update rm2state to apply to repet as well
update copynumber tracks to new lastz results
add reminder of old copy_cv track that unwittingly was lost in last change
option to never use log when running setTrackScaling
add extractMonomers script to reproduce polyns and polyas tracks
revise polya poly n business
fix bug where cleanTermini wasnt run on overlap and palindrome tracks
add some options to trackRanking
small cleanup of preprocessor.  now add basic flag to xml to govern action taken.  still needs some work especially for tsd generation scheme
Merge remote-tracking branch 'origin/development'