stdio MCP server breaks the client with `Unexpected token ... is not valid JSON`: send logs to stderr

Symptom

The client logs Unexpected token 'S', "Server sta"... is not valid JSON, and again on every tool call that logs something.

Environment and tested versions

Debian GNU/Linux 13 (trixie) x86_64, node 20.19.2, npm 11.21.1; stdio transport; SDK used for both server and client

• @modelcontextprotocol/sdk (TypeScript) 1.32.2
• node 20.19.2

Client used in the test: Reproduced with the official MCP TypeScript SDK stdio client (StdioClientTransport) 1.32.2 as a stand-in for a desktop app (Claude Desktop, Cursor, etc.), which can't run on the Linux test box. Not tested in the desktop app itself.

Root cause

In stdio transport, stdout carries JSON-RPC messages and nothing else. A console.log (or Python print) writes plain text into that stream and the client can't parse it.

Fix steps

1. Find every write to stdout in the server (console.log, print, startup banners).
2. Send logs and diagnostics to stderr instead: console.error in Node, print(..., file=sys.stderr) or logging in Python.
3. Restart the client and confirm the tool list loads without parse errors.

Verification

Tested 31 Oct 2026 in a throwaway directory on a Linux box (fake credentials only). Before (A) and after the fix:

== console.log
TRANSPORT_ERROR: Unexpected token 'S', "Server sta"... is not valid JSON
CONNECTED tools: ping
TRANSPORT_ERROR: Unexpected token 'H', "Handling ping..." is not valid JSON
== console.error
CONNECTED tools: ping
CALL: [{"type":"text","text":"pong"}]
SERVER_STDERR: Server starting, loading config...

Sources

• https://github.com/microsoft/azure-devops-mcp/issues/147