I want to create a small shared hosting on a VPS. Every client will get the same PHP applications, but over the ftp he can only change the template. The application is built under CodeIgniter using MVC Structure. Controllers and models are stored somewhere in the system. I am choosing this method, instead of encoding files with zend/ioncube, because they can be decoded and my work is lost.

This is why I don't want to have a client which will upload the shell and steal my scripts.