WIP: port over two files to using proper numeric indices for taxa
Trying defining AnnotatedTree to include the LabelTable.  Refactor Visualize under this assumption.
Pushing through the refactor of Labels.  Its pretty ugly.  NewickTrees should have been an ADT.  This rev typechecks but is still not finished.
WIP: thread arguments through parser.  But need to use a single map.
Fixed the known problems, but still seeing a bad distance matrix coming out
Fixed the problem and have good RFdistance again
There was a stack leak in the previous, which should be fixed now.  There is still no speed improvement (yet) from the new label representation.
No speedup from fixing the space leak, but switching over to IntSet does help a fair bit.  1.6 sec for 150 taxa 100 trees on my laptop