BEAST:
o add commmand line option for setting package user directory
o more robust -version_file handling
o make beast script find BEAGLE easier on arm cpu
o allow BEAGLE usage for irreversible models, and make BEAGLE rootFrequencies input aware
o more robust AVMN operator, uncertain alignment
BEAUti:
o fix bug that prevented BEAUti from saving files if directory was removed
o make sure tip date operator is added when tips-only for MRCA prior is set
o add functionality for auto-configuring tip date
o allow 'Cancel' to stop BEAUti from closing
o make short-cut keys on OS-X use command key instead of control
Package manager
o selects CBAN clone if the default is not available
o add -dir option to switch user package directory
