The UML markup for the various classes is found in Graph+Edge+Node UML.png and CyFinder other uml.txt (the names are self-explanatory). It is placed there because there is far too much UML to place as-is inside the diagram, so use that as a reference.

The graph probably doesn't have as many links as it should as the program is more or less about single objects that process other objects instead of object-object relationships (which is seen in the graph thing). Often the objects inherit from other ones (see: Algorithm). And yes, CygrouperEdge doesn't reference CygrouperNode at all.