nano-brain 2026.7.3 → 2026.7.6

package/dist/embeddings.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"embeddings.d.ts","sourceRoot":"","sources":["../src/embeddings.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,eAAe,EAAE,eAAe,EAAE,MAAM,YAAY,CAAC;AAInE,MAAM,WAAW,iBAAiB;IAChC,KAAK,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,eAAe,CAAC,CAAC;IAC9C,UAAU,CAAC,KAAK,EAAE,MAAM,EAAE,GAAG,OAAO,CAAC,eAAe,EAAE,CAAC,CAAC;IACxD,aAAa,IAAI,MAAM,CAAC;IACxB,QAAQ,IAAI,MAAM,CAAC;IACnB,WAAW,IAAI,MAAM,CAAC;IACtB,OAAO,IAAI,IAAI,CAAC;CACjB;AAED,MAAM,WAAW,wBAAwB;IACvC,eAAe,CAAC,EAAE,eAAe,CAAC;IAClC,YAAY,CAAC,EAAE,CAAC,KAAK,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,KAAK,IAAI,CAAC;CACxD;AAED,iBAAS,iBAAiB,CAAC,KAAK,EAAE,MAAM,GAAG,MAAM,CAEhD;AAED,iBAAS,oBAAoB,CAAC,KAAK,EAAE,MAAM,EAAE,OAAO,EAAE,MAAM,GAAG,MAAM,CAEpE;AAGD,wBAAgB,eAAe,IAAI,MAAM,CAExC;AAED,wBAAsB,iBAAiB,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC;IAAE,SAAS,EAAE,OAAO,CAAC;IAAC,MAAM,CAAC,EAAE,MAAM,EAAE,CAAC;IAAC,KAAK,CAAC,EAAE,MAAM,CAAA;CAAE,CAAC,CAWvH;AAED,wBAAsB,iBAAiB,CACrC,OAAO,EAAE,MAAM,EACf,MAAM,EAAE,MAAM,EACd,KAAK,EAAE,MAAM,GACZ,OAAO,CAAC;IAAE,SAAS,EAAE,OAAO,CAAC;IAAC,KAAK,CAAC,EAAE,MAAM,CAAC;IAAC,KAAK,CAAC,EAAE,MAAM,CAAA;CAAE,CAAC,CAwBjE;AAiUD,wBAAsB,uBAAuB,CAC3C,OAAO,CAAC,EAAE,wBAAwB,GACjC,OAAO,CAAC,iBAAiB,GAAG,IAAI,CAAC,CAmDnC;AAED,OAAO,EAAE,iBAAiB,EAAE,oBAAoB,EAAE,CAAC"}
+{"version":3,"file":"embeddings.d.ts","sourceRoot":"","sources":["../src/embeddings.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,eAAe,EAAE,eAAe,EAAE,MAAM,YAAY,CAAC;AAInE,MAAM,WAAW,iBAAiB;IAChC,KAAK,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,eAAe,CAAC,CAAC;IAC9C,UAAU,CAAC,KAAK,EAAE,MAAM,EAAE,GAAG,OAAO,CAAC,eAAe,EAAE,CAAC,CAAC;IACxD,aAAa,IAAI,MAAM,CAAC;IACxB,QAAQ,IAAI,MAAM,CAAC;IACnB,WAAW,IAAI,MAAM,CAAC;IACtB,OAAO,IAAI,IAAI,CAAC;CACjB;AAED,MAAM,WAAW,wBAAwB;IACvC,eAAe,CAAC,EAAE,eAAe,CAAC;IAClC,YAAY,CAAC,EAAE,CAAC,KAAK,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,KAAK,IAAI,CAAC;CACxD;AAED,iBAAS,iBAAiB,CAAC,KAAK,EAAE,MAAM,GAAG,MAAM,CAEhD;AAED,iBAAS,oBAAoB,CAAC,KAAK,EAAE,MAAM,EAAE,OAAO,EAAE,MAAM,GAAG,MAAM,CAEpE;AAGD,wBAAgB,eAAe,IAAI,MAAM,CAExC;AAED,wBAAsB,iBAAiB,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC;IAAE,SAAS,EAAE,OAAO,CAAC;IAAC,MAAM,CAAC,EAAE,MAAM,EAAE,CAAC;IAAC,KAAK,CAAC,EAAE,MAAM,CAAA;CAAE,CAAC,CAWvH;AAED,wBAAsB,iBAAiB,CACrC,OAAO,EAAE,MAAM,EACf,MAAM,EAAE,MAAM,EACd,KAAK,EAAE,MAAM,GACZ,OAAO,CAAC;IAAE,SAAS,EAAE,OAAO,CAAC;IAAC,KAAK,CAAC,EAAE,MAAM,CAAC;IAAC,KAAK,CAAC,EAAE,MAAM,CAAA;CAAE,CAAC,CAwBjE;AAuWD,wBAAsB,uBAAuB,CAC3C,OAAO,CAAC,EAAE,wBAAwB,GACjC,OAAO,CAAC,iBAAiB,GAAG,IAAI,CAAC,CAmDnC;AAED,OAAO,EAAE,iBAAiB,EAAE,oBAAoB,EAAE,CAAC"}

