Update SCM to the latest ccpp-physics/framework main

[grantfirl]

This pull request catches the SCM up to the latest ccpp-physics main as of Jan 25, 2022 and implements changes to be consistent with the fv3atm pull requests listed below.

Associated PRs:
ccpp-physics

• Fixed bug in cloud diagnostics, removed over counting. ccpp-physics#806
• Modification of momentum roughness length over ice in the surface layer scheme ccpp-physics#808
• Using relatively new Thompson cloud fraction scheme, tune a few things to cause fewer overall clouds, particularly high clouds ccpp-physics#809
• Enforce tracer column mass conservation in TVD schemes ccpp-physics#812
• fix the tsurf issue in Noah MP driver ccpp-physics#816
• Wrapper for #806, #807, and #813 ccpp-physics#817
• Wrapper for #808 and #816 ccpp-physics#818
• Wrapper for #812 ccpp-physics#819
• Bug fix for dimensions of eta level variables in metadata, remove duplicate Fortran modules from CMakeLists.txt ccpp-physics#821
• MYNN sfclay restart reproducibility ccpp-physics#822
• Radar-derived microphysics temperature tendencies similar to operational HRRR ccpp-physics#823
• Sm nov222021 ccpp-physics#824

ccpp-framework

• Update README.md, remove README_TODO.txt ccpp-framework#425

fv3atm

• CCPP cloud cover change for Thompson MP associated with Xu Randall NOAA-EMC/ufsatm#443
• Use 'model set run clock' routine in FV3 NUOPC cap. NOAA-EMC/ufsatm#450
• Bug fix for dimensions of eta level variables and WAM variables in Fortran code and CCPP metadata NOAA-EMC/ufsatm#431
• MYNN sfclay (RAP suite) restart reproducibility, P8 suite definition files NOAA-EMC/ufsatm#455
• Radar-derived microphysics temperature tendencies similar to operational HRRR NOAA-EMC/ufsatm#457

Testing

• ran multi_run_scm.py, plotted and visually checked results for TWPICE case
• ran SCM RTs: all tests completed successfully with different results for the GSD_v1, RRFS_v1alpha, and GFS_v16 suites due to changes (at least) to the Thompson MP (GSD_v1, RRFS) and satmedmfvdifq PBL (GFS_v16) schemes.

[climbfuji]

One type in GFS_typedefs.F90, which is probably also in FV3atm and should be corrected at some point.

[grantfirl]

@mkavulich This is an example of a SCM pull request that "catches up" with the other repos (ccpp-physics, ccpp-framework, and fv3atm). All changes in here have been reviewed somewhere else, so this is typically an easy review. Would you like to take a look before I merge?