port} (PIDs: ${stoppedPids.join(', ')})`);
-                stopped = true;
-              }
-            } catch {
-              // Ignore command failures
-            }
-          }
-        }
-      } catch {
-        // Ignore health check failures
-      }
-    }
-
-    if (!stopped) {
-      if (force) {
-        cliOutput('No running server found');
-      } else if (skippedUnsafe.length > 0) {
-        cliOutput('No safe nano-brain server PID found to stop.');
-        for (const item of skippedUnsafe) {
-          const details = item.command ? ` (${item.command})` : '';
-          cliOutput(`  skipped ${item.source} PID ${item.pid}${details}`);
-        }
-        cliOutput('Use `npx nano-brain serve stop --force` only if you verified the target PID manually.');
-      } else {
-        cliOutput('No running server found');
-      }
-    }
-    return;
-  }
-
-  // serve status
-  if (subcommand === 'status') {
-    let pidAlive = false;
-    let pid: number | null = null;
-    try {
-      pid = parseInt(fs.readFileSync(SERVE_PID_FILE, 'utf-8').trim(), 10);
-      process.kill(pid, 0);
-      pidAlive = true;
-    } catch {}
-    const portActive = await detectRunningServer(port);
-    if (pidAlive && pid) {
-      cliOutput(`nano-brain server is running (PID: ${pid}, port: ${port})`);
-    } else if (portActive) {
-      cliOutput(`nano-brain server is responding on port ${port} but PID file is stale. Run: npx nano-brain serve stop --force`);
-    } else {
-      cliOutput('nano-brain server is not running');
-    }
-    return;
-  }
-
-  // serve install
-  if (subcommand === 'install') {
-    const result = installService({ force, port });
-    if (result.success) {
-      cliOutput(`✅ ${result.message}`);
-      cliOutput(`   The server will start automatically on login.`);
-      cliOutput(`   Port: ${port}`);
-    } else {
-      cliError(`❌ ${result.message}`);
-      process.exit(1);
-    }
-    return;
-  }
-
-  // serve uninstall
-  if (subcommand === 'uninstall') {
-    const result = uninstallService();
-    if (result.success) {
-      cliOutput(`✅ ${result.message}`);
-    } else {
-      cliError(`❌ ${result.message}`);
-      process.exit(1);
-    }
-    return;
-  }
-
-  // serve (start)
-  if (foreground) {
-    return handleMcp(globalOpts, ['--http', `--port=${port}`, '--host=0.0.0.0', '--daemon', ...(root ? [`--root=${root}`] : [])]);
-  }
-
-  // --force: stop existing server before starting
-  if (force) {
-    try {
-      if (fs.existsSync(SERVE_PID_FILE)) {
-        const existingPid = parseInt(fs.readFileSync(SERVE_PID_FILE, 'utf-8').trim(), 10);
-        try { process.kill(existingPid, 'SIGTERM'); } catch {}
-        cliOutput(`Stopped existing server (PID: ${existingPid})`);
-        fs.unlinkSync(SERVE_PID_FILE);
-        await new Promise(r => setTimeout(r, 1000));
-      }
-    } catch {}
-    const portBusy = await detectRunningServer(port);
-    if (portBusy) {
-      const platform = process.platform;
-      if (platform === 'darwin' || platform === 'linux') {
-        try {
-          const cmd = platform === 'darwin' ? `lsof -ti tcp:${port}` : `lsof -ti tcp:${port} 2>/dev/null || fuser ${port}/tcp 2>/dev/null`;
-          const raw = execSync(cmd, { encoding: 'utf-8' }).trim();
-          for (const pidStr of raw.split(/\s+/)) {
-            const pid = parseInt(pidStr, 10);
-            if (pid > 0) { try { process.kill(pid, 'SIGKILL'); } catch {} }
-          }
-          await new Promise(r => setTimeout(r, 500));
-        } catch {}
-      }
-    }
-  }
-
-  // Check if already running via PID file
-  let pidAlive = false;
-  try {
-    if (fs.existsSync(SERVE_PID_FILE)) {
-      const existingPid = parseInt(fs.readFileSync(SERVE_PID_FILE, 'utf-8').trim(), 10);
-      process.kill(existingPid, 0);
-      pidAlive = true;
-      cliOutput(`Server already running (PID: ${existingPid}). Stop first or use: npx nano-brain serve start --force`);
-      return;
-    }
-  } catch {
-    try { fs.unlinkSync(SERVE_PID_FILE); } catch {}
-  }
-
-  // Secondary check: verify if port is already in use by another instance
-  const isPortActive = await detectRunningServer(port);
-  if (isPortActive) {
-    cliOutput(`Port ${port} is in use by an orphaned process. Run: npx nano-brain serve start --force`);
-    return;
-  }
-
-  // Spawn detached child
-  const logsDir = path.join(NANO_BRAIN_HOME, 'logs');
-  fs.mkdirSync(logsDir, { recursive: true });
-
-  const cliPath = path.resolve(path.dirname(new URL(import.meta.url).pathname), '../bin/cli.js');
-  const args = [cliPath, 'mcp', '--http', `--port=${port}`, '--host=0.0.0.0', '--daemon'];
-  if (root) {
-    args.push(`--root=${root}`);
-  }
-  if (globalOpts.configPath !== DEFAULT_CONFIG) {
-    args.push(`--config=${globalOpts.configPath}`);
-  }
-
-  const logFd = fs.openSync(SERVE_LOG_FILE, 'a');
-  const child = spawn(process.argv[0], args, {
-    detached: true,
-    stdio: ['ignore', logFd, logFd],
-  });
-
-  if (child.pid) {
-    fs.writeFileSync(SERVE_PID_FILE, String(child.pid));
-    child.unref();
-    cliOutput(`nano-brain server started on http://0.0.0.0:${port} (PID: ${child.pid})`);
-    cliOutput(`  SSE endpoint: http://localhost:${port}/sse`);
-    cliOutput(`  Health check: http://localhost:${port}/health`);
-    cliOutput(`  Logs: ${SERVE_LOG_FILE}`);
-    cliOutput(`  Stop: npx nano-brain serve stop`);
-  } else {
-    cliError('Failed to start server');
-    process.exit(1);
-  }
-
-  fs.closeSync(logFd);
-  process.exit(0);
-}
 
