Clean up MPAS-Hydro repo to allow for generic nuopc cap development

MPAS-Hydro has a head start on a nuopc cap for MPAS standalone.  (Soren/Dan).
MPAS NUOPC cross project sync meeting:  Soren agree to clean up the code base to allow for generic nuopc cap development across Hydro, LIS, and MOM6.  (Fire model not funded yet).

https://github.com/NCAR/MPAS-Model-NUOPC-dev/tree/mpas-hydro