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Ok, you could have uploaded the files in the HTML folder to your site's root folder, which woiuld make the url be
http://www.yourserver.com/index.php. What you can do now is download the files from your server to your harddrive, change the paths in mainfile.php manually, removing the html/xoops/ parts, and upload the files to your server root folder. Update the cache files by going to system admin -> preferences -> general settings, and click go at the bottom of the page. This should do the trick!
Herko