Refactor Werkzeug requirement into flask

This is a PR for discussion is a rewrite of the code base that removes Werkzeug and replaces the server code with a Flask implementation - see issue #38 .
The *_dev scripts are only meant for development. The ga4gh_* version are actually the installed versions and are intended to to be used more widely, and are installed in the virtualenv that was created earlier in the instructions. So, I would back out of these changes to README, except for the spelling fixes on 'indicies'.