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I just moved the files to a subfolder, CHMOD mainfile.php to 777 so I could update the information in in, then CHMOD it back to 444. After that, I could get the index.php file, but when I tried to log in, I got redirected to the location for my old user.php. I had to leave the computer a while and when I came back, I tried again and it worked. It was probably some cache function in my browser that messed with me, now everything seems to work just fine. I updated all my modules just in case and then I had to fix the settings for all my blocks since the update function resets all the settings..
