Iw as hoping maybe someone might have come across a similar situation. I was updating my theme and on autopilot when I realized that I had thrown all the file into the Root directory. bad move on my part. After sifting through them and removing them, the site seemed find but I am using WP Supercache so I most likely didn't see the changes.
After a while, I started receiving this error: "Fatal error: Call to undefined function get_header() in"
Realizing that I had placed the theme Index.php file in the root, I quickly did a full re-install of Wordpress to make sure there were no other culprits. I also re-installed the theme as well. The tree structure in the root directory looks just like Wordpress. Problem, however, still remains. I thought I was getting a cached version so I deactivated all plugins and deleted the WP Supercache's current cache. I switched the theme to Twenty Eleven basic the and I still get the same Error.
The Index.php file in my root directory matches that of the current Wordpress file and everything looks fine but I still am getting the Error and I am a bit stumped as to where this would be coming from or why given that I am using the Wordpress theme twenty eleven.
Just thought I would ask to see if anyone else had a similar issue in the past and if they could share some wisdom. Thanks in advance