Refactor Werkzeug requirement into flask

This is an early PR for discussion; it will be updated and cleaned up before proposed merging. This is a rewrite of the code base that removes Werkzeug and replaces the server code with a Flask implementation - see issue #38 .  For now much of the server lies in ga4gh/__init__.py and it's a bit kludgy

Topics for Discussion:
* Do we want the server in ga4gh.__init__.py ?
* Should ga4gh/protocols.py be renamed models.py?
* Should this be a branch?