bugfixes:
bugfixes:

- made sure that prespecified files didn't cause problems if they're
  in canonical locations
- added explicit memory usages to all java invocations
- renamed some cachepipe calls

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