Fluxnet observation converter and obs_def_rttov13_mod.f90 bug-fixes

Fluxnet obs converter (#478):

• Generates a new observation converter (Fluxnetfull_to_obs) for eddy covariance flux tower data (carbon, water energy fluxes)
• Documentation changes made to the older, deprecated ameriflux converter (level4_to_obs) and the broken links have been fixed
• New flux tower observation types added to accomodate the forward operator approach for time aggregated fluxes (daily through monthly)

obs_def_rttov13_mod.f90 bug-fixes:

• Added public get_channel to obs_def_rttov13_mod.f90 to compile WRF successfully with rttov13. #532
• Removed cloud_overlap (integer) from the function: get_rttov_option_logical #537

CAM-FV shell scripts

Performance improvements for CAM-FV shell scripts:

• Avoid listing files if the CAM_PHIS file already exists.
• Avoid using /var/tmp
• RUNDIR defined after CIME_OUTPUT_ROOT change.
• Warn if no inflation files found.

MPAS-ATM constants update and readthedocs fix

• MPAS-ATM model_mod.f90 constants updated to MPAS v5+ #251
  see mpas_atm for how to run with v4 constants.
• readthedocs build info updated. #526

Bug-fixes for MOM6 and WRF

• bug-fixes:

  • MOM6 read_model_time converts to dart time to match observation sequences #494
  • MOM6 salinity units converted to MSU during model_interpolate #509
  • WRF get_dist calculation fixed for observations with VERTISUNDEF #486

• doc-fixes:

  • WOD and GTSPP converter documentation notes about salinity units #509
  • MOM6 documentation for setting the Gregorian calendar in CESM #494
  • comment fix in filter_mod.f90 #508

CAM-DART observation preprocessor

• Tool to remove observations above a given CAM level from an obs sequence file #459
• bug-fixes:
  • MOM6 added check for too deep observations #490
  • test_interpolate_range write format corrected #487
  • removed unused code from mpas_atm directory #496 #498
• doc: removed outdated references to prep_buf.html #452

Smoother removal

• Dead smoother code removed. #479
• Documentation fix for quality control. #481
• Cray Compiler Environment mkmf.template #470

Please reach out to dart@ucar.edu if you are interested in implementing a smoother in DART Manhattan.

Documentation fix

conf.py changes for latest readthedocs. Fixes search and flyout menu. #471

CLM-DART: CAM reanalysis site-level bias correction tool

• Initial version of bias correction for CAM reanalysis forcing for site-level assimilation with CLM-DART. #446
• mkmf change: make clean removes .mod files. #444
• bug-fix: readthedocs yaml file for online documentation build. #471

MOM6

CESM-MOM6 interface added to DART #451

• An early functional release of the MOM6 ocean component has been made available to CESM users beginning with CESM2.2.
• This DART-MOM6 interface was developed for MOM6 within the CESM framework to use with the
  CESM functional release.

Bug-fixes for the WRF Tutorial and developer test quickbuilds

• Fixes the broken link to WRF DART tutorial input.nml.template #464
• Fixes the developer_tests quickbuild.sh files #466