switch to autoprogram for all scripts

synchronize tests
remove out-dated files
Install sphinx-contrib.autoprogram when needed
add PDF generation to Makefile, doc env vars
remove references to the word 'hash'
mention unification behind @camillescott's khmer_args
make clean is now failproof
Merge pull request #344 from ged-lab/feature/new-docs

use the sphinxcontrib.autoprogram extension to pull the argparse parsers from each script so that the documentation auto-syncs with changes in each script's option