Add utility script documentation to the Users Guide, moved to standard sphinx directory structure and names

[edwardhartnett]

DESCRIPTION OF CHANGES:

In this PR I set up sphinx/readthedocs so that the python scripts in the ush directory are included in the documentation. Not all scripts have documentation written yet - but that will come in future PRs. Also moved files into standard sphinx directory structure.

No code changes in this PR, only documentation. I had to add a lot of .rst files to the repo. Unfortunately, this is just a byproduct of sphinx. It seems to be how everyone does things, so we just have to live with them.

TESTS CONDUCTED:

N/A

Machines/Platforms:

N/A

Test cases:

N/A

ISSUE:

Part of #502

[MatthewPyle-NOAA]

No fears on merging documentation changes - will get this one merged in case other outstanding PRs require more work to merge.