Use a Repository to read JGit configuration rather than a FileBasedConfig

I was unable to find any sequence of arguments which would allow a
FileBasedConfig to return useful results.  Rather than spending time
trying to find the magic arguments to make it work, I switched to
create a Repository on the passed in git directory.

Even that change only allows the branch to be taken successfully in a
single test case.
Include an assertion which passes in JGit and fails in CliGit