Upgrade to JGit 3.0.0

This allows to get rid of the workaround for checking out a branch after
clone, see the following bug which was fixed in 3.0.0:

https://bugs.eclipse.org/bugs/show_bug.cgi?id=390994

WindowCache became internal, but it's no longer necessary with the
different approach for checking out a commit, so remove the code.
Merge pull request #9 from robinst/jgit-3.0

Upgrade to JGit 3.0.0 (by @robinst)