This fixes `git_submodule_sync` to correctly update the remote URL
of the default branch of the submodule along with the URL in the
parent repository config (i.e. match core Git's behavior).

Also move some useful helper logic from the submodule code into
a shared config API `git_config__update_entry` that can either set
or delete an entry with constraints like not overwriting or not
creating a new entry.  I used that helper to update a couple other
places in the code.