[BUG] Custom local MCP server tools disabled in Cowork and Claude Code, but work in Claude Chat Desktop app

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

A custom local MCP server (self-hosted, running locally) works correctly in the Claude desktop Chat interface, but all its tools are non-functional in Cowork mode and Claude Code. The tools are recognized and appear in the tool list, but any invocation returns:

This tool has been disabled in your connector settings.

What Should Happen?

The local MCP connector should work across the Claude Desktop application if tools are allowed.

Error Messages/Logs

This tool has been disabled in your connector settings.

Steps to Reproduce

1. Set up a custom local MCP server running locally by adding into claude_desktop_config.json
2. Connect it to Claude — tools work correctly in the chat interface
3. Open the same MCP connection in Cowork mode or Claude Code
4. Attempt to call any tool from the MCP server
5. Observe the error

Claude Model

Sonnet (default)

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

2.1.90

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

Windows Terminal

Additional Information

_No response_