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If you are leaving the xoops_lib and xoops_data folders inside your web root directory, you should rename them with a random prefix as eg b3f6_xoops_data and change the value in mainfile.php for it.
I also have doubts on how much security is gained with this separation to inside and outside webroot.
If it is really required, then you should not allow installation on servers, that don't offer the possibility of having directories outside the webroot and executing PHP code from it.
From my understanding, was the main purpose of this outside webroot idea, that one can not enter the site on this code and could not harm the site. This makes the programming in a way easier, because the program didn't have to be hardend for various kinds of attacks. You have only one interface (the code left in the normal module directory in the webroot) and this should gard the info passed on to the outside code.
But when you allow it anyway from inside the root, then there is no possibility for this kind of 'lazy programming' and the program should be hardened to its full (Ironically demonstrated by the countless website attacks on the Protector module these days).
With that, the need to have it on a separated directory is no longer much of a security gain.