Test clone from bare repo, referencing a working directory

Reported on the Jenkins mailing list, fixed by
b6473d636f9f8f00f954ef294cfd5ed296b6a738
Merge pull request #78 from MarkEWaite/master-add-referenced-working-dir-in-clone

Test clone from bare repo, referencing a working directory
Merge remote-tracking branch 'upstream/master' into master-isBareRepository-JGit-fixes