Okay so I was, and may still be, using wordpress 3.5 on a client's site. They were getting annoyed by the upgrade now message on the dashboard and asked me to upgrade it for them. I had never upgraded before and just downloaded the new version and copied it over the old one. Now on the server I can delete and change anything I want (css files, html pages, header images, etc.) but it doesn't do anything to the actual site. WordPress itself still operates. I can add pages, upload images, create users etc. and would not have a problem if I didn't have an html home page that while on the server comes up with a 404 error. I also would like to add a couple plugins but since it is done on a server level it won't show up. I have been trying to fix this for over a month now and am really frustrated at this point. I have deleted everything from the database, that only removed the wordpress info, but the problem persisted. What else can I do? Any help is greatly appreciated.