 async function handleCollection(globalOpts: GlobalOptions, commandArgs: string[]): Promise<void> {
   const subcommand = commandArgs[0];
@@ -1411,8 +1116,8 @@ async function handleEmbed(globalOpts: GlobalOptions, commandArgs: string[]): Pr
   if (isRunningInContainer()) {
     const serverRunning = await detectRunningServerContainer(DEFAULT_HTTP_PORT);
     if (!serverRunning) {
-      cliError('Error: Daemon not running. Start it on the host:');
-      cliError('  npx nano-brain serve install && launchctl load ~/Library/LaunchAgents/com.nano-brain.server.plist');
+      cliError(`Error: nano-brain server not reachable at ${getHttpHost()}:${getHttpPort()}. Ensure the Docker container is running:`);
+      cliError('  docker start nano-brain');
       process.exit(1);
     }
     try {
@@ -1555,8 +1260,8 @@ async function handleSearch(
     : await detectRunningServer(DEFAULT_HTTP_PORT);
 
   if (inContainer && !serverRunning) {
-    cliError('Error: Daemon not running. Start it on the host:');
-    cliError('  npx nano-brain serve install && launchctl load ~/Library/LaunchAgents/com.nano-brain.server.plist');
+    cliError(`Error: nano-brain server not reachable at ${getHttpHost()}:${getHttpPort()}. Ensure the Docker container is running:`);
+    cliError('  docker start nano-brain');
     process.exit(1);
   }
 
