bugfix: combine alignments AFTER all chunks are done
bugfix: combine alignments AFTER all chunks are done

-numjobs now affects parsing

ability to toggle sentence-level filtering

changed how thrax dir is generated to ensure (increase the chances
of?) uniqueness

lukeorland/joshua,lukeorland/joshua,thammegowda/incubator-joshua,fhieber/incubator-joshua,kpu/joshua,gwenniger/joshua,fhieber/incubator-joshua,thammegowda/incubator-joshua,gwenniger/joshua,kpu/joshua,gwenniger/joshua,kpu/joshua,thammegowda/incubator-joshua,fhieber/incubator-joshua,thammegowda/incubator-joshua,lukeorland/joshua,thammegowda/incubator-joshua,fhieber/incubator-joshua,fhieber/incubator-joshua,lukeorland/joshua,gwenniger/joshua,kpu/joshua,lukeorland/joshua,gwenniger/joshua,thammegowda/incubator-joshua,lukeorland/joshua,fhieber/incubator-joshua,thammegowda/incubator-joshua,fhieber/incubator-joshua,lukeorland/joshua,thammegowda/incubator-joshua,thammegowda/incubator-joshua,fhieber/incubator-joshua,kpu/joshua,thammegowda/incubator-joshua,fhieber/incubator-joshua,gwenniger/joshua,kpu/joshua,lukeorland/joshua,lukeorland/joshua