windows compatibility and misc fixes

Three changes for Windows compatibility:
* use f.read().splitlines() instead of removing '\n' in FAVE-extract
* use os.mkdir() instead of os.system('mkdir') in FAVE-align
* use shutil.rmtree() instead of os.sytem('rm -rf') in FAVE-align

Also, stopWords wasn't being logged correctly if you use a custom stopWords file, so I changed all the stopWords references to just use opts.stopWords since everything that needs stopWords also has access to opts