refactor(01-03): extract services/skills/gateway/mcp into services.ts, reduce index.ts to 140 lines

- Extract initSkills(), initMcp(), loadSystemPrompt(), initPairingManager(), createGateway(), startServices() into services.ts
- daemon/index.ts reduced from 386 to 140 lines (64% reduction, 87% from 1087 baseline)
- Organize imports with section comments (External, Config, Daemon Modules, Infrastructure)
- Add section dividers in startDaemon() (Data & Sessions, Core Services, Model & Prompt, Gateway & Channels, Tier 1 Tools, Lifecycle)
- Convert unused value imports to type-only imports
- DaemonContext interface and re-exports unchanged

src/daemon/index.ts

@@ -1,32 +1,35 @@
-import { Lifecycle } from './lifecycle.js';
-import { createModelRouter } from './models.js';
-import { initMemory } from './memory.js';
-import { createMessageRouter } from './routing.js';
-import { initAgents } from './agents.js';
-import { initTools } from './tools.js';
-import { registerChannels } from './channels.js';
-import type { Config } from '../config/index.js';
-import type { AudioTranscriptionConfig } from '../models/media.js';
-import { ModelRouter } from '../models/index.js';
-import { AgentOrchestrator } from '../backends/index.js';
-import { OutboundAttachmentCollector } from '../backends/native/attachments.js';
-import { SessionStore, SessionManager, parseDuration } from '../session/index.js';
-import { HookEngine } from '../hooks/index.js';
-import type { ToolRegistry, ToolExecutor, BrowserManager } from '../tools/index.js';
-import { createSessionTools, createAgentsListTool, createMessageSendTool, createCronTools } from '../tools/index.js';
-import { GatewayServer } from '../gateway/index.js';
-import { ChannelRegistry, PairingManager } from '../channels/index.js';
-import type { CronScheduler } from '../automation/index.js';
-import { HeartbeatMonitor } from '../automation/index.js';
-import { McpManager } from '../mcp/index.js';
-import { SkillRegistry, SkillInstaller, loadAllSkills } from '../skills/index.js';
-import { assembleSystemPrompt } from '../prompt/index.js';
-import type { AgentConfigRegistry, AgentRouter } from '../agents/index.js';
-import type { SandboxManager } from '../sandbox/index.js';
+// ── External ──
 import { resolve } from 'path';
 import { homedir } from 'os';
 import { mkdirSync } from 'fs';
 
+// ── Config & Types ──
+import type { Config } from '../config/index.js';
+import type { AudioTranscriptionConfig } from '../models/media.js';
+import type { ToolRegistry, ToolExecutor, BrowserManager } from '../tools/index.js';
+import type { AgentConfigRegistry, AgentRouter } from '../agents/index.js';
+import type { SandboxManager } from '../sandbox/index.js';
+
+// ── Daemon Modules ──
+import { Lifecycle } from './lifecycle.js';
+import { createModelRouter } from './models.js';
+import { initMemory } from './memory.js';
+import { initTools } from './tools.js';
+import { initAgents } from './agents.js';
+import { createMessageRouter } from './routing.js';
+import { registerChannels } from './channels.js';
+import { initSkills, initMcp, loadSystemPrompt, initPairingManager, createGateway, startServices } from './services.js';
+
+// ── Infrastructure ──
+import type { ModelRouter } from '../models/index.js';
+import { SessionStore, SessionManager, parseDuration } from '../session/index.js';
+import { HookEngine } from '../hooks/index.js';
+import { createSessionTools, createAgentsListTool, createMessageSendTool, createCronTools } from '../tools/index.js';
+import { ChannelRegistry } from '../channels/index.js';
+import type { McpManager } from '../mcp/index.js';
+import type { SkillRegistry, SkillInstaller } from '../skills/index.js';
+import type { GatewayServer } from '../gateway/index.js';
+
 export interface DaemonContext {
   config: Config;
   lifecycle: Lifecycle;
@@ -47,33 +50,13 @@ export interface DaemonContext {
   browserManager?: BrowserManager;
 }
 
-function loadSystemPrompt(config: Config): string {
-  const searchDirs = [
-    process.cwd(),
-    resolve(import.meta.dirname, '../..'),
-    ...(config.prompt.search_dirs ?? []),
-  ];
-
-  const result = assembleSystemPrompt({
-    searchDirs,
-    extraSections: config.prompt.extra_sections,
-  });
-
-  if (result.loadedFiles.length > 0) {
-    console.log(`Loaded prompt templates: ${result.loadedFiles.map(f => f.split('/').pop()).join(', ')}`);
-  }
-
-  return result.prompt;
-}
-
 export async function startDaemon(config: Config): Promise<DaemonContext> {
   const lifecycle = new Lifecycle();
 
