And use it to set annex-config-uuid in git config. This makes
using the origin special remote work after cloning.
Without the added Logs.Remote.configSet, instantiating the remote will
look at the annex-config-uuid's config in the remote log, which will be
empty, and so it will fail to find a special remote.
The added deletion of files in the alternatejournaldir is just to make
100% sure they don't get committed to the git-annex branch. Now that
they contain things that definitely should not be committed.
