Working on #1 : What works and what doesn't:
The example in inst/tests/inheritance.R should run using the class
definitions in R/inherited_classes.R.  Other class definitions are
obsoleted by these updates and should eventually be removed.
The ape methods should be unaffected, since the S4 classes have the
same structure as before, only defined through inheritance instead.

ToDo:
- Remove the obsoleted methods in classes.R, nexml_read.R and nexml_write.R
- Check the ape.R unit tests, update other unit tests
- Write remaining essential classes out by hand based on
inheritance and schema definitions: e.g. edge, otu, otus, tree, trees, nexml