The "Stage All" button seems to NOP when there is something it doesn't understand in the "Changes" list on the Source Control navigator. See how you have those "?" items? I believe that is what messes it up - it can't "Stage All" because it can't Stage these. I staged the ones it could one-by-one and then cleaned up the question mark ones. How to deal with the question mark ones? It depends. In my case I created a separate commit record and pushed it, figuring i could always back that out later manually. It basically pushed nothing so I left it.