package/dist/embeddings.js

@@ -117,13 +117,13 @@ class OllamaEmbeddingProvider {
             dimensions: this.dimensions,
         };
     }
-    async embedBatch(texts) {
+    async _sendBatch(inputs) {
         const response = await fetch(`${this.url}/api/embed`, {
             method: 'POST',
             headers: { 'Content-Type': 'application/json' },
             body: JSON.stringify({
                 model: this.model,
-                input: texts.map(t => this.truncate(t)),
+                input: inputs.map(t => this.truncate(t)),
             }),
             signal: AbortSignal.timeout(180000),
         });
@@ -140,6 +140,38 @@ class OllamaEmbeddingProvider {
             dimensions: emb.length,
         }));
     }
+    async embedBatch(texts) {
+        const MAX_CHARS_PER_BATCH = 100_000; // ~25K tokens safety margin
+        const MAX_ITEMS_PER_BATCH = 50; // Also limit item count
+        const results = [];
+        // Split into sub-batches by cumulative character count
+        let currentBatch = [];
+        let currentChars = 0;
+        let batchCount = 0;
+        for (const text of texts) {
+            if (currentBatch.length > 0 &&
+                (currentChars + text.length > MAX_CHARS_PER_BATCH ||
+                    currentBatch.length >= MAX_ITEMS_PER_BATCH)) {
+                batchCount++;
+                const embeddings = await this._sendBatch(currentBatch);
+                results.push(...embeddings);
+                currentBatch = [];
+                currentChars = 0;
+            }
+            currentBatch.push(text);
+            currentChars += text.length;
+        }
+        // Send remaining
+        if (currentBatch.length > 0) {
+            batchCount++;
+            const embeddings = await this._sendBatch(currentBatch);
+            results.push(...embeddings);
+        }
+        if (batchCount > 1) {
+            log('embed', `Ollama sub-batching: ${texts.length} items into ${batchCount} batches`);
+        }
+        return results;
+    }
     getDimensions() {
         return this.dimensions;
     }

package/dist/embeddings.js.map

@@ -1 +1 @@
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package/dist/index.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAeA,OAAO,KAAK,EAAE,YAAY,EAAE,gBAAgB,EAAE,KAAK,EAAuB,MAAM,YAAY,CAAC;AA8G7F,MAAM,WAAW,aAAa;IAC5B,MAAM,EAAE,MAAM,CAAC;IACf,UAAU,EAAE,MAAM,CAAC;IACnB,SAAS,EAAE,MAAM,EAAE,CAAC;CACrB;AAED,wBAAgB,kBAAkB,CAAC,IAAI,EAAE,MAAM,EAAE,GAAG,aAAa,CA4BhE;AAGD;;;;;GAKG;AACH,wBAAgB,aAAa,CAAC,MAAM,EAAE,MAAM,EAAE,aAAa,EAAE,MAAM,GAAG,MAAM,CAM3E;AACD,wBAAgB,QAAQ,IAAI,IAAI,CAoJ/B;AAED,wBAAgB,WAAW,IAAI,IAAI,CAQlC;AAED,wBAAgB,kBAAkB,CAAC,OAAO,EAAE,YAAY,EAAE,EAAE,MAAM,EAAE,MAAM,GAAG,MAAM,GAAG,OAAO,GAAG,MAAM,CAmBrG;AAukFD,wBAAgB,0BAA0B,CACxC,UAAU,EAAE,MAAM,EAClB,MAAM,EAAE,gBAAgB,GAAG,IAAI,EAC/B,KAAK,EAAE,KAAK,GACX;IAAE,WAAW,EAAE,MAAM,CAAC;IAAC,aAAa,EAAE,MAAM,GAAG,IAAI,CAAA;CAAE,CAoDvD"}

