Adding CESM Makefile

Adding the used for building MPAS-O within the CESM.
Fixing an issue with wind stress in forcing.

Creating surfaceWindStress variable to house the forcing at the surface
of the ocean.

Modifying coupled forcing module to use this variable rather than the
old windStress version.
Fixing issues with forcing var_struct.

Moving some variables in, and fixing incorrect variable names used in
forcing var_struct.
Causing makefile to pass CPP flags to CPP

This affects Registry. The CPP of Registry doesn't currently pass
$(CPPFLAGS) or $(CPPINCLUDES), so sections of Registry.xml aren't
appropriately ifdef'd out.
Comment out non-existent time average coupler.

Also, setup coupling alarm id.
Fixing references to windStress in coupler driver.
Fixing up references to state that should be forcing.
Temporarily making variables not input.

vertCoordMovementWeights is now not an input.
seaSurfacePressure is not not an input.

Both of these changes are just to allow MPAS-O to build/run in CESM.
Adding a pointer association for surfaceWindStress
Adding coupled time averager.

This is responsible for updating the fields that get sent back to the
coupler for computation of fluxes.
Some cleanup to get MPASO working in CESM.

Adding calls to init constants, fixing up coupled time averager.
Turning off history attribute read in (CESM's PIO dies on this).
Some fixes for surface fluxes.

Fixing units and masking on surface fluxes.
Making ESMF_Finalize not called if built in CESM.

Previously this would finalize MPI after the ocean was done running, and
cause an issue where CESM would still call MPI after MPAS finalized it.
REMOVE LATER: Fixing an issue with tracer_min

This is incorporated into another branch and should be removed from this
branch later.
Initial setup of mpas_units module

The mpas_units module is intended to allow access and modification to
the unit numbers for stdout or stderr.
Update ocean core to use units from mpas_units

Modifying write statements to use the unit numbers from mpas_units
instead of hard coded unit 0 and 6.
Fixing an issue with mpas_units.
Adding grad_ssh computations.
Removing print of Tk value.

It was used for debugging earlier, and is no longer needed.
Adding sea ice formation flux.

This flux is called the q-flux in POP terms, but it computes the
formation of frazil ice on the ocean time steps.

Currently it's using a hard-coded freezing temperature of -1.8C, and
hard-coded density values which are provided through mpas_ocn_constants.
Fixing some small issues:

Allowing the unit numbers to start at 0, for the case of stderr.

Uncommenting out the 360day calendar.
Cleanup of some comments for coupled forcing.