start integrating Melissas phyloP module
add enable def to compiler opts
rejig phylop build parameters to hopefully work on linux and mac.  some cleaning still needed
fix from melissa
test dir from melissa
make test.sh executable
reduce output float precision to 3
merge development
revamp hal2maf to use halBedScanner
add --baseComp option to halStats
add option to copy the halfile to the assemblyhub outdir
add hal4dExtract tool and consolidate mask and extract dirs
try to avoid leaving empty output files
let refSequence and refTargets get used together
add get tree
add script for phylop neutral model
add missing extract files from prev commits
switch halPhyloP argument order to be more consistent with other hal tools
turn outWiggle from option to argument
add halPhyloPMP wrapper