I stumbled upon this while reading some magazine, Minix is an OS. It doesn't have anything to do with PHP. However, i like the way it's made. In short, here is how it works: We have the Minix core, and outside that we have all the "modules". This gives alot more stability, and in PHP, it would also give alot more flexibility. Then you create a simple core and outside that, you make all your modules. Lets say you have a framework, then you just make some system folders for all the standard classes (instead of modules), and in another folder called application, the user can make his own classes there. Rest of the thinking is up to you, anyways, what do you think of it?
So you are saying the way minix is setup would work well with PHP?
If so, i would recommend you look at some PHP frameworks, they are setup just as you show, particularly Cake PHP, all the backend is in a completely different folder away from development.
If you meant use this as an OS for an PHP web server, i would say its going too far for small scale websites use LAMP (linux apache mysql php) and for larger applications, start moving away from apache and mysql to say lighttpd and oracle, but linux and PHP are very scalable and will run even the largest of websites!