Removed mac endlines in .nex files; added (void **) casts to SafeFree calls
added (void **) casts to SafeFree calls
Runtime selection of BEAGLE implemented
Turned off moves that do not work with codon models.
Two BEAGLE flags are working; however, need to make specification at the data-partition level
 fix "set usebeagle=no"
Initial BEAGLE options seem to all be there
pinvar fix
fixed compilation without BEAGLE_ENABLED
Fix of omega variations.
Added stubs for the BEST model.
Specifying precision for user
omega variation fix 2. 
Note that due to different random number generation sequence results look still different between Beagle and MrBayes but that is not a bug.
Solved problem with starting values associated with changing the number of chains.
changed BEAGLE settings to be passed as preferences, so fallback to BEAGLE CPU is automatic
Added best files.
Some progress towards integrating best.
added some TODO comments to mcmc.c with suggestions for improvements to how BEAGLE is called