Fix test which broke because it's internal class moved.

The test `querying.clj` depended on `org.eclipse.jgit.storage.file.RefDirectory$LooseUnpeeled` but it moved in JGit 3.3.2 (or earlier).  So the test didn't pass as-is and I fixed the package name which is now `org.eclipse.jgit.internal.storage.file`.  The JGit version bump is just because I tried it both ways and both have the same problem.  There surely is a better way to do the test but I just loaded up this code and don't know yet what that is.