[eluser]Dam1an[/eluser]
But would he not just be able to mess it up wherever its stored?
I know you can change the location of the view folder by changing the constuctor in the Loader file (in system/libraries)
The model loading is also done via that class, so it's bound to be in there somewhere
As for changing the controllers location, that would be somewhere in router.php I'd imagine
If you do decide to take this route, be sure to extend the classes with your own so they don't get lost if/when you upgrade