Fix hal2maf for bed version > 9
conserved 4d site extraction

Also reading frame preservation, fixes, and tests
Fix 4d site problem w/ multiple sequences
Fix 4dExtract problem w/ intra-exon duplication

(hopefully)
Fix wiggleLiftover on extremely small genomes
Fix not being able to reuse WiggleLiftover classes

WiggleLiftover calls WiggleTiles.clear() after one conversion, but
clear() didn't set the genome length to 0, which caused WiggleLiftover
not to re-initialize the tiles properly.
update from melissa to add include for pcre in phast.
Update README.md

add contributors list
change exception to warning when running hal2maf with default params on empty genome or seuqnce
add header to empty maf
revert last change
add clang check before adding stdlib in include.mk
Merge remote-tracking branch 'origin/development' into chains