How do I make sure that a folder-based class can find its methods after the application have been compiled for deployment with MATLAB compiler?

I have an application with a bunch of folder-based classes. In the GUI for the 2014a version of matlab deployment tool, when adding all the necessary files, if I add a folder it just adds all the files it contains individually. That makes all the methods of different folder-based classes to mix up.

But that's not a problem as my classes don't contain methods of the same names. What is a problem is that it seems like the main program can't call them!

The main program is a class itself and one of the first things it does is it calls one of its own methods. It works fine when run in matlab, but the compiled version only pops out an error reading:

No appropriate method, property, or field BLAH<method_name> for class BLAH<class_name>

Is there any way to show the MATLAB compiler where the methods are stored? Can I make it work?