I forked a repo, then cloned it to my Mac into a /YATC
directory. I had a previously-created Xcode project (TwitterTimeline) in another directory, which I copied in
Not sure exactly what's happening but I was in the same situation
git add -A .
I got around it by renaming the subdir, doing git add
from a parent dir, then renaming the subdir back to the original name. Somehow that seemed to get git back in a working state.