After upgrading to 1.9, changes that I made were staged automatically.

NOTE: This might be an upgrade-only issue. I saw it when upgrading from 1.8.1 to 1.9, then I did not see it again after going back to 1.8.1 and then upgrading to 1.9 again. Since I've seen a complaint about the "Use Staging Area" option being off by default in 1.9, this could be related to that problem.