Test cases related to JENKINS-21434 - alternates file wrong content

Checks that cloned copies have the alternates file with expected
content when the clone is performed with a reference repository, and
that cloned copies do not have the alternates file when clone does not
use a reference repository.
Merge pull request #77 from MarkEWaite/master-test-JENKINS-21434-fixed

Test cases related to JENKINS-21434 - alternates file wrong content
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-work