The Application component maintains the state of the application. It gets input from the interface and it tells the VisGen what geometry to generate. This is where a lot of the application dependent code is stored. This helps make the interface component simpler and at the same time facilitates reuse since both the CAVE tool and the Desktop tool use the same Application component.
Since the Application component maintains the state of the application, it can also be made to store that state. This would allow the user to "save" the state in some session file and restore that state at a later time.