fix(api): remove MCP server

MCP server is overkill for this use case — all 5 MCP tools are
thin wrappers over the REST API. Paperclip agents should use the
REST API directly with bearer token auth instead.

Co-Authored-By: Paperclip <noreply@paperclip.ing>

apps/api/src/index.ts

@@ -7,7 +7,6 @@ import { serve } from '@hono/node-server';
 import * as k8s from '@kubernetes/client-node';
 import { createApp } from './app.js';
 import { loadConfig } from './config.js';
-import { startMcpServer } from './mcp/server.js';
 import { connectTemporal, disconnectTemporal } from './services/temporal-client.js';
 
 async function main(): Promise<void> {
@@ -35,21 +34,14 @@ async function main(): Promise<void> {
     coreApi,
   });
 
-  // 5. Start MCP server (runs alongside the Hono API on a separate port)
-  const mcpServer = await startMcpServer(
-    { config, temporalClient: temporal.client, batchApi, coreApi },
-    config.mcpPort,
-  );
-
-  // 6. Start Hono server
+  // 5. Start Hono server
   const server = serve({ fetch: app.fetch, port: config.port }, (info) => {
     console.log(`Shannon API server listening on port ${info.port}`);
   });
 
-  // 7. Graceful shutdown
+  // 6. Graceful shutdown
   const shutdown = async (): Promise<void> => {
     console.log('Shutting down...');
-    mcpServer.close();
     server.close();
     await disconnectTemporal(temporal);
     process.exit(0);