It kept crossing my mind that the code for NeXML was a little skimpy. I kind of felt like I was missing something. However, I had only been looking under org.cipres.treebase.domain.nexus.nexml. When studying this a little closer, I realized I am missing out on more than half the relevant code. Within the nexml-1.5-SNAPSHOT.jar, there is a whole set of important classes. Sure enough, Rutger even told me to study org.nexml.model*
And now the frustration sets in....GRRR.