@@ -1722,8 +1427,8 @@ async function handleWrite(globalOpts: GlobalOptions, commandArgs: string[]): Pr
   if (isRunningInContainer()) {
     const serverRunning = await detectRunningServerContainer(DEFAULT_HTTP_PORT);
     if (!serverRunning) {
-      cliError('Error: Daemon not running. Start it on the host:');
-      cliError('  npx nano-brain serve install && launchctl load ~/Library/LaunchAgents/com.nano-brain.server.plist');
+      cliError(`Error: nano-brain server not reachable at ${getHttpHost()}:${getHttpPort()}. Ensure the Docker container is running:`);
+      cliError('  docker start nano-brain');
       process.exit(1);
     }
     try {
@@ -2319,8 +2024,8 @@ async function handleReindex(globalOpts: GlobalOptions, commandArgs: string[]):
   if (isRunningInContainer()) {
     const serverRunning = await detectRunningServerContainer(DEFAULT_HTTP_PORT);
     if (!serverRunning) {
-      cliError('Error: Daemon not running. Start it on the host:');
-      cliError('  npx nano-brain serve install && launchctl load ~/Library/LaunchAgents/com.nano-brain.server.plist');
+      cliError(`Error: nano-brain server not reachable at ${getHttpHost()}:${getHttpPort()}. Ensure the Docker container is running:`);
+      cliError('  docker start nano-brain');
       process.exit(1);
     }
     try {
@@ -4094,7 +3799,7 @@ async function main() {
   // Resolve per-workspace DB path.
   // Daemon mode (serve or mcp --daemon) skips early resolution — startServer() resolves
   // using the correct workspace root from config.yml instead of process.cwd()
-  const isDaemonMode = command === 'serve' || (command === 'mcp' && commandArgs.includes('--daemon'));
+  const isDaemonMode = command === 'mcp' && commandArgs.includes('--daemon');
   if (command !== 'init' && command !== 'docker' && !isDaemonMode) {
     globalOpts.dbPath = resolveDbPath(globalOpts.dbPath, process.cwd());
   }
@@ -4102,8 +3807,6 @@ async function main() {
   switch (command) {
     case 'mcp':
       return handleMcp(globalOpts, commandArgs);
-    case 'serve':
-      return handleServe(globalOpts, commandArgs);
     case 'init':
       return handleInit(globalOpts, commandArgs);
     case 'collection':

package/src/server.ts

@@ -2908,10 +2908,19 @@ export async function startServer(options: ServerOptions): Promise<void> {
   const server = createMcpServer(deps);
 
   let watcher: ReturnType<typeof startWatcher> | null = null;
+  let watcherStarted = false;
   const startFileWatcher = () => {
-    if (watcher) {
+    if (watcherStarted) {
       return;
     }
+    watcherStarted = true;
+
+    // Stop any existing watcher before creating a new one (defensive cleanup)
+    if (watcher) {
+      try { watcher.stop(); } catch {}
+      watcher = null;
+    }
+
     log('server', 'Starting file watcher');
 
     // Detect overlapping workspaces
@@ -3314,6 +3323,7 @@ export async function startServer(options: ServerOptions): Promise<void> {
           watcher.stop();
           watcher = null;
         }
+        watcherStarted = false;
         try {
           symbolGraphDb.pragma('wal_checkpoint(TRUNCATE)');
         } catch (err) {

