Add comments and doc changes from walkthrough sessions

[mcgibbon]

Purpose

Over the past two months we've held fv3core walkthrough sessions with Lucas and others from GFDL. This PR adds the comments and documentation changes we wrote during those sessions to the dynamical core, including many TODOs.

Code changes:

• Renamed some internal functions and variables, updated docstrings and added comments in pace.fv3core

Checklist

Before submitting this PR, please make sure:

• You have followed the coding standards guidelines established at Code Review Checklist.
• Docstrings and type hints are added to new and updated routines, as appropriate
• All relevant documentation has been updated or added (e.g. README, CONTRIBUTING docs)
• For each public change and fix in pace-util, HISTORY has been updated
• Unit tests are added or updated for non-stencil code changes

[elynnwu]

launch jenkins