Hm well then I'll go without subfolders, though that will get messy with 60+ files xD

What's the matter? I don't think you understand. Graal will create a folder with the name of the playerworld, for basically everything on clientside (should it include file/folder modification) in the scriptfiles folder. You cannot avoid that.
Are folder names really that important to you?

Well they aren't but I didn't want it server-based :p

Do you want to create something you can use on several servers?

ya
well atleast that shares its data if the script is used on 2 servs

Can always use an IRC channel to synchronize data in between servers.

Well its not between servers, more like a script should be able to access teh same data (saved on the players pc) from several servers

Well, I don't really have any experience with file manipulation clientsided, but if that doesn't work out as you want you can always use requestURL to send/load personalized data from a webserver (assuming you have access to one).