Update to JGit 3.3.0 and other more recent versions

This intentionally updates to JGit 3.3.0 even though JGit 3.3.1 is now
available.  The git-client-plugin still uses 3.3.0 and the git-plugin
should not depend on a newer version than the git-client-plugin.

Once the git-client-plugin updates to 3.3.1, git-plugin may update also.