All inheritance-based classes appearing in inst/examples/trees.xml now implemented
inherited classes now replace all the original classes
start cleaning up old read/write methods obsoleted by toNeXML/fromNeXML methods
test_ape.R unit tests now passing.
Should still revise the coercion methods in nexml_write.R to something more clever.  We aren't
coercing a tree to a nexml, we are building a nexml from a tree.  Likewise handling
the otu assignments of species names should be done directly
updated nexml->ape conversion to get tip.labels from otus
instead of just using the otu attribute on the node, which simply corresponds to the id of the otu element in otu.
the taxon (species name) is in the label of the matching element instead.  Still needs some testing and a unit test
to confirm the label is correct.  This addresses 1/2 of #8.

Still need to handle the case of coercing ape->nexml, in which a method generates the otus node from the tip.label list
and matches the id to node's otu attribute.  This means that ape->tree doesn't look at tip.label, but just generates
locally unique keys for the node otu attribute