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 .
Flask is best launched with a config.py, but this does go against the CLI.  We should make a design choice if we want a command line or config (or both)  As the code grows and we're able to host variants, reads and references, I think the amount of config that will need to happen on the command line will grow to the point where a config.py file will be the better solutions.