Fix daemon startup, migrations, and project auto-creation

- Add start.ts entry point for daemon (creates DB, runs migrations, starts server)
- Copy migration SQL files to dist/ during build
- Install pino-pretty for structured logging
- Auto-create project on first memory save (fixes FK constraint)
- Fix SSE type: add sync.offline event to union
- Fix quality gate: proper type casting for DB results

Tested end-to-end: init → daemon start → create memory → search → doctor ✅

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: KD-K2N2

packages/server/package.json

@@ -44,7 +44,8 @@
     "node": ">=18.0.0"
   },
   "scripts": {
-    "build": "tsup src/index.ts --format esm --dts --clean --external better-sqlite3",
+    "build": "tsup src/index.ts --format esm --dts --clean --external better-sqlite3 && tsup src/start.ts --format esm --external better-sqlite3 --no-dts && mkdir -p dist/migrations && cp src/db/migrations/*.sql dist/migrations/",
+    "start": "node dist/start.js",
     "dev": "tsup src/index.ts --format esm --dts --watch --external better-sqlite3",
     "test": "vitest run",
     "test:coverage": "vitest run --coverage",
@@ -62,6 +63,7 @@
     "better-sqlite3": "^11.0.0",
     "fastify": "^5.8.2",
     "openai": "^6.32.0",
+    "pino-pretty": "^13.1.3",
     "uuid": "^10.0.0"
   },
   "devDependencies": {

packages/server/src/api/routes/memories.ts

@@ -95,6 +95,16 @@ export function registerMemoryRoutes(
       });
     }
 
+    // Auto-create project if it doesn't exist
+    const existingProject = db.prepare('SELECT id FROM projects WHERE id = ?').get(project_id);
+    if (!existingProject) {
+      const { v4: projUuid } = await import('uuid');
+      db.prepare(
+        `INSERT OR IGNORE INTO projects (id, name, path, git_remote, tech_stack, context_budget, memory_limit, created_at, last_session_at)
+         VALUES (?, ?, NULL, NULL, '[]', 4000, 500, strftime('%Y-%m-%dT%H:%M:%fZ', 'now'), strftime('%Y-%m-%dT%H:%M:%fZ', 'now'))`,
+      ).run(project_id, project_id);
+    }
+
     // Quality gate
     const gateResult = runQualityGate(parsed.data, db, project_id);
     if (!gateResult.passed) {

packages/server/src/quality/gate.ts

@@ -100,10 +100,10 @@ export function runQualityGate(
     .prepare(
       'SELECT content FROM memories WHERE project_id = ? AND deleted_at IS NULL AND superseded_by IS NULL',
     )
-    .all(projectId)
-    .map((r: { content: string }) => r.content);
+    .all(projectId) as { content: string }[];
+  const existingTexts = existingContents.map((r) => r.content);
 
-  const duplicateResult = checkDuplicate(input.content, existingContents);
+  const duplicateResult = checkDuplicate(input.content, existingTexts);
   if (!duplicateResult.passed) {
     return {
       passed: false,

packages/server/src/start.ts

@@ -0,0 +1,48 @@
+#!/usr/bin/env node
+/**
+ * Cortex daemon entry point.
+ * Creates database, runs migrations, starts API server + MCP server.
+ */
+
+import { createDatabase, runMigrations } from './db/index.js';
+import { startAPIServer } from './api/server.js';
+import { SSEEmitter } from './api/sse/emitter.js';
+import { startMCPServer } from './mcp/server.js';
+import os from 'node:os';
+import path from 'node:path';
+import fs from 'node:fs';
+
+const PORT = parseInt(process.env.CORTEX_PORT || '7434', 10);
+const DB_PATH = process.env.CORTEX_DB_PATH || path.join(os.homedir(), '.cortex', 'memory.db');
+const STDIO_MODE = process.argv.includes('--stdio');
+
+// Ensure data directory exists
+const dataDir = path.dirname(DB_PATH);
+if (!fs.existsSync(dataDir)) {
+  fs.mkdirSync(dataDir, { recursive: true });
+}
+
+// Create database and run migrations
+const db = createDatabase(DB_PATH);
+runMigrations(db);
+
+// Create SSE emitter
+const sseEmitter = new SSEEmitter();
+
+if (STDIO_MODE) {
+  // MCP mode — Claude Code connects via stdio
+  startMCPServer(db).catch((err) => {
+    console.error('[cortex] MCP server failed:', err);
+    process.exit(1);
+  });
+} else {
+  // Daemon mode — REST API server
+  startAPIServer(db, sseEmitter, PORT)
+    .then((address) => {
+      console.log(`[cortex] Daemon running at ${address}`);
+    })
+    .catch((err) => {
+      console.error('[cortex] Failed to start:', err);
+      process.exit(1);
+    });
+}

packages/shared/src/types/sse.ts

@@ -102,6 +102,11 @@ export interface SSESyncError {
   data: { code: string; message: string };
 }
 
+export interface SSESyncOffline {
+  type: 'sync.offline';
+  data: { offlineCount: number; latency_ms: number };
+}
+
 export interface SSEDaemonError {
   type: 'daemon.error';
   data: { code: string; message: string };
@@ -122,6 +127,7 @@ export type SSEEvent =
   | SSERateLimitWarning
   | SSEReviewReminder
   | SSESyncError
+  | SSESyncOffline
   | SSEDaemonError;
 
 /**