MCP servers configured in local repo custom agents don't get started anymore

[tlmii]

Describe the bug

An MCP server configured in a custom agent that is defined in .github/agents/ inside the working directory for the copilot cli doesn't seem to ever get started.

Affected version

0.0.382 Commit: 18bf0ae

Steps to reproduce the behavior

A simple repro (though it requires .NET 10 because the MCP server uses dnx) is to:

1. Clone https://github.com/tlmii/CopilotFeatureSupportChecks
2. Load the repo in copilot cli
3. Load the nuget-tooling-agent agent using /agent
4. Ask it to tell you the latest version of (for e.g.) the Newtonsoft.Json package (you can ask it to specifically use the nuget tools if you want, doesn't seem to matter).

Expected behavior

The configured mcp server would be started and the tools it provides would be available to the model

Additional context

This worked in 0.0.364 (it started the mcp server, discovered the tools and used the correct one to answer the question) and does not work now in 0.0.382 (it never starts the mcp server or even acknowledges that it exists). I'm not sure when in-between it stopped working but I know there was some refactoring going on. I just happened to have 0.0.364 still installed on a machine.

I was able to confirm with another member of our team that it worked when he first tried it but stopped working at some point over the last few weeks. So I don't think its a "my machine" thing.

I do wonder if it is related to repo-level custom agents not supporting mcp servers in CCA if they share the same engine. This is the local variant of that scenario so I could see there being something going on there, but just a guess.