If you arent worried about encryption, GDK has some commands that take advantage of I think its windows built in file compression, to store directories and files as a "pak" file.
The commands I think you might want to have a look at are called :
dbReadDirBlock();
dbReadFileBlock();
dbWriteDirBlock();
dbWriteFileBlock();
GDK has a bunch of inbuilt file handling commands, most of them are just wrappers around the windows functionality, but if you arent familiar with these operations in native windows, the GDK commands will make it easy to get an idea of how it is all working.
But, like I said, the drawback is that there would be no encryption that you could call secure. So the above methods would be more for tidy organisation of files rather than keeping people from prying into them.
If it ain't broke.... DONT FIX IT !!!