[BUG] Claude Code Desktop eager loading MCPs while Claude Code CLI lazy loading

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?

Eager loading mcp tools at init in Claude Code Desktop app --

<img width="530" height="542" alt="Image" src="https://github.com/user-attachments/assets/3c1a5bca-3387-42fd-a7a4-47daf14d120d" />

What Should Happen?

Lazy loading MCP on claude code CLI

<img width="980" height="650" alt="Image" src="https://github.com/user-attachments/assets/a4f1c039-c04e-4984-858f-6b2b5365379b" />

Error Messages/Logs

Steps to Reproduce

1. open claude code cli and type /context -- observe mcp usage
2. open claude code desktop and type /context observe mcp usage

Claude Model

Opus

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

Claude 1.10628.0 (b4f860) 2026-06-02T05:48:19.000Z

Platform

AWS Bedrock

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

_No response_