The project Model contain some tools to modify directly the geometry such as scaling, translating, and rotating. This really affects the geometry and not only the transformation matrices.
When you create your own geometry classes you have to provide a "model" method to be able to work with this project on your geometries. The method gets the transformation matrix as parameter and has to performs the transformation.
Copyright © by the Sonderforschungsbereich 256 at the Institut für Angewandte Mathematik, Universität Bonn.