Update doxygen documentation in fv3atm so that doxygen builds without warnings

[edwardhartnett]

Description

As discussed at a recent meeting, we will update the doxygen documentation in fv3atm. We want to build doxygen with all warnings turned on, and have the fv3atm documentation build without warning. When this is the case, we can turn on documentation checking in CI, and no one will be able to merge code without full documentation.

Solution

We have to add missing documentation elements everywhere. Programmers must fill in missing information. This will take a while!

@AlexanderRichert-NOAA and @edwardhartnett will add the missing doxygen elements, but only fv3atm programmers can provide the needed information.

Alternatives

Doxygen is what we use all across the EMC, so we don't want fv3atm to be different from all other EMC software. Also doxygen is effective, simple, and provides all the features we need. It's also very common and well-understood by the programming community.

Testing:

The CI build has been modified to build docs and upload them to GitHub, so anyone can download a zip file from GitHub actions and see the built documentation.

Dependent PRs:

N/A.