Purge of old trees.
Deleting old Matlab formatting scripts to avoid confusion.
High level organisation of loading trees and running inference in main.c, based on command line options.
Super ugly but backwards-compatible implementation of saving output to file.
1) Generate trees in /whole, /split/1 or /split/2 as appropriate
2) Delete unused intermediary tree files to save space
3) Handle rare dendropy errors in the split tree case