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