Fixes a number of warnings in the documentation build:

• add empty lines where sphinx requires
• Fix explicit markup warning (*.cmake is interpreted by sphinx as the start of a bold markup)
• Fixed ill-formed admonition (this admonition wasn't showing up in the document)
• Fixed duplicate label

Also, my emacs write-hook clears trailing white space so there are a few white space-only diffs. Let me know if you would prefer that I not do that.

Clean (remove _build folder) and build.
Only warning is the 404.rst consistency warning about toctree inclusion.