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Did you compare these files with the originals from The XOOPS archive? What was altered?
Mosttimes when a lot of files are altered this means that someone has got access to your site by compromising the server software (in this case probably several other sites which are also located on this shared server are also affected) or through your ftp access (in this case, the probable cause is a virus, keylogger or other malware on your PC).
After correcting the cause and blocking the access path, reupload the original files from an earlier backup and alter all passwords (FTP, server, MySQL, XOOPS admin).