Fixes #3118 : Upgrade Jgit to 2.1

A dependency upgrade for Jgit 

Here we upgrade to Jgit 2.1 (before was 1.3)

I made another pull request to upgrade to Jgit 2.2 ( last release was from mid-december) https://github.com/Normation/cf-clerk/pull/3

This one should not cause any problem