Lots of changes to further merge domain model objects and document pipeline

Quite a few changes here.

Pay particular attention to handling of authored examples and the newly added customizations package.  I think we need some way to organize the various customizations but I'm not sure if this is the best way or not.

With this PR, you should be able to generate interactive help with all JSON and Shorthand examples plus any authored examples that have been added.  There aren't many yet.  You should also be able to run ``make html`` in the ``doc`` directory and generate the HTML docs, also including all examples.