Bump Rugged to 0.28.0

This version bump makes things consistent between Gitaly and
fixes a significant number of bugs:
https://github.com/libgit2/libgit2/releases

This also decreases disk space of Omnibus builds by ~30 MB.

There is also a workaround for
https://github.com/libgit2/rugged/issues/785. If Gitaly or another
process changes .gitconfig while Rugged has the file loaded,
Rugged::Repository#each_key will report stale values unless a lookup is
done first.

This bug only manifests in a spec because we are using both Gitaly and
Rugged at the same time there, and we normally don't use Rugged in the
CE/EE code in this way.