Controllers
Controllers are scripts containing the main PHP logic for creating output for a web page.
Controllers do not contain any visual elements, as they gather all the data necessary for displaying content and send it to a template view for stitching the data with the visuals.
Page Controllers
Page controllers are located in the folder named pages/ e.g. pages/index.inc.php. Their purpose is to control the output of a web page.
Partials Controllers
Partial controllers, also known as boxes, are the files located in the folder ~/includes/boxes/ e.g. ~/includes/boxes/box_latest_products.inc.php. Their purpose is to control the output of a partial area of a web page.