CORE-3451: use the Forester library to parse most tree files
CORE-3451: made several changes suggested by lein-kibit and lein-eastwood
CORE-3451: added code to identify NeXML files
CORE-3451: began implementing the code to handle NeXML files
CORE-3451: finished implementing the code to handle NeXML tree files
CORE-3451: made some more changes suggested by lein-kibit
CORE-3451: removed some unused configuration settings and dependencies
CORE-3451: write text directly to a file when serializing NeXML trees as Newick
CORE-3451: documentation updates