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rosata, Welcome to the XOOPS forum!
You have to move the two directories (if possible) outside the web root. This is to the directory where your public _htm is in.
For renaming, just put 4 random letters and/or digits in front of the name.
You have to alter the definitions in mainfile.php accordingly. (Beware to lift the readonly of mainfile.php!)
Fantastico is not always on the latest version, see 2.4.4 on the home page here. In the article, there is also a link to an installation manual.