refactor: scaffold module registries and default-module layout

Additive change — existing code paths still run via inline fallbacks.
Prepares core for per-module extractions in PR #3 onward.

Four registries added with empty defaults:
  - delivery action handlers (delivery.ts)
  - router inbound gate (router.ts)
  - response dispatcher (index.ts)
  - MCP tool self-registration (container/agent-runner/src/mcp-tools/server.ts)

Default modules moved to src/modules/ for signaling:
  - src/modules/typing/       (extracted from delivery.ts)
  - src/modules/mount-security/ (moved from src/mount-security.ts)

Both are imported directly by core — no hook, no registry. Removal
requires editing core imports.

Migrator now keys applied rows by name (uniqueness) so module
migrations can pick arbitrary version numbers. Stored version column
is auto-assigned as an applied-order sequence.

sqlite_master guards added around core calls into module-owned tables
(user_roles, agent_destinations, pending_questions). No-ops today;
load-bearing after the owning modules are extracted.

MODULE-HOOK markers placed at scheduling's two skill-edit sites
(host-sweep.ts recurrence call, poll-loop.ts pre-task gate). PR #4
replaces the marked blocks when scheduling moves to its module.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

container/agent-runner/src/mcp-tools/agents.ts

@@ -9,6 +9,7 @@
  * (see mcp-tools/index.ts). The host re-checks permission on receive.
  */
 import { writeMessageOut } from '../db/messages-out.js';
+import { registerTools } from './server.js';
 import type { McpToolDefinition } from './types.js';
 
 function log(msg: string): void {
@@ -62,4 +63,4 @@ export const createAgent: McpToolDefinition = {
   },
 };
 
-export const agentTools: McpToolDefinition[] = [createAgent];
+registerTools([createAgent]);

container/agent-runner/src/mcp-tools/core.ts

@@ -12,6 +12,7 @@ import path from 'path';
 import { findByName, getAllDestinations } from '../destinations.js';
 import { getMessageIdBySeq, getRoutingBySeq, writeMessageOut } from '../db/messages-out.js';
 import { getSessionRouting } from '../db/session-routing.js';
+import { registerTools } from './server.js';
 import type { McpToolDefinition } from './types.js';
 
 function log(msg: string): void {
@@ -258,4 +259,4 @@ export const addReaction: McpToolDefinition = {
   },
 };
 
-export const coreTools: McpToolDefinition[] = [sendMessage, sendFile, editMessage, addReaction];
+registerTools([sendMessage, sendFile, editMessage, addReaction]);

container/agent-runner/src/mcp-tools/index.ts

@@ -1,59 +1,21 @@
 /**
- * MCP tools barrel — collects all tool modules and starts the server.
+ * MCP tools barrel — imports each tool module for its side-effect
+ * `registerTools([...])` call, then starts the MCP server.
  *
- * Each module exports a McpToolDefinition[] array. This file registers
- * them all with the MCP server. Adding a new tool module requires only
- * importing it here and spreading its tools array.
+ * Adding a new tool module: create the file, call `registerTools([...])`
+ * at module scope, and append the import here. No central list.
  */
-import { Server } from '@modelcontextprotocol/sdk/server/index.js';
-import { StdioServerTransport } from '@modelcontextprotocol/sdk/server/stdio.js';
-import { CallToolRequestSchema, ListToolsRequestSchema } from '@modelcontextprotocol/sdk/types.js';
-
-import type { McpToolDefinition } from './types.js';
-import { coreTools } from './core.js';
-import { schedulingTools } from './scheduling.js';
-import { interactiveTools } from './interactive.js';
-import { agentTools } from './agents.js';
-import { selfModTools } from './self-mod.js';
+import './core.js';
+import './scheduling.js';
+import './interactive.js';
+import './agents.js';
+import './self-mod.js';
+import { startMcpServer } from './server.js';
 
 function log(msg: string): void {
   console.error(`[mcp-tools] ${msg}`);
 }
 
-const allTools: McpToolDefinition[] = [
-  ...coreTools,
-  ...schedulingTools,
-  ...interactiveTools,
-  ...agentTools,
-  ...selfModTools,
-];
-
-const toolMap = new Map<string, McpToolDefinition>();
-for (const t of allTools) {
-  toolMap.set(t.tool.name, t);
-}
-
-async function startMcpServer(): Promise<void> {
-  const server = new Server({ name: 'nanoclaw', version: '2.0.0' }, { capabilities: { tools: {} } });
-
-  server.setRequestHandler(ListToolsRequestSchema, async () => ({
-    tools: allTools.map((t) => t.tool),
-  }));
-
-  server.setRequestHandler(CallToolRequestSchema, async (request) => {
-    const { name, arguments: args } = request.params;
-    const tool = toolMap.get(name);
-    if (!tool) {
-      return { content: [{ type: 'text', text: `Unknown tool: ${name}` }] };
-    }
-    return tool.handler(args ?? {});
-  });
-
-  const transport = new StdioServerTransport();
-  await server.connect(transport);
-  log(`MCP server started with ${allTools.length} tools: ${allTools.map((t) => t.tool.name).join(', ')}`);
-}
-
 startMcpServer().catch((err) => {
   log(`MCP server error: ${err instanceof Error ? err.message : String(err)}`);
   process.exit(1);

