VS Code MCP Config Overrides Personal Copilot MCP Config

[mishapos]

Describe the bug

When I open copilot in a repo, it claims to have loaded the MCP servers from my personal configuration at C:\Users\<user>\.copilot/mcp-config.json but when I ask it to use those tools, it doesnt recognize them.

I figured out that instead, the .vscode\mcp.json was overwriting them and only loading the MCP tools in that file and completely ignoring the C:\Users\<user>\.copilot/mcp-config.json, even though it explicitly stated that it loaded them at the beginning in the startup text.

Affected version

GitHub Copilot CLI 0.0.415-0.

Steps to reproduce the behavior

1. Create a repo with a .vscode/mcp.json file.
2. Load different MCP configurations into the .vscode/mcp.json file and your C:\Users\<user>\.copilot/mcp-config.json
3. Open copilot in the repo's directory
4. Ask copilot to list which MCP servers/tools it has configured
5. Notice that even though it says it loaded from C:\Users\<user>\.copilot/mcp-config.json , those MCP servers are not configured.

Expected behavior

I expect that the CLI would merge the MCP servers from both configurations instead of silently removing the personal configuration even after explicitly stating that it loaded them.

Additional context

No response