begin to add doxygenation to the code

[edwardhartnett]

We will doxygenate the source code as we have done for many other EMC projects.

I will provide a sample and some training, and we will start to update as we touch the code in development or testing.

Testing can provide many opportunities for documentation improvement. @AlysonStahl-NOAA anything you learn from @webisu via meetings or other interactions should make it into the code base as documentation updates. For example, if you are testing some function, and have to ask a bunch of questions to figure it out, make sure that the answers make it into the docs.

We'll start this after the 3.4.0 release.