This directory contains different configuration stages. More info you can find in other section of documentation.
Engine directory is heart of CMS. Here under the hood main horsepower =).
Libraries that can be installed via packages system. Read more information about packages in other section.
Modules are also part of packages. But here we can find default two modules: Core and User.
Core module contains code for general classes of CMS. Also it implements admin panel logic.
User module pointed on work with users.
One more type of package. Plugins exist for defining additional logic by system events (events handlers).
Var directory is for main garbage =). Contains: logs, temp files (that currently processing), system data (metadata about packages), cache.