you want directories? really?

[Angus]

I would use subdirectories for local backup of programs and data. You can easily delete or modify a program by mistake. If you are in the field and don't have access to your computer there is no chance to recover the functionality of the prime....
Some kind of write/delete protection could do the job or, maybe, there already is some concept I don't now?

When thinking about the apps. Storing different copies of app data (complete Variable set maybe) in a subtirectory of that app could be handy to switch between them. Just load a set and do calculations on that.

However I am aware that I am kind of trapped in old-style thinking. Discussions like this are really helpful.