The current version of JGit being used by the plugin is several versions behind. 0.7.1 contains all of the patches that were submitted and 0.4 should be removed. I've got a clean compile using the version at eclipse, but there appears to be a problem with their maven repo so until that is fixed, I'll hold off on providing a patch.

https://bugs.eclipse.org/bugs/show_bug.cgi?id=311293