Full support for multi-repo setups

Coming from a multi-repo workspace setup for VS Code, there is a lot of friction getting Copilot CLI to have the same tooling and instructions as the agents running in the IDE, despite the close relationship.

With /add-dir or by starting in the parent directory, the Copilot CLI can work across repos, but only one directory seems to be used for:

1. skill discovery
2. instructions
3. MCP discovery (or that might actually still only go through the user configuration)

some of these can be configured with flags and env-var, but it would be great to have some kind of parity with VS Code so that it does not matter if one is running Copilot one place or the other.

## Related issues?
https://github.com/github/copilot-cli/issues/1826