package/dist/index.js

@@ -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';
@@ -23,14 +22,15 @@ import * as fs from 'fs';
 import * as path from 'path';
 import * as os from 'os';
 import * as crypto from 'crypto';
-import { execSync, spawn } from 'child_process';
-import { log, initLogger, cliOutput, cliError } from './logger.js';
+import { execSync } from 'child_process';
+import { log, initLogger, cliOutput, cliError, setStdioMode } from './logger.js';
 const DEFAULT_HTTP_PORT = 3100;
-async function detectRunningServer(port = DEFAULT_HTTP_PORT) {
+async function detectRunningServer(port = getHttpPort()) {
+    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;
     }
@@ -38,46 +38,14 @@ async function detectRunningServer(port = DEFAULT_HTTP_PORT) {
         return false;
     }
 }
-const UNSAFE_SERVE_STOP_PATTERNS = [
-    /docker/i,
-    /docker-proxy/i,
-    /com\.docker/i,
-    /vpnkit/i,
-    /containerd/i,
-];
-function getProcessCommand(pid) {
-    if (!Number.isInteger(pid) || pid <= 0)
-        return '';
-    try {
-        return execSync(`ps -p ${pid} -o command=`, { encoding: 'utf-8' }).trim();
-    }
-    catch {
-        return '';
-    }
-}
-function isUnsafeServeStopTarget(command) {
-    if (!command)
-        return true;
-    return UNSAFE_SERVE_STOP_PATTERNS.some((pattern) => pattern.test(command));
-}
-function isLikelyNanoBrainServerCommand(command) {
-    if (!command)
-        return false;
-    const normalized = command.toLowerCase();
-    const hasNanoBrainMarker = normalized.includes('nano-brain') ||
-        normalized.includes('/bin/cli.js') ||
-        normalized.includes('/src/index.ts');
-    const hasServerModeMarker = normalized.includes(' mcp') ||
-        normalized.includes(' serve') ||
-        normalized.includes('--daemon');
-    return hasNanoBrainMarker && hasServerModeMarker;
-}
 async function proxyGet(port, path) {
-    const resp = await fetch(`http://localhost:${port}${path}`);
+    const host = getHttpHost();
+    const resp = await fetch(`http://${host}:${port}${path}`);
     return resp.json();
 }
 async function proxyPost(port, path, body) {
-    const resp = await fetch(`http://localhost:${port}${path}`, {
+    const host = getHttpHost();
+    const resp = await fetch(`http://${host}:${port}${path}`, {
         method: 'POST',
         headers: { 'Content-Type': 'application/json' },
         body: JSON.stringify(body),
@@ -93,9 +61,16 @@ function isRunningInContainer() {
     }
 }
 function getHttpHost() {
+    if (process.env.NANO_BRAIN_HOST)
+        return process.env.NANO_BRAIN_HOST;
     return isRunningInContainer() ? 'host.docker.internal' : 'localhost';
 }
-async function detectRunningServerContainer(port = DEFAULT_HTTP_PORT) {
+function getHttpPort() {
+    if (process.env.NANO_BRAIN_PORT)
+        return parseInt(process.env.NANO_BRAIN_PORT, 10);
+    return DEFAULT_HTTP_PORT;
+}
+async function detectRunningServerContainer(port = getHttpPort()) {
     const host = getHttpHost();
     try {
         const controller = new AbortController();
@@ -202,14 +177,6 @@ nano-brain - Memory system with hybrid search
     --host=<addr>   Bind address (default: 127.0.0.1)
     --daemon        Run as background daemon
     stop            Stop running daemon
-  serve             Start SSE server as background daemon (shortcut)
-    --port=<n>      HTTP port (default: 3100)
-    --foreground    Run in foreground instead of detaching
-    stop [--force]  Stop running server (safe PID checks)
-    status          Show server status
-    install         Install as system service (launchd on macOS, systemd on Linux)
-      --force       Overwrite existing service file
-    uninstall       Remove system service
   status            Show index health, embedding server status, and stats
     --all           Show status for all workspaces
