Agency plugin causes local .mcp.json to be ignored

### Short summary

If an agency plugin is configured with an .mcp.json, local .mcp.json config is ignored

### Affected version or release

v1.1.10

### Installation context

_No response_

### What happened?

I had an agency plugin installed at the global scope which contained a .mcp.json configuration. After that, a new session in a repo with a local .mcp.json file was unable to load the mcp servers defined in the local file.

Removing the agency plugin returned the behavior to the expected.

### Steps to reproduce

_No response_

### Expected behavior

_No response_

### Additional context

_No response_

Start by reproducing the issue with a global agency plugin containing .mcp.json and a repository with its own local .mcp.json. Trace how the two configurations are discovered and loaded. Done means local MCP servers load as expected when the agency plugin is present, with a regression test covering both files.

Written by the indexing model from the issue text.