Keep MCP stdio logs off stdout

[mirageN1349]

Summary

• route diagnostic MCP server logs to stderr instead of stdout
• install the stdout JSON-RPC guard before startup discovery runs
• keep stdout reserved for MCP JSON-RPC messages

Verification

• npm run build
• started dist/mcp-server.js over stdio and sent an initialize request; stdout contained only the JSON-RPC response while discovery logs were written to stderr