package/src/store.ts

@@ -1567,11 +1567,17 @@ export function createStore(dbPath: string): Store {
           // Table exists with correct dimensions — check consistency
           const vecCount = (db.prepare('SELECT COUNT(*) as count FROM vectors_vec').get() as { count: number }).count;
           const cvCount = (db.prepare('SELECT COUNT(*) as count FROM content_vectors').get() as { count: number }).count;
-          if (vecCount === 0 && cvCount > 0) {
+          // When an external vector provider (e.g. Qdrant) is active, vectors_vec is always
+          // empty by design — vectors live in the external store, not sqlite-vec.
+          // Only treat empty vectors_vec as stale when using sqlite-vec as the provider.
+          const usingExternalVectorStore = vectorStore && !(vectorStore instanceof SqliteVecStore);
+          if (vecCount === 0 && cvCount > 0 && !usingExternalVectorStore) {
             // vectors_vec was rebuilt but content_vectors has stale tracking rows
             log('store', 'ensureVecTable clearing stale content_vectors count=' + cvCount);
             log('store', `vectors_vec empty but content_vectors has ${cvCount} stale rows, clearing for re-embedding`, 'error');
             db.exec(`DELETE FROM content_vectors`);
+          } else if (vecCount === 0 && cvCount > 0 && usingExternalVectorStore) {
+            log('store', `ensureVecTable: vectors_vec empty but external vector store active, skipping content_vectors clear (${cvCount} rows preserved)`);
           }
           return;
         } catch {

package/src/watcher.ts

@@ -174,7 +174,7 @@ export function startWatcher(options: WatcherOptions): Watcher {
 
   const handleFileChange = (filePath: string) => {
     if (stopped) return
-    
+
     log('watcher', 'File change detected: ' + filePath)
     dirty = true
     lastFileChangeAt = Date.now()
@@ -199,17 +199,17 @@ export function startWatcher(options: WatcherOptions): Watcher {
 
