Second reconciliation PR from production/RRFSv1

[grantfirl]

Description

This PR is analogous to #789 into production/RRFS.v1

Note that although the original PR contained a temporary fix for the -check all issue for NCO adoption, this temporary fix is no longer needed due to other changes in the CCPP framework and fv3atm that have already been merged. The associated changes to the ccpp-framework and atmos_cubed_sphere are not needed (and are not included in this PR) since we're no longer allocating all variables to zero size. Variables can successfully remain unallocated.

This PR does contain the following changes:
There was also some cleanup done to remove variables that are declared in GFS_ and CCPP_typedefs.F90 but are not being used anywhere anymore. In addition, the ACTIVE attribute in the metadata files was double-checked for every conditionally-allocated variable.

Some of the changes to the active attribute required follow-on changes in the CCPP physics: ufs-community/ccpp-physics#228

Issue(s) addressed

None

Testing

This was testing using the full rt.conf on Hera. The -check all flag was added to the debug mode in the Intel.cmake file for testing and no runtime errors were noted in the RTs

Dependencies

waiting on ufs-community/ccpp-physics#228

Requirements before merging

• All new code in this PR is tested by at least one unit test
• All new code in this PR includes Doxygen documentation
• All new code in this PR does not add new compilation warnings (check CI output)