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 .
I agree with Jerome that Wrkzeug -> Flask should be a single PR, with only
necessary changes in it. I know that it is a pain to break up a change into
several small minimal units, but it allows for more in-depth review of
complex parts and easy progress on simple parts of the change. For example,
we can discuss the hamlish-jinja addition separately from the choice to use
Flask.
Kerry

On Mon, Dec 8, 2014 at 3:08 PM, Steve Hershman <notifications@github.com>
wrote:

> In config.py:
>
> > @@ -0,0 +1,2 @@
> > +DEBUG = True  # Turns on debugging features in Flask
> > +BEACON = True
>
> 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.
>
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> <https://github.com/ga4gh/server/pull/40/files#r21480981>.
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