Fix -check all runtime errors (for CCPP) using zero-size allocations

[grantfirl]

Description

This PR at least partially addresses ufs-community/ufs-weather-model#2023 (at least any runtime errors associated with the CCPP). The strategy is to simply make sure that every variable is allocated, although for variables that had been conditionally-allocated to save memory, they are now being allocated with zero size. This has a ripple effect in other repos where one needs to change from checking whether a variable is allocated to whether the size is > 0.

Note: 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.

Issue(s) addressed

ufs-community/ufs-weather-model#2023

Testing

This was tested with the full RT suite on Hera with the -check all compilation flag added in the ufs-weather-model Intel.cmake file. All tests completed successfully with no BL changes.

Dependencies

• waiting on Fix -check all using zero-size allocations ufs-community/ccpp-physics#159
• waiting on a PR for https://github.com/climbfuji/ccpp-framework/tree/feature/dummy_allocate_inactive
• waiting on Change wgrs to zero-size allocation NOAA-GFDL/GFDL_atmos_cubed_sphere#315

[grantfirl]

This is replaced by #789 that is targeted at the RRFS release branch. This will likely NOT need to go to develop since a longer-term fix is forthcoming.