Adding better usage notes that list commands and handling when no command is specified
Dropped comments referring to code long gone
Merge remote-tracking branch 'gsf/master' into gather_updates
address most but not all of pylint's complaints
don't hardcode Dnatural and ReDD versions in init method
use Dnatural/0.17 for full instantiations with only recommended directories
Merge pull request #7 from cokernel/update_dnatural_to_0.17

Update dnatural to 0.17