Configuring mcp tools for custom agents does not work

Feedback source

Other

GitHub Copilot plugin version

0.15.0.202601270459

Eclipse IDE and version

2025-12 (4.38)

Steps to reproduce

Steps to reproduce the behavior:
Precondition: Have agent tat uses non bult-in mcp tool.

1. Go to Copilot Settings -> MCP Settings
   

2. Click on "Configute tools for" and change it from "Agent mode" to the custom agent.
   

3. Select non built-in mcp tools.
   

4. Apply settings
   

5. Run the agent and see that it cannot use the non built-in mcp tool
   

6. Go in to the settings and see that the previously selected tools are unselected again.
   

Logs (optional)

No response

Expected behavior

Custom agents should work with all mcp tools.

Actual behavior

When creating custom agents, in the settings it is possible to configure the mcp tools the agent can use. Per default all built in tools are avaialable but when using other mcp servers these tools are disabled by default.
When enabling the tools, the settings are not applied and the custom agent can still not use the tools.

Additional information

No response