Refs that do not belong to ostree should not be automatically pruned

[jlebon]

There are multiple apps now that also need to store data in the system repo. These apps might not want ostree to automatically prune their refs (see ostree_admin_cleanup()).

We need to make ostree smarter so that it only prunes the refs that belong to it.
See also PR #257.

[cgwalters]

So...we ended up using a separate repo for this, but I have a suspicion this is still going to bite people down the line.

[jlebon]

Yup, for this reason I had to add refs to the base layers for package layering (although to be fair, in that case the commit does "belong" to ostree, but we should probably still have some configurability here so we don't have to hack around it).