Allow for more customization/separation for mcp configuration

### Describe the feature or problem you'd like to solve

When a project has .vscode/mcp.json, it will override ~/.copilot/mcp-config.json even when they are set differently due to being run within VSCode and cli

### Proposed solution

It would be useful to have either a flag in the config to determine that CLI should ignore/prioritize one over the other for CLI, or to be able to turn off reading from the mcp.json within .vscode.

### Example prompts or workflows

_No response_

### Additional context

_No response_