update jgit to latest release 3.0

This PR updates jgit to its latest version.

jgit 3.0 moved the 'FileRepository' to an internal package, therefore refactored most of the code to use a 'Repository' only. 
The only place I did not do it is in 'JGitAPIImpl.openDummyRepository()', as there is an overwrite of close method done.