   const triggerReindex = async (force?: boolean): Promise<void> => {
     if (isReindexing || stopped) return
-    
+
     if (!force && lastReindexAt && Date.now() - lastReindexAt < reindexCooldownMs) {
       const remainingMs = reindexCooldownMs - (Date.now() - lastReindexAt)
       const remainingMin = Math.ceil(remainingMs / 60000)
       log('watcher', `Reindex skipped: cooldown active (${remainingMin}m remaining)`)
       return
     }
-    
+
     isReindexing = true
     log('watcher', 'Starting reindex')
-    
+
     try {
       for (const collection of collections) {
         try {
@@ -218,10 +218,10 @@ export function startWatcher(options: WatcherOptions): Watcher {
           for (let fileIdx = 0; fileIdx < files.length; fileIdx++) {
             const filePath = files[fileIdx];
             if (!fs.existsSync(filePath)) continue
-            
+
             const content = fs.readFileSync(filePath, 'utf-8')
             const hash = computeHash(content)
-            
+
             const existingDoc = store.findDocument(filePath)
             if (!existingDoc || existingDoc.hash !== hash) {
               const title = extractTitle(content)
@@ -230,12 +230,12 @@ export function startWatcher(options: WatcherOptions): Watcher {
                 : projectHash;
               indexDocument(store, collection.name, filePath, content, title, effectiveProjectHash)
             }
-            
+
             activePaths.push(filePath)
-            
+
             if (fileIdx % 20 === 0) await yieldToEventLoop();
           }
-          
+
           await yieldToEventLoop();
           store.bulkDeactivateExcept(collection.name, activePaths)
           await yieldToEventLoop();
@@ -243,7 +243,7 @@ export function startWatcher(options: WatcherOptions): Watcher {
           log('watcher', `Collection scan failed for ${collection.name}: ${err}`)
         }
       }
-      
+
       await yieldToEventLoop();
       if (codebaseConfig?.enabled) {
         try {
@@ -259,7 +259,7 @@ export function startWatcher(options: WatcherOptions): Watcher {
           log('watcher', `Embedding failed for primary workspace: ${err}`)
         }
       }
-      
+
       if (allWorkspaces && dataDir) {
         for (const [wsPath, wsConfig] of Object.entries(allWorkspaces)) {
           if (!wsConfig.codebase?.enabled) continue;
@@ -283,7 +283,7 @@ export function startWatcher(options: WatcherOptions): Watcher {
           }
         }
       }
-      
+
       dirty = false
       pendingPaths.clear()
       lastReindexAt = Date.now()
@@ -296,33 +296,33 @@ export function startWatcher(options: WatcherOptions): Watcher {
   const startupIntegrityCheck = async () => {
     const health = store.getIndexHealth();
     let mismatches = 0;
-    
+
     for (const collectionInfo of health.collections) {
       const collection = collections.find(c => c.name === collectionInfo.name);
       if (!collection) continue;
-      
+
       const files = await scanCollectionFiles(collection);
-      
+
       for (let fileIdx = 0; fileIdx < files.length; fileIdx++) {
         const filePath = files[fileIdx];
         if (!fs.existsSync(filePath)) continue;
-        
+
         const existingDoc = store.findDocument(filePath);
         if (!existingDoc) continue;
-        
+
         const content = fs.readFileSync(filePath, 'utf-8');
         const hash = computeHash(content);
-        
+
         if (existingDoc.hash !== hash) {
           mismatches++;
           dirty = true;
           pendingPaths.add(filePath);
         }
-        
+
         if (fileIdx % 20 === 0) await yieldToEventLoop();
       }
     }
-    
+
     if (mismatches > 0) {
       log('watcher', 'Integrity check found ' + mismatches + ' mismatches')
       log('watcher', `Integrity check: ${mismatches} file(s) need re-indexing`);
@@ -401,7 +401,7 @@ export function startWatcher(options: WatcherOptions): Watcher {
         await triggerReindex();
       }
     }, pollIntervalMs);
-    
+
     sessionPollInterval = setInterval(async () => {
       if (stopped) return;
       if (storageConfig) {
@@ -411,32 +411,32 @@ export function startWatcher(options: WatcherOptions): Watcher {
           return;
         }
       }
-      
+
       try {
         const sessions = await harvestSessions({
           sessionDir: sessionStorageDir,
           outputDir,
         });
-        
+
         if (sessions.length > 0) {
           log('watcher', 'Session harvest: ' + sessions.length + ' session(s) harvested')
           await triggerReindex();
         }
-        
+
         if (storageConfig && dbPath) {
           const expiredCount = evictExpiredSessions(outputDir, storageConfig.retention, store);
           if (expiredCount > 0) {
             log('watcher', 'Storage eviction: ' + expiredCount + ' expired session(s)')
             log('storage', `Evicted ${expiredCount} expired session(s)`);
           }
-          
+
           const sizeEvictedCount = evictBySize(outputDir, dbPath, storageConfig.maxSize, store);
           if (sizeEvictedCount > 0) {
             log('watcher', 'Storage eviction: ' + sizeEvictedCount + ' session(s) due to size limit')
             log('storage', `Evicted ${sizeEvictedCount} session(s) due to size limit`);
           }
         }
-        
+
         harvestCycleCount++;
         if (harvestCycleCount % 10 === 0) {
           const orphansDeleted = store.cleanOrphanedEmbeddings();
@@ -445,7 +445,7 @@ export function startWatcher(options: WatcherOptions): Watcher {
             log('storage', `Cleaned ${orphansDeleted} orphaned embedding(s)`);
           }
         }
-        
+
         try {
           const purged = store.purgeTelemetry(90);
           if (purged > 0) {
@@ -460,6 +460,7 @@ export function startWatcher(options: WatcherOptions): Watcher {
     }, sessionPollMs);
 
