Sorry, I should have gotten back to you earlier. It's a bad time of year for this because the weather here is so nice that I'm spending all of my time outside.
The diff was definitely problematic because it didn't pick up the new locations for any of the files. I also had some problems with inconsistencies between our source trees because of changes I've made since you last pulled from the repository.
Unfortunately, at this point I think the simplest solution is going to be to pull down a fresh copy of the Git repo, reproduce your file moves with git mv, and then copy over the changed files from the original edited source tree (so don't overwrite it with the new copy
). The git diff for that should cover all the changes and as long as I don't make any further changes it should apply cleanly here.
You could also try git adding all of the moved files again, but I'm not sure if that will retain their history and it won't solve the inconsistency problem.