* Start of fswthru by components

* Remove CESM2 MCT drivers

* Updated fswthru by components

* Update documentation

Update Version Index to Release Table

…Consortium#488)

* updated orbital calculations needed for cesm

* fixed problems in updated orbital calculations needed for cesm

* update CICE6 to support coupling with UFS

* put in changes so that both ufsatm and cesm requirements for potential temperature and density are satisfied

* update icepack submodule

* Revert "update icepack submodule"

This reverts commit e70d1ab.

* update comp_ice.backend with temporary ice_timers fix

* Fix threading problem in init_bgc

* Fix additional OMP problems

* changes for coldstart running

* Move the forapps directory

* remove cesmcoupled ifdefs

* Fix logging issues for NUOPC

* removal of many cpp-ifdefs

* fix compile errors

* fixes to get cesm working

* fixed white space issue

* Add restart_coszen namelist option

* Move restart_coszen to forcing_nml

* Update documentation on restart_coszen

Co-authored-by: Mariana Vertenstein <mvertens@ucar.edu>
Co-authored-by: apcraig <anthony.p.craig@gmail.com>
Co-authored-by: Denise Worthen <denise.worthen@noaa.gov>

* Update CPPs
Rename ncdf to USE_NETCDF (ncdf still works) and update USE_NETCDF implementation
Update NO_I8
Update NO_R16
Remove popcice

* Convert ORCA_GRID CPP to orca_halogrid namelist
Convert a RASM_MODS CPP to bathymetry_format namelist to support reading a pop vertical grid file
Convert gather_scatter_barrier CPP to add_mpi_barriers namelist
Document

* update documentation

* update documentation, remove coupled macros as this is going away soon and change cpp directive to cpp macro

Co-authored-by: Philippe Blain <levraiphilippeblain@gmail.com>

* Remove "coupled" CPP flag and replace as needed
  Remove "fake MPI" capability in serial/ice_communicate.F90
  Add ssh_stress variable/namelist with options 'geostrophic' or 'slope' to specify the computation of the sea surface height stress term.
  Add ssh_stress to ice_in, set to 'geostrophic'.
  Add ssh_stress to namelist documentation
  Change "coupled" to CESMCOUPLED in ice_init on check for oceanmixed_ice setting
  Clean up drivers
    remove "coupled" and CESMCOUPLED from standalone/cice as if neither were set
    remove "coupled" macro end_run call in nuopc/cmeps, CESMCOUPLED left mostly alone
    remove "coupled" and CESMCOUPLED from mct/cesm1 as if both were set
    remove "coupled" and CESMCOUPLED from direct/hadgem as if both were set
    no changes to nuopc/dmi, prefer dmi make those changes
Fix error in coriolis namelist documentation where Cstar was in the wrong place

NOTE: Coupled systems should leverage the new ssh_stress namelist to turn on the 'slope' option.  The coupled CPP flag is no longer in use.

* rename ssh_stress option from slope to coupled and update documentation

* update documentation

* update warning message for oceanmixed_ice

…ut, script warning messages for --set conflicts (CICE-Consortium#494)

* Add support for .cice_set (CICE-Consortium#464)
Add warning messages when multiple set options overlap (CICE-Consortium#243)
Fix namelist output diagnostic for atmbndy (CICE-Consortium#493)
Modify git clone in script to use --depth=1 (CICE-Consortium#492)

* update doc precedence

* update documentation, add info about .cice_set format

Co-authored-by: Philippe Blain <levraiphilippeblain@gmail.com>

Send broadband fswthrun by categories to coupler.

This integrates the sw_redist changes from Icepack into CICE.

Add three new namelist, sw_redist, sw_frac, and sw_dtemp.

The alt03 and alt04 test cases have been updated so that ktherm=1 is bfb. The default settings are such that ktherm=2 is bfb. This is the other piece to addressing issue CICE-Consortium#485 and CICE-Consortium/Icepack#280.

* update icepack to 4c42a82

* remove two failing test configurations with iobinary due to bathymetry netcdf file requirements

* updated orbital calculations needed for cesm

* fixed problems in updated orbital calculations needed for cesm

* update CICE6 to support coupling with UFS

* put in changes so that both ufsatm and cesm requirements for potential temperature and density are satisfied

* update icepack submodule

* Revert "update icepack submodule"

This reverts commit e70d1ab.

* update comp_ice.backend with temporary ice_timers fix

* Fix threading problem in init_bgc

* Fix additional OMP problems

* changes for coldstart running

* Move the forapps directory

* remove cesmcoupled ifdefs

* Fix logging issues for NUOPC

* removal of many cpp-ifdefs

* fix compile errors

* fixes to get cesm working

* fixed white space issue

* Add restart_coszen namelist option

* Update NUOPC cap to work with latest CICE6 master

* nuopc,cmeps or s2s build updates

* fixes for dbug_flag

* Update nuopc2 to latest CICE master

* Fix some merge problems

* Fix dbug variable

* Manual merge of UFS changes

Co-authored-by: Mariana Vertenstein <mvertens@ucar.edu>
Co-authored-by: apcraig <anthony.p.craig@gmail.com>
Co-authored-by: Denise Worthen <denise.worthen@noaa.gov>