[jameslk]

That's not what the OP is getting at. He's referring to the common file organization of projects where, for example, in MVC, the models are located under a models directory, the controllers under a controllers directory and the views under a views directory.

If I want to understand what the code does, looking over the code and seeing just a bunch of models or controllers is next to useless. Instead, the code should be organized semantically by the domains of the application. I should be able to look over the various directories and files and have a high level understanding of what the application does, not that it's just another MVC application.

This semantic organization also promotes encapsulation since only things related to each other are near each other, instead of scattered throughout many directories organized by arbitrary architectural concepts.