[BUG] Design issue: confusing responsibilities of .mcp.json in claude plugin projects

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?

For a claude plugin project, the .mcp.json file in the root directory of the project have confusions.

• MCP servers used for development work of the plugin project being shared at project level
• MCP servers bundled together with the claude plugin, will be automatically installed on the plugin consumer side.

What Should Happen?

I would suggest for MCP servers used for development being shared at project level, the .mcp.json file should be put in .claude directory under the project.
Then .mcp.json file in root directory of a claude plugin will only be for bundled MCP servers.

Error Messages/Logs

Steps to Reproduce

1. Create a claude plugin project
2. Create .mcp.json in the root dir of the project and configure one mcp server in it.
3. Install this plugin to a new project
4. You will see the new project with the plugin installed will have a mcp server under the plugin domain.

Claude Model

Not sure / Multiple models

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.1.100

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

_No response_