…ure/capgen into main/20240308) Combined PR ufs-community#2190 (ufs-community#2181)

* FV3 - Update submodule pointers for ccpp-framework and ccpp-physics. Change units flashes 5 min-1 to flashes min-1 and update long name to make clear this is per 5 minutes.
    * ccpp-physics - In physics/Interstitials/UFS_SCM_NEPTUNE/maximum_hourly_diagnostics.meta: change units flashes 5 min-1 to flashes min-1 and update long name to make clear this is per 5 minutes.
    * ccpp-framework - Update main from feature/capgen as of 2024-03-08 (includes optional argument updates in feature/capgen). Only commit on top of the merge is NCAR/ccpp-framework@6cdd38a which is required to parse the metadata in the Unified Forecast System / ccpp-physics (underscores in units, e.g. degree_north).

…allow-argument-mismatch' flag (ufs-community#1147)

* UFSWM - Fix type mismatch compiler error when gfortran 10 is used without '-fallow-argument-mismatch' flag.
  * FV3 - Fix type mismatch compiler error when gfortran 10 is used without '-fallow-argument-mismatch' flag.
    * ccpp-physics - Resolve various subroutine argument mismatches.
    * ccpp-framework - Add support to use mpi_f08 MPI module .
  * stochastic_physics - Fix type mismatch compiler error when gfortran 10 is used without '-fallow-argument-mismatch' flag.

- update module paths in Hera intel/gnu lua files for Rocky8 OS spack-stack libraries.

…ity#2197), add xr_cnvcld flag to FV3 (ufs-community#2185) (ufs-community#2202)

* UFSWM - atparse.bash: correctly handle input that doesn't end with an end-of-line character. Fix some bugs in Rocoto support and clean up rt.sh.
  * FV3 - namelist flag xr_cnvcld to control if suspended grid-mean convective cloud condensate should be included in cloud fraction and optical depth calculation in radiation in the GFS suite
    * ccpp - physics-level changes to implement new namelist variable
  * MOM6 - update MOM6 code to eliminate all compiler warnings

  * WW3 - Langmuir turbulence parameterization

…#2193)

* UFSWM - Update module_write_netcdf to avoid hangs in RRFS runs
  * FV3 - Update module_write_netcdf to avoid hangs in RRFS runs

…ommunity#2175)

  * CMEPS - allow additional dimension in cpl_scalars for CSG and regional ATM domains for use in mediator history files 
  * CMEPS - fix mapping mask for lnd->atm
  * FV3 - add export of cpl_scalars
  * NOAHMP - add export of cpl_scalars

…fs-community#2223)

cubed_sphere hash update: f060e85 for a bug- fix in the HAILCAST diagnostic code (units issue)

Update to CICE-Consortium/CICE aca8357. Adds implementation of namelist PIO options for CICE

…m wrong for nests (ufs-community#2201)

* UFSWM - None.
  * FV3 - Write component will use kchunk3d. Model init sends the right tile number to CCPP.
    * atmos_cubed_sphere - Initialize the hailwat variable. Pass global_tile index to model.

*doc/UserGuide
   *requirements.txt - updates inda version from 3.6 to 3.7

* UFSWM 
  * doc/Userguide
    * source
      * conf.py
      * Configurations.rst
      * FAQ.rst
      * InputsOutputs.rst
      * Introduction.rst

…Adds -v Verbose option. (ufs-community#2218)  Remove nowarn Intel compiler flag (ufs-community#2225)

* UFSWM
- Add bash linting to CI:
  - uses superlinter to check for consistent bash code writing
- Cleans up .sh scripts to comply with superlinter
- Cleans up .sh scripts to be more consistent, easier to read.
- Add's -v verbose option if debugging outputs needed, otherwise simplifies rt.sh run echo's.
- Addresses smaller bugs
  - quota/timeout search logic adjusted.
  - check for dirs existing (DISKNM, STMP, PTMP) before starting.
  - adjustments/cleanup to ecflow/rocoto sections
  - rt.sh will attempt to start ecflow, and only stop ecflow if it started from rt.sh.
  - fix for issue where run_dir will not delete properly.
* FV3: Address compiler warnings
  * atmos_cubed_sphere: Address compiler warnings.

* UFSWM - Update inline post
  * FV3 - Update upp submodule for inline post