Checkout branches when possible

Even when tracking a SHA, first try checking out the branch to see if the current head matches the desired ref. This will leave the nested repository in a better state for ongoing development.

Start by locating the checkout and ref-resolution logic for nested repositories, then read any nearby tests. Verify the existing behavior when tracking a SHA, and confirm that branch checkout is attempted first when the branch head matches the desired ref, leaving the nested repository on that branch when possible.

Written by the indexing model from the issue text.