-  // Ensure data directory exists (FLYNN_DATA_DIR overrides default for Docker/custom deployments)
+  // ── Data & Sessions ──
   const dataDir = process.env.FLYNN_DATA_DIR ?? resolve(homedir(), '.local/share/flynn');
   mkdirSync(dataDir, { recursive: true });
 
-  // Initialize session store and manager
   const sessionStore = new SessionStore(resolve(dataDir, 'sessions.db'));
   const sessionManager = new SessionManager(sessionStore);
 
@@ -82,304 +65,76 @@ export async function startDaemon(config: Config): Promise<DaemonContext> {
     console.log('Session store closed');
   });
 
-  // Session pruning timer (TTL-based cleanup)
   const ttlMs = parseDuration(config.sessions?.ttl ?? '30d');
   if (ttlMs) {
     const pruneInterval = setInterval(() => {
-      const cutoff = Math.floor((Date.now() - ttlMs) / 1000); // created_at is unix seconds
+      const cutoff = Math.floor((Date.now() - ttlMs) / 1000);
       const pruned = sessionStore.pruneStale(cutoff);
       if (pruned.length > 0) {
         sessionManager.evictSessions(pruned);
         console.log(`Pruned ${pruned.length} stale session(s) (TTL: ${config.sessions?.ttl ?? '30d'})`);
       }
-    }, 3_600_000); // every hour
-
-    lifecycle.onShutdown(async () => {
-      clearInterval(pruneInterval);
-    });
+    }, 3_600_000);
+    lifecycle.onShutdown(async () => { clearInterval(pruneInterval); });
   }
 
-  // Initialize hook engine
+  // ── Core Services ──
   const hookEngine = new HookEngine(config.hooks);
-
-  // Initialize tool registry, executor, web search, process tools, browser tools, and tool policy
   const { toolRegistry, toolExecutor, browserManager } = initTools({ config, lifecycle, hookEngine });
-
-  // Initialize memory store, vector search, and memory tools
-  const { memoryStore, hybridSearch, memoryDir } = await initMemory({ config, dataDir, lifecycle, toolRegistry });
-
-  // Initialize MCP manager and start configured servers
-  const mcpManager = new McpManager(toolRegistry);
-
-  if (config.mcp.servers.length > 0) {
-    console.log(`Starting ${config.mcp.servers.length} MCP server(s)...`);
-    await mcpManager.startAll(config.mcp.servers);
-  }
-
-  lifecycle.onShutdown(async () => {
-    await mcpManager.stopAll();
-    console.log('MCP servers stopped');
-  });
-
-  // Initialize skills system
-  const defaultManagedDir = resolve(homedir(), '.flynn/workspace/skills');
-  const skillRegistry = new SkillRegistry();
-  const skillInstaller = new SkillInstaller(config.skills.managed_dir ?? defaultManagedDir);
-
-  const skills = loadAllSkills({
-    bundledDir: config.skills.bundled_dir,
-    managedDir: config.skills.managed_dir ?? defaultManagedDir,
-    workspaceDir: config.skills.workspace_dir,
-  });
-
-  for (const skill of skills) {
-    skillRegistry.register(skill);
-  }
-
-  if (skills.length > 0) {
-    const available = skillRegistry.listAvailable().length;
-    console.log(`Loaded ${skills.length} skill(s) (${available} available)`);
-  }
-
-  // Initialize agent config registry, router, and sandbox manager
+  const { memoryStore, memoryDir } = await initMemory({ config, dataDir, lifecycle, toolRegistry });
+  const mcpManager = await initMcp(config, lifecycle, toolRegistry);
+  const { skillRegistry, skillInstaller } = initSkills(config);
   const { agentConfigRegistry, agentRouter, sandboxManager } = await initAgents({ config, lifecycle });
 
-  // Initialize audio transcription config
+  // ── Model & Prompt ──
   const audioConfig: AudioTranscriptionConfig = {
     endpoint: config.audio.transcription_endpoint,
     apiKey: config.audio.transcription_api_key,
     model: config.audio.transcription_model,
   };
-
-  // Initialize model router
   const modelRouter = createModelRouter(config);
+  const systemPrompt = loadSystemPrompt(config, skillRegistry);
 
-  // Load system prompt and append skill instructions
-  let systemPrompt = loadSystemPrompt(config);
-  const skillAdditions = skillRegistry.getSystemPromptAdditions();
-  if (skillAdditions) {
-    systemPrompt = `${systemPrompt}\n\n# Available Skills\n\n${skillAdditions}`;
-  }
-
-  // Initialize channel registry (created early so the gateway can reference it)
+  // ── Gateway & Channels ──
   const channelRegistry = new ChannelRegistry();
+  const pairingManager = initPairingManager(config);
 
