Hi Tom, thanks for your reply. I moved everything that was in /staff into the root, not just the index.php. I did try just the index.php initially and tried to play around with .htaccess, but couldn't get it to work so I moved it all and fixed as many location-related dependencies as I could find.
That's why it seems odd that loading index.php brings up a login screen when I'm already logged in.

Maybe you modified some references to files that were originally in the staff folder and concequently broke it? You only need to fix the dependencies to files outside the staff folder because their relative positions were changed when you moved files/subfolders from staff to the root. On the other hand, the relative positions among the files and subfodlers inside the staff folder remain the same, so you shouldn't modify the dependencies among them. If you do, something undesirable will happen.