   collection        Manage collections
@@ -396,6 +363,10 @@ async function handleMcp(globalOpts, commandArgs) {
             return;
         }
     }
+    if (!useHttp) {
+        // In stdio transport mode, stdout/stderr must be reserved for MCP JSON-RPC frames.
+        setStdioMode(true);
+    }
     log('cli', 'mcp server start transport=' + (useHttp ? `http:${host}:${port}` : 'stdio'));
     await startServer({
         dbPath: globalOpts.dbPath,
@@ -406,270 +377,6 @@ async function handleMcp(globalOpts, commandArgs) {
         root,
     });
 }
-async function handleServe(globalOpts, commandArgs) {
-    const SERVE_PID_FILE = path.join(NANO_BRAIN_HOME, 'serve.pid');
-    const SERVE_LOG_FILE = path.join(NANO_BRAIN_HOME, 'logs', 'server.log');
-    let port = 3100;
-    let foreground = false;
-    let subcommand;
-    let root;
-    let force = false;
-    for (const arg of commandArgs) {
-        if (arg.startsWith('--port=')) {
-            port = parseInt(arg.substring(7), 10);
-        }
-        else if (arg.startsWith('--root=')) {
-            root = arg.substring(7);
-        }
-        else if (arg === '--foreground' || arg === '-f') {
-            foreground = true;
-        }
-        else if (arg === '--force') {
-            force = true;
-        }
-        else if (arg === 'stop' || arg === 'status' || arg === 'install' || arg === 'uninstall') {
-            subcommand = arg;
-        }
-    }
-    // serve stop
-    if (subcommand === 'stop') {
-        let stopped = false;
-        const skippedUnsafe = [];
-        const tryStopPid = (pid, source) => {
-            if (!Number.isInteger(pid) || pid <= 0)
-                return false;
-            const command = getProcessCommand(pid);
-            if (!force && (isUnsafeServeStopTarget(command) || !isLikelyNanoBrainServerCommand(command))) {
-                skippedUnsafe.push({ pid, command, source });
-                return false;
-            }
-            try {
-                process.kill(pid, 'SIGTERM');
-                cliOutput(`Stopped nano-brain server (${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 = [];
-                            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 = 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, commandArgs) {
     const subcommand = commandArgs[0];
     if (!subcommand) {
@@ -1341,8 +1048,8 @@ async function handleEmbed(globalOpts, commandArgs) {
     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 {
@@ -1486,8 +1193,8 @@ async function handleSearch(globalOpts, commandArgs, mode) {
         ? await detectRunningServerContainer(DEFAULT_HTTP_PORT)
         : 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);
     }
     if (serverRunning) {
@@ -1635,8 +1342,8 @@ async function handleWrite(globalOpts, commandArgs) {
     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 {
@@ -2166,8 +1873,8 @@ async function handleReindex(globalOpts, commandArgs) {
     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 {
@@ -3773,19 +3480,22 @@ async function main() {
     initLogger(cliConfig ?? undefined);
     const command = globalOpts.remaining[0] || 'mcp';
     const commandArgs = globalOpts.remaining.slice(1);
+    // Enable stdio-safe logging as early as possible for MCP stdio mode.
+    // This prevents top-level CLI logs from polluting MCP JSON-RPC transport.
+    if (command === 'mcp' && !commandArgs.includes('--http')) {
+        setStdioMode(true);
+    }
     log('cli', 'command=' + command);
     // 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());
     }
     switch (command) {
         case 'mcp':
             return handleMcp(globalOpts, commandArgs);
-        case 'serve':
-            return handleServe(globalOpts, commandArgs);
         case 'init':
             return handleInit(globalOpts, commandArgs);
         case 'collection':