feat: wire up all Phase 2-6 features into daemon and config

Integrate all new features into the shared infrastructure:
- Config schema: add memory, discord, slack, process, web_search schemas
- Daemon wiring: memory store init, tool registration, channel adapters
- Orchestrator: memory injection into system prompt, extraction on compaction
- Agent: add setSystemPrompt() for dynamic prompt updates
- Channel/tool index: export new adapters and tool factories
- Add @slack/bolt, discord.js, turndown, linkedom, @mozilla/readability deps
- Update state.json with Phase 3b completion (494 tests passing)

src/daemon/index.ts

@@ -5,9 +5,11 @@ import type { ModelClient } from '../models/index.js';
 import { AgentOrchestrator, type DelegationConfig } from '../backends/index.js';
 import { SessionStore, SessionManager } from '../session/index.js';
 import { HookEngine } from '../hooks/index.js';
-import { ToolRegistry, ToolExecutor, allBuiltinTools } from '../tools/index.js';
+import { ToolRegistry, ToolExecutor, allBuiltinTools, createWebSearchTools, createProcessTools, ProcessManager } from '../tools/index.js';
+import { MemoryStore } from '../memory/index.js';
+import { createMemoryTools } from '../tools/builtin/index.js';
 import { GatewayServer } from '../gateway/index.js';
-import { ChannelRegistry, TelegramAdapter, WebChatAdapter } from '../channels/index.js';
+import { ChannelRegistry, TelegramAdapter, WebChatAdapter, DiscordAdapter, SlackAdapter } from '../channels/index.js';
 import { CronScheduler } from '../automation/index.js';
 import type { InboundMessage, OutboundMessage } from '../channels/index.js';
 import { McpManager } from '../mcp/index.js';
@@ -144,6 +146,7 @@ function createMessageRouter(deps: {
   toolRegistry: ToolRegistry;
   toolExecutor: ToolExecutor;
   config: Config;
+  memoryStore?: MemoryStore;
 }) {
   // Cache agents by session ID to avoid recreating on every message
   const agents = new Map<string, AgentOrchestrator>();
@@ -176,6 +179,7 @@ function createMessageRouter(deps: {
         } : undefined,
         modelName: deps.config.models.default.model,
         contextWindow: deps.config.models.default.context_window,
+        memoryStore: deps.memoryStore,
       });
       agents.set(sessionId, agent);
     }
@@ -228,6 +232,13 @@ export async function startDaemon(config: Config): Promise<DaemonContext> {
   const dataDir = resolve(homedir(), '.local/share/flynn');
   mkdirSync(dataDir, { recursive: true });
 
+  // Initialize memory store
+  const memoryDir = config.memory.dir ?? resolve(dataDir, 'memory');
+  mkdirSync(memoryDir, { recursive: true });
+  const memoryStore = config.memory.enabled
+    ? new MemoryStore({ dir: memoryDir, maxContextTokens: config.memory.max_context_tokens })
+    : undefined;
+
   // Initialize session store and manager
   const sessionStore = new SessionStore(resolve(dataDir, 'sessions.db'));
   const sessionManager = new SessionManager(sessionStore);
@@ -245,6 +256,42 @@ export async function startDaemon(config: Config): Promise<DaemonContext> {
   for (const tool of allBuiltinTools) {
     toolRegistry.register(tool);
   }
+
+  // Register memory tools if memory is enabled
+  if (memoryStore) {
+    for (const tool of createMemoryTools(memoryStore)) {
+      toolRegistry.register(tool);
+    }
+  }
+
+  // Register web search tool if configured with credentials
+  if (config.web_search.api_key || config.web_search.endpoint) {
+    for (const tool of createWebSearchTools({
+      provider: config.web_search.provider,
+      apiKey: config.web_search.api_key,
+      endpoint: config.web_search.endpoint,
+      maxResults: config.web_search.max_results,
+    })) {
+      toolRegistry.register(tool);
+    }
+  }
+
+  // Initialize process manager and register process tools
+  const processManager = new ProcessManager({
+    maxConcurrent: config.process.max_concurrent,
+    maxRuntimeMinutes: config.process.max_runtime_minutes,
+    bufferSize: config.process.buffer_size,
+  });
+
+  for (const tool of createProcessTools(processManager)) {
+    toolRegistry.register(tool);
+  }
+
+  lifecycle.onShutdown(async () => {
+    await processManager.shutdown();
+    console.log('Process manager stopped');
+  });
+
   const toolExecutor = new ToolExecutor(toolRegistry, hookEngine);
 
   // Initialize MCP manager and start configured servers
@@ -321,6 +368,7 @@ export async function startDaemon(config: Config): Promise<DaemonContext> {
     toolRegistry,
     toolExecutor,
     config,
+    memoryStore,
   }));
 
   // Register Telegram adapter
@@ -331,6 +379,28 @@ export async function startDaemon(config: Config): Promise<DaemonContext> {
   });
   channelRegistry.register(telegramAdapter);
 
+  // Register Discord adapter (if configured)
+  if (config.discord) {
+    const discordAdapter = new DiscordAdapter({
+      botToken: config.discord.bot_token,
+      allowedGuildIds: config.discord.allowed_guild_ids.length > 0 ? config.discord.allowed_guild_ids : undefined,
+      allowedChannelIds: config.discord.allowed_channel_ids.length > 0 ? config.discord.allowed_channel_ids : undefined,
+      requireMention: config.discord.require_mention,
+    });
+    channelRegistry.register(discordAdapter);
+  }
+
+  // Register Slack adapter (if configured)
+  if (config.slack) {
+    const slackAdapter = new SlackAdapter({
+      botToken: config.slack.bot_token,
+      appToken: config.slack.app_token,
+      signingSecret: config.slack.signing_secret,
+      allowedChannelIds: config.slack.allowed_channel_ids.length > 0 ? config.slack.allowed_channel_ids : undefined,
+    });
+    channelRegistry.register(slackAdapter);
+  }
+
   // Register WebChat adapter (wraps the gateway)
   const webChatAdapter = new WebChatAdapter({ gateway });
   channelRegistry.register(webChatAdapter);