container/agent-runner/src/mcp-tools/interactive.ts

@@ -7,6 +7,7 @@
 import { findQuestionResponse, markCompleted } from '../db/messages-in.js';
 import { writeMessageOut } from '../db/messages-out.js';
 import { getSessionRouting } from '../db/session-routing.js';
+import { registerTools } from './server.js';
 import type { McpToolDefinition } from './types.js';
 
 function log(msg: string): void {
@@ -165,4 +166,4 @@ export const sendCard: McpToolDefinition = {
   },
 };
 
-export const interactiveTools: McpToolDefinition[] = [askUserQuestion, sendCard];
+registerTools([askUserQuestion, sendCard]);

container/agent-runner/src/mcp-tools/scheduling.ts

@@ -8,6 +8,7 @@
 import { getInboundDb } from '../db/connection.js';
 import { writeMessageOut } from '../db/messages-out.js';
 import { getSessionRouting } from '../db/session-routing.js';
+import { registerTools } from './server.js';
 import type { McpToolDefinition } from './types.js';
 
 function log(msg: string): void {
@@ -265,4 +266,4 @@ export const updateTask: McpToolDefinition = {
   },
 };
 
-export const schedulingTools: McpToolDefinition[] = [scheduleTask, listTasks, updateTask, cancelTask, pauseTask, resumeTask];
+registerTools([scheduleTask, listTasks, updateTask, cancelTask, pauseTask, resumeTask]);

container/agent-runner/src/mcp-tools/self-mod.ts

@@ -9,6 +9,7 @@
  * the host side (defense in depth).
  */
 import { writeMessageOut } from '../db/messages-out.js';
+import { registerTools } from './server.js';
 import type { McpToolDefinition } from './types.js';
 
 function log(msg: string): void {
@@ -140,4 +141,4 @@ export const requestRebuild: McpToolDefinition = {
   },
 };
 
-export const selfModTools: McpToolDefinition[] = [installPackages, addMcpServer, requestRebuild];
+registerTools([installPackages, addMcpServer, requestRebuild]);

container/agent-runner/src/mcp-tools/server.ts

@@ -0,0 +1,54 @@
+/**
+ * MCP server bootstrap + tool self-registration.
+ *
+ * Each tool module calls `registerTools([...])` at import time. The
+ * barrel (`index.ts`) imports every tool module for side effects, then
+ * calls `startMcpServer()` which uses whatever was registered.
+ *
+ * Default when only `core.ts` is imported: the core `send_message` /
+ * `send_file` / `edit_message` / `add_reaction` tools are available.
+ */
+import { Server } from '@modelcontextprotocol/sdk/server/index.js';
+import { StdioServerTransport } from '@modelcontextprotocol/sdk/server/stdio.js';
+import { CallToolRequestSchema, ListToolsRequestSchema } from '@modelcontextprotocol/sdk/types.js';
+
+import type { McpToolDefinition } from './types.js';
+
+function log(msg: string): void {
+  console.error(`[mcp-tools] ${msg}`);
+}
+
+const allTools: McpToolDefinition[] = [];
+const toolMap = new Map<string, McpToolDefinition>();
+
+export function registerTools(tools: McpToolDefinition[]): void {
+  for (const t of tools) {
+    if (toolMap.has(t.tool.name)) {
+      log(`Warning: tool "${t.tool.name}" already registered, skipping duplicate`);
+      continue;
+    }
+    allTools.push(t);
+    toolMap.set(t.tool.name, t);
+  }
+}
+
+export async function startMcpServer(): Promise<void> {
+  const server = new Server({ name: 'nanoclaw', version: '2.0.0' }, { capabilities: { tools: {} } });
+
+  server.setRequestHandler(ListToolsRequestSchema, async () => ({
+    tools: allTools.map((t) => t.tool),
+  }));
+
+  server.setRequestHandler(CallToolRequestSchema, async (request) => {
+    const { name, arguments: args } = request.params;
+    const tool = toolMap.get(name);
+    if (!tool) {
+      return { content: [{ type: 'text', text: `Unknown tool: ${name}` }] };
+    }
+    return tool.handler(args ?? {});
+  });
+
+  const transport = new StdioServerTransport();
+  await server.connect(transport);
+  log(`MCP server started with ${allTools.length} tools: ${allTools.map((t) => t.tool.name).join(', ')}`);
+}