     if (embedder) {
+      let lastQuietSkipLogAt = 0;
       const scheduleNextEmbedCycle = () => {
         if (stopped) return;
         embeddingTimeout = setTimeout(async () => {
@@ -470,8 +471,12 @@ export function startWatcher(options: WatcherOptions): Watcher {
           isEmbedding = true;
           try {
             if (lastFileChangeAt > 0 && Date.now() - lastFileChangeAt < embedQuietPeriodMs) {
-              const sinceSec = Math.round((Date.now() - lastFileChangeAt) / 1000)
-              log('watcher', `Embedding skipped: quiet period active (${sinceSec}s since last change, need ${Math.round(embedQuietPeriodMs / 1000)}s)`)
+              const now = Date.now();
+              if (now - lastQuietSkipLogAt >= 60_000) {
+                const sinceSec = Math.round((now - lastFileChangeAt) / 1000)
+                log('watcher', `Embedding skipped: quiet period active (${sinceSec}s since last change, need ${Math.round(embedQuietPeriodMs / 1000)}s)`)
+                lastQuietSkipLogAt = now;
+              }
               isEmbedding = false;
               scheduleNextEmbedCycle();
               return;
@@ -486,7 +491,7 @@ export function startWatcher(options: WatcherOptions): Watcher {
               for (const [wsPath, wsConfig] of Object.entries(allWorkspaces)) {
                 if (!wsConfig.codebase?.enabled) continue;
                 if (wsPath === workspaceRoot) continue;
-                
+
                 try {
                   const wsStore = openWorkspaceStore(dataDir, wsPath);
                   if (!wsStore) {
@@ -549,7 +554,7 @@ export function startWatcher(options: WatcherOptions): Watcher {
         if (stopped) return;
         learningTimeout = setTimeout(async () => {
           if (stopped) return;
-          
+
           try {
             const banditState = sampler.getState();
             const flatStats = banditState.flatMap(config =>
@@ -561,11 +566,11 @@ export function startWatcher(options: WatcherOptions): Watcher {
               }))
             );
             store.saveBanditStats(flatStats, projectHash);
-            
+
             const configJson = JSON.stringify(sampler.selectSearchConfig());
             const telemetryCount = store.getTelemetryCount();
             store.saveConfigVersion(configJson, telemetryCount > 0 ? telemetryCount : null);
-            
+
             const latestVersion = store.getLatestConfigVersion();
             if (latestVersion && latestVersion.expand_rate !== null) {
               const prevVersion = store.getConfigVersion(latestVersion.version_id - 1);
@@ -577,7 +582,7 @@ export function startWatcher(options: WatcherOptions): Watcher {
                 }
               }
             }
-            
+
             lastLearningRun = Date.now();
             log('watcher', 'Learning cycle complete: saved bandit stats and config version');
 
@@ -763,17 +768,17 @@ export function startWatcher(options: WatcherOptions): Watcher {
   return {
     stop() {
       stopped = true;
-      
+
       if (debounceTimer) {
         clearTimeout(debounceTimer);
         debounceTimer = null;
       }
-      
+
       if (pollInterval) {
         clearInterval(pollInterval);
         pollInterval = null;
       }
-      
+
       if (sessionPollInterval) {
         clearInterval(sessionPollInterval);
         sessionPollInterval = null;
@@ -823,21 +828,21 @@ export function startWatcher(options: WatcherOptions): Watcher {
         clearTimeout(mergeTimeout);
         mergeTimeout = null;
       }
-      
+
       if (watcher) {
         watcher.close();
         watcher = null;
       }
     },
-    
+
     isDirty() {
       return dirty;
     },
-    
+
     async triggerReindex(force?: boolean) {
       await triggerReindex(force);
     },
-    
+
     getStats(): WatcherStats {
       return {
         filesWatched: watchedPaths.size,
@@ -852,13 +857,13 @@ export function startWatcher(options: WatcherOptions): Watcher {
 
 function extractTitle(content: string): string {
   const lines = content.split('\n');
-  
+
   for (const line of lines) {
     const trimmed = line.trim();
     if (trimmed.startsWith('# ')) {
       return trimmed.substring(2).trim();
     }
   }
-  
+
   return 'Untitled';
 }

