chore: remove unused MCP server from API package

The MCP server was never wired into the API entry point — dead code.
The REST API + Paperclip skill provides sufficient surface area.

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

apps/api/package.json

@@ -12,7 +12,6 @@
   "dependencies": {
     "@hono/node-server": "^1.14.0",
     "@kubernetes/client-node": "^1.4.0",
-    "@modelcontextprotocol/sdk": "^1.29.0",
     "@trebuchet/worker": "workspace:*",
     "@temporalio/client": "^1.11.0",
     "hono": "^4.7.0",