Default JGit changelog command to start at HEAD ref if no ref specified

Makes the behavior consistent with CliGit and allows two tests which
were marked as not implemented in JGit to be executed.
Correct isBareRepository tests for JGit

Previous tests mistakenly asserted the repository was not bare when it
had been created as a bare repository.  JGit correctly failed the
flawed assertion.  My mistake to assume that the CliGit implementation
is always the better reference implementation.  In this case, the JGit
implementation was the better reference implementation.