Previously transcript-protein links were assumed to always be
indexed by transcript, and cached entries were allowed to have
a `null` protein (meaning caching the knowledget that there is
no link for this transcript).

Now we can cache links in both directions. Both transcript and
protein are allowed to be `null` (but not at the same time),
and the protein column has a new unique constraint.

The Werkzeug reloader is disabled by default due to a bug with
using it in combination with `python -m mutalyzer.entrypoints.website`.

https://github.com/mitsuhiko/werkzeug/issues/461#issuecomment-139369694

By default, the first request to the SOAP service will trigger a
build of the WSDL document, using the context (service location)
from that request. For example, if the first request is on
`http://localhost/` and subsequent requests are on
`https://mutalyzer.nl/services/`, they will not have a valid WSDL
document.

This is actually what we do on our production infrastructure,
where the service is tested (on localhost) after it has been
started.

The fix is to force a build of the WSDL document and specifying
the location to use.

http://spyne.io/docs/2.10/reference/server.html#spyne.server.wsgi.WsgiApplication

This is quite a large commit, touching many things related to developer
documentation. It is all focussed on getting as much of this as possible
into the new Sphinx-based documentation.

Some highlights:

- Start Sphinx-based developer documentation, including fairly complete
  instructions for installation and configuration.
- Remove epydoc API docs.
- Rework some docstrings to conform to reStructuredText, so they can be
  used in the API docs generated by Sphinx.
- Move all of the top-level text files to reStructuredText so they can
  linked from the Sphinx-based docs and for consistency.
- Remove many obsolete things from the extras/ directory, including old
  installation scripts and migrations.

Many of the installation related documentation and scripts are removed
or adapted in light of the new automated deployment using Ansible.