package/src/service-installer.ts

@@ -1,260 +0,0 @@
-import * as fs from 'fs';
-import * as path from 'path';
-import * as os from 'os';
-import { execSync } from 'child_process';
-
-export type Platform = 'macos' | 'linux' | 'unsupported';
-
-export function detectPlatform(): Platform {
-  if (process.platform === 'darwin') return 'macos';
-  if (process.platform === 'linux') return 'linux';
-  return 'unsupported';
-}
-
-export interface ServiceConfig {
-  port: number;
-  nodePath: string;
-  cliPath: string;
-  homeDir: string;
-  logsDir: string;
-}
-
-export function getDefaultServiceConfig(): ServiceConfig {
-  const homeDir = os.homedir();
-  const logsDir = path.join(homeDir, '.nano-brain', 'logs');
-  
-  // Resolve a stable npx path — avoid ephemeral npx cache paths
-  let npxPath: string;
-  try {
-    npxPath = execSync('which npx', { encoding: 'utf-8' }).trim();
-  } catch {
-    npxPath = path.join(path.dirname(process.execPath), 'npx');
-  }
-  
-  return {
-    port: 3100,
-    nodePath: npxPath,
-    cliPath: 'nano-brain',  // npx will resolve this to the latest installed version
-    homeDir,
-    logsDir,
-  };
-}
-
-export function generateLaunchdPlist(config: ServiceConfig): string {
-  return `<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
-<plist version="1.0">
-<dict>
-  <key>Label</key>
-  <string>com.nano-brain.server</string>
-  <key>ProgramArguments</key>
-  <array>
-    <string>${config.nodePath}</string>
-    <string>${config.cliPath}</string>
-    <string>serve</string>
-    <string>--port</string>
-    <string>${config.port}</string>
-  </array>
-  <key>KeepAlive</key>
-  <true/>
-  <key>RunAtLoad</key>
-  <true/>
-  <key>StandardOutPath</key>
-  <string>${config.logsDir}/server.log</string>
-  <key>StandardErrorPath</key>
-  <string>${config.logsDir}/server.err</string>
-  <key>WorkingDirectory</key>
-  <string>${config.homeDir}</string>
-  <key>EnvironmentVariables</key>
-  <dict>
-    <key>PATH</key>
-    <string>/usr/local/bin:/usr/bin:/bin:${path.dirname(config.nodePath)}</string>
-  </dict>
-  <key>ThrottleInterval</key>
-  <integer>30</integer>
-</dict>
-</plist>
-`;
-}
-
-export function generateSystemdService(config: ServiceConfig): string {
-  return `[Unit]
-Description=nano-brain MCP server
-After=network.target
-
-[Service]
-Type=simple
-ExecStart=${config.nodePath} ${config.cliPath} serve --port ${config.port}
-Restart=always
-RestartSec=2
-StartLimitBurst=5
-StartLimitIntervalSec=600
-WorkingDirectory=${config.homeDir}
-Environment=PATH=/usr/local/bin:/usr/bin:/bin:${path.dirname(config.nodePath)}
-StandardOutput=append:${config.logsDir}/server.log
-StandardError=append:${config.logsDir}/server.err
-
-[Install]
-WantedBy=default.target
-`;
-}
-
-export function getLaunchdPlistPath(): string {
-  return path.join(os.homedir(), 'Library', 'LaunchAgents', 'com.nano-brain.server.plist');
-}
-
-export function getSystemdServicePath(): string {
-  return path.join(os.homedir(), '.config', 'systemd', 'user', 'nano-brain.service');
-}
-
-export interface InstallResult {
-  success: boolean;
-  path: string;
-  message: string;
-}
-
-export function installService(options: { force?: boolean; port?: number } = {}): InstallResult {
-  const platform = detectPlatform();
-  
-  if (platform === 'unsupported') {
-    return {
-      success: false,
-      path: '',
-      message: `Unsupported platform: ${process.platform}. Only macOS and Linux are supported.`,
-    };
-  }
-  
-  const config = getDefaultServiceConfig();
