fixed parsing and serializing of ape trees.
See new tests: (new) test at bottom of test_ape.R now runs successfully
Some restructuring file structure for methods definitions: classes is just classes,
methods now separated into write and read. Could still benefit from some cleaner logic.

Top level coercions to nexml and serializing to XML need work.
In particular, need to define otus seperately. Should define
defaults with some basic metadata too (licenses? author?)