An unintended consequence of #788 is that the diff after a pull is now being performed in the reverse direction, for example files added are being treated as files deleted.

This is because on this line, both diffbase and diffCompare are now being used, to accommodate checkout, rather than previously only diffCompare. When diffCompare is set then .. is added:

As an example if a branch is currently at commit ID 1234 and a pull is performed the diff is now being performed as git diff ..1234 rather than the previous (and intended) git diff 1234. One can easily observe what is happening here by observing the difference between git diff HEAD~1 and git diff ..HEAD~1 on practically any Git repository.