brief commit before merging with trombone; minor changes
Merge branch 'master' of http://github.com/dbarkan/pcss

Conflicts:
	doc/todo.txt
	lib/pcssIO.pyc
	lib/pcssTools.pyc
	test/runs/develop/annotationOutput.txt
commit trombone in preparation for merging with new ff sequence feature files
merging with changes to ff files on trombone
commit before trying out on cluster for the first time