[BUG] mcp add project overwrites existing mcps in project

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?

claude mcp add -s project violator -- violate overwrites existing mcp servers.

What Should Happen?

new mcp should be inserted instead of overwriting existing

Error Messages/Logs

Steps to Reproduce

cat .mcp.json
{
  "mcpServers": {
    "secret": {
      "type": "stdio",
      "command" : "secret",
      "args": [
        "${SECRET}"
      ],
      "env": [
        "SECRET", "${SECRET}"
      ]
    }
  }
}

claude mcp add -s project violator -- violate
Added stdio MCP server violator with command: violate  to project config
File modified: /Users/jimweller/tmp/_crap/.mcp.json

cat .mcp.json
{
  "mcpServers": {
    "violator": {
      "type": "stdio",
      "command": "violate",
      "args": [],
      "env": {}
    }
  }
}                                

claude --version
2.1.50 (Claude Code)

Claude Model

None

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.1.50

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

iTerm2

Additional Information

_No response_