I have been doing a lot of research on MVC and file structure. Mainly I've been looking at how to start a new layout. I have downloaded a few open source applications to take a look at file structure and how files are developed.
In the first application it was set up to use the standard way (at least the way it seems to me) of putting all the controllers, models and views each in their respective folders. This is the way that all the books say to do it.
In the second application, all folders are in a modules_core or modules folder where each controller (at least what I would assume to be controllers) are in a folder in there that contain three folders: controller, model, view.
Which of the two versions is accepted as standard and common practice? Are the two applications different because of versions of Codeigniter?