Set Up Sphinx to support all sub-modules

[radumas]

Following Rick's Sphinx instructions, and the Sphinx-Gallery and Sphinx-RTD tutorials about folder structure.
Also bearing in mind this issue with multiple modules

• Move most Sphinx configuration stuff to the doc/ root folder and set it up to work with all of the sub-modules.
• It would be really nice to have Sphinx work with Markdown rather than .rst files so we don't have to duplicate README documentation...

[radumas]

Promising for markdown organization