-  if (options.port) {
-    config.port = options.port;
-  }
-  
-  fs.mkdirSync(config.logsDir, { recursive: true });
-  
-  if (platform === 'macos') {
-    const plistPath = getLaunchdPlistPath();
-    
-    if (fs.existsSync(plistPath) && !options.force) {
-      return {
-        success: false,
-        path: plistPath,
-        message: `Service already installed at ${plistPath}. Use --force to overwrite.`,
-      };
-    }
-    
-    fs.mkdirSync(path.dirname(plistPath), { recursive: true });
-    const plistContent = generateLaunchdPlist(config);
-    fs.writeFileSync(plistPath, plistContent);
-    
-    try {
-      const uid = execSync('id -u', { encoding: 'utf-8' }).trim();
-      execSync(`launchctl bootstrap gui/${uid} "${plistPath}"`, { stdio: 'pipe' });
-    } catch {
-      try {
-        execSync(`launchctl load "${plistPath}"`, { stdio: 'pipe' });
-      } catch {}
-    }
-    
-    return {
-      success: true,
-      path: plistPath,
-      message: `Service installed at ${plistPath}`,
-    };
-  }
-  
-  const servicePath = getSystemdServicePath();
-  
-  if (fs.existsSync(servicePath) && !options.force) {
-    return {
-      success: false,
-      path: servicePath,
-      message: `Service already installed at ${servicePath}. Use --force to overwrite.`,
-    };
-  }
-  
-  fs.mkdirSync(path.dirname(servicePath), { recursive: true });
-  const serviceContent = generateSystemdService(config);
-  fs.writeFileSync(servicePath, serviceContent);
-  
-  try {
-    execSync('systemctl --user daemon-reload', { stdio: 'pipe' });
-    execSync('systemctl --user enable nano-brain', { stdio: 'pipe' });
-    execSync('systemctl --user start nano-brain', { stdio: 'pipe' });
-  } catch {
-  }
-  
-  return {
-    success: true,
-    path: servicePath,
-    message: `Service installed at ${servicePath}`,
-  };
-}
-
-export function uninstallService(): InstallResult {
-  const platform = detectPlatform();
-  
-  if (platform === 'unsupported') {
-    return {
-      success: false,
-      path: '',
-      message: `Unsupported platform: ${process.platform}. Only macOS and Linux are supported.`,
-    };
-  }
-  
-  if (platform === 'macos') {
-    const plistPath = getLaunchdPlistPath();
-    
-    if (!fs.existsSync(plistPath)) {
-      return {
-        success: false,
-        path: plistPath,
-        message: `Service not installed at ${plistPath}`,
-      };
-    }
-    
-    try {
-      const uid = execSync('id -u', { encoding: 'utf-8' }).trim();
-      execSync(`launchctl bootout gui/${uid}/com.nano-brain.server`, { stdio: 'pipe' });
-    } catch {
-      try {
-        execSync(`launchctl unload "${plistPath}"`, { stdio: 'pipe' });
-      } catch {}
-    }
-    
-    fs.unlinkSync(plistPath);
-    
-    return {
-      success: true,
-      path: plistPath,
-      message: `Service uninstalled from ${plistPath}`,
-    };
-  }
-  
-  const servicePath = getSystemdServicePath();
-  
-  if (!fs.existsSync(servicePath)) {
-    return {
-      success: false,
-      path: servicePath,
-      message: `Service not installed at ${servicePath}`,
-    };
-  }
-  
-  try {
-    execSync('systemctl --user disable --now nano-brain', { stdio: 'pipe' });
-  } catch {
-  }
-  
-  fs.unlinkSync(servicePath);
-  
-  try {
-    execSync('systemctl --user daemon-reload', { stdio: 'pipe' });
-  } catch {
-  }
-  
-  return {
-    success: true,
-    path: servicePath,
-    message: `Service uninstalled from ${servicePath}`,
-  };
-}