Updated scripts to use add_threading_args from khmer_args (issue #383)

Removed khmer/threading_args.py as it is now depreicated and irrelephant.

Resolves #383

Removes code. Yaaaay.

- [x] Is it mergable
- [x] Did it pass the tests?
- [x] If it introduces new functionality in scripts/ is it tested?
  Check for code coverage.
- [x] Is it well formatted? Look at `pep8`/`pylint`, `cppcheck`, and
  `make doc` output. Use `autopep8` and `astyle -A10 --max-code-length=80`
  if needed.
- [x] Is it documented in the Changelog?
- [x] Was spellcheck run on the source code and documentation after changes
  were made?
I believe @mr-c wanted consistency with the command line args and changing such would be an API change. Or.. Something along those lines