-  // Create PairingManager if pairing is enabled
-  let pairingManager: PairingManager | undefined;
-  if (config.pairing.enabled) {
-    // Parse code_ttl: supports '5m', '1h', '30s' → milliseconds
-    const ttlMatch = config.pairing.code_ttl.match(/^(\d+)(s|m|h)$/);
-    const codeTtlMs = ttlMatch
-      ? Number(ttlMatch[1]) * ({ s: 1000, m: 60_000, h: 3_600_000 }[ttlMatch[2] as 's' | 'm' | 'h'])
-      : 5 * 60_000; // default 5 minutes
+  let channelAgents: ReturnType<typeof createMessageRouter>['agents'] | null = null;
 
-    pairingManager = new PairingManager({
-      enabled: true,
-      codeTtl: codeTtlMs,
-      codeLength: config.pairing.code_length,
-    });
-    console.log(`Pairing codes enabled (TTL: ${config.pairing.code_ttl}, length: ${config.pairing.code_length})`);
-  }
-
-  // Mutable reference to channel agents map — set after createMessageRouter() below.
-  // This allows the gateway's getTokenUsage callback to access channel agent usage data.
-  let channelAgents: Map<string, { orchestrator: AgentOrchestrator; collector: OutboundAttachmentCollector }> | null = null;
-
-  // Initialize gateway WebSocket server
-  const gateway = new GatewayServer({
-    port: config.server.port,
-    host: config.server.localhost ? '127.0.0.1' : '0.0.0.0',
-    sessionManager,
-    modelClient: modelRouter,
-    systemPrompt,
-    toolRegistry,
-    toolExecutor,
-    auth: {
-      token: config.server.token,
-      tailscaleIdentity: config.server.tailscale_identity,
-    },
-    authHttp: config.server.auth_http,
-    lock: config.server.lock,
-    uiDir: resolve(import.meta.dirname, '../gateway/ui'),
-    config,
-    channelRegistry,
-    pairingManager,
-    restart: async () => {
-      console.log('Restart requested via gateway');
-      await lifecycle.shutdown();
-      // Exit with code 75 (EX_TEMPFAIL) — process supervisor should restart
-      process.exit(75);
-    },
-    getTokenUsage: () => {
-      const results: Array<{
-        sessionId: string;
-        primary: { inputTokens: number; outputTokens: number; calls: number };
-        delegation: Record<string, { inputTokens: number; outputTokens: number; calls: number }>;
-        total: { inputTokens: number; outputTokens: number; calls: number; estimatedCost: number };
-      }> = [];
-
-      // Collect usage from gateway WebSocket sessions (NativeAgent-based)
-      const sessionBridge = gateway.getSessionBridge();
-      for (const entry of sessionBridge.getAllUsage()) {
-        results.push(entry);
-      }
-
-      // Collect usage from channel agents (AgentOrchestrator-based, has full delegation data)
-      if (channelAgents) {
-        for (const [sessionId, { orchestrator }] of channelAgents) {
-          const usage = orchestrator.getUsage();
-          results.push({
-            sessionId,
-            primary: usage.primary,
-            delegation: usage.delegation,
-            total: usage.total,
-          });
-        }
-      }
-
-      return results;
-    },
+  const gateway = createGateway({
+    config, sessionManager, modelRouter, systemPrompt, toolRegistry, toolExecutor,
+    channelRegistry, pairingManager, lifecycle,
+    getChannelAgents: () => channelAgents,
   });
 
-  if (config.server.token) {
-    console.log(`Gateway auth: token required${config.server.tailscale_identity ? ' + Tailscale identity' : ''}`);
-  }
-
-  // ── Channel Registry ──────────────────────────────────────────
-
-  // Set up the unified message handler
   const messageRouter = createMessageRouter({
-    sessionManager,
-    modelRouter,
-    systemPrompt,
-    toolRegistry,
-    toolExecutor,
-    config,
-    memoryStore,
-    agentConfigRegistry,
-    agentRouter,
-    sandboxManager,
-    audioConfig,
+    sessionManager, modelRouter, systemPrompt, toolRegistry, toolExecutor,
+    config, memoryStore, agentConfigRegistry, agentRouter, sandboxManager, audioConfig,
   });
   channelRegistry.setMessageHandler(messageRouter.handler);
-
-  // Wire channel agents into the getTokenUsage callback (late binding)
   channelAgents = messageRouter.agents;
 
