Question: Is there a way to REMOVE a DIV of the master page? not hide, there are some hyperlinks in the div, so I want to remove them from the code as well. thanks

Answer: 
Hierarchical model–view–controller (HMVC) is a software architectural pattern, a variation of Model–view–controller (MVC) similar to Presentation-abstraction-control (PAC)，[more info in wiki](http://en.wikipedia.org/wiki/HMVC)  

I hope you have enjoyed [this tutorial](http://net.tutsplus.com/tutorials/php/hvmc-an-introduction-and-application/).
I suggest you use links placed in the directory you desire pointing to the folders in the application folder. I wouldn't recommend moving those folders out of the application folder. 

Cheers.