I'm still new to the open source world so I hope this is the right place to post about issues like this. From a recent clone of the jgit source (1.2.0 I believe). The DiffEntry.scan method appears to be filtering out files with no content(sha) changes. This is causing changes to executable permissions on a file to be missed in differences. Normal git diff on two commits will report permissions changes but the jgit command line will not which I think stems from here. I've gone through the contributor guide wiki page and did a search on the jgit bugzilla project and wasn't quite sure how to proceed from here... Any advice would be greatly appreciated.