-  // Register all channel adapters (Telegram, Discord, Slack, WhatsApp, WebChat, cron, webhooks, Gmail)
   const { cronScheduler } = registerChannels({ config, channelRegistry, hookEngine, pairingManager, gateway });
 
-  // ── Register Tier 1 agent tools ─────────────────────────────
-
-  // Session management tools (list, history, create, delete)
-  for (const tool of createSessionTools(sessionManager)) {
-    toolRegistry.register(tool);
-  }
-
-  // Agent discovery tool
+  // ── Tier 1 Tools ──
+  for (const tool of createSessionTools(sessionManager)) { toolRegistry.register(tool); }
   toolRegistry.register(createAgentsListTool(agentConfigRegistry));
-
-  // Cross-channel messaging tool
   toolRegistry.register(createMessageSendTool(channelRegistry));
-
-  // Cron management tools (if scheduler is active)
   if (cronScheduler) {
-    for (const tool of createCronTools(cronScheduler)) {
-      toolRegistry.register(tool);
-    }
+    for (const tool of createCronTools(cronScheduler)) { toolRegistry.register(tool); }
   }
 
-  // ── Signal Handlers ───────────────────────────────────────────
-
-  const signalHandler = () => {
-    lifecycle.shutdown().then(() => process.exit(0));
-  };
-
-  process.on('SIGINT', signalHandler);
-  process.on('SIGTERM', signalHandler);
-
-  lifecycle.onShutdown(async () => {
-    process.off('SIGINT', signalHandler);
-    process.off('SIGTERM', signalHandler);
-  });
-
-  // ── Start Services ────────────────────────────────────────────
-
-  // Register shutdown handler for channels (stops Telegram bot etc.)
-  lifecycle.onShutdown(async () => {
-    await channelRegistry.stopAll();
-    console.log('Channel adapters stopped');
-  });
-
-  // Start all channel adapters (Telegram long polling, WebChat status)
-  await channelRegistry.startAll();
-
-  // Start gateway (HTTP + WS server)
-  lifecycle.onShutdown(async () => {
-    await gateway.stop();
-    console.log('Gateway server stopped');
-  });
-
-  await gateway.start();
-
-  // ── Tailscale Serve ────────────────────────────────────────────
-  if (config.server.tailscale?.serve) {
-    const { startTailscaleServe, stopTailscaleServe } = await import('../gateway/tailscale.js');
-    const tsConfig = {
-      localPort: config.server.port,
-      servePort: config.server.tailscale.port,
-      hostname: config.server.tailscale.hostname,
-    };
-    try {
-      await startTailscaleServe(tsConfig);
-      lifecycle.onShutdown(async () => {
-        await stopTailscaleServe(tsConfig);
-      });
-    } catch {
-      console.warn('Tailscale Serve failed to start — gateway still accessible on local port');
-    }
-  }
-
-  // ── Heartbeat Monitor ──────────────────────────────────────────
-  const heartbeatMonitor = new HeartbeatMonitor({
-    config: config.automation.heartbeat,
-    getGatewayPort: () => config.server.port,
-    modelRouter,
-    channelLister: channelRegistry,
-    memoryDir: config.memory.enabled ? memoryDir : undefined,
-    dataDir,
-    channelLookup: channelRegistry,
-  });
-
-  heartbeatMonitor.start();
-
-  lifecycle.onShutdown(async () => {
-    heartbeatMonitor.stop();
-    console.log('Heartbeat monitor stopped');
-  });
-
-  console.log('Flynn daemon started');
+  // ── Lifecycle ──
+  await startServices({ config, lifecycle, channelRegistry, gateway, modelRouter, memoryDir, dataDir });
 
   return {
-    config,
-    lifecycle,
-    sessionStore,
-    sessionManager,
-    hookEngine,
-    modelRouter,
-    toolRegistry,
-    toolExecutor,
-    gateway,
-    channelRegistry,
-    mcpManager,
-    skillRegistry,
-    skillInstaller,
-    agentConfigRegistry,
-    agentRouter,
-    sandboxManager,
-    browserManager,
+    config, lifecycle, sessionStore, sessionManager, hookEngine, modelRouter,
+    toolRegistry, toolExecutor, gateway, channelRegistry, mcpManager,
+    skillRegistry, skillInstaller, agentConfigRegistry, agentRouter,
+    sandboxManager, browserManager,
   };
 }
 
+// ── Re-exports for backward compatibility ──
 export { Lifecycle } from './lifecycle.js';
 export { createClientFromConfig, anthropicToGitHubModel, createAutoFallbackClient, createModelRouter } from './models.js';