CLI Commands using the new framework should read the checked-out branch from repo_state.json instead of using the server's default branch.

A server's default branch is set when the server is created and cannot change. If the checked out branch changes while the server is running, the server does not see the change, and future connections to the server will get the original checked-out branch as the default.

For most cases this doesn't matter, because we don't typically allow changing the checked out branch while the server is running. But one place where this is allowed is when a user is using the command line to connect to a locally running server. In that case, the commands still have access to the file system, and `dolt checkout` can change the checked out branch.

But after the checkout, subsequent commands will not run on the newly checked out branch because instead of getting the checked out branch from the filesystem, they connect to the already running server and use that server's default. We should change this to make the commands supply the checked out branch to the server when they connect.

This is important for running our BATs tests in the "remote-engine" configuration.