Bug-fix for obs converter builds and MPAS_ATM perf improvement

• Bug fix for converter builds using the template model_mod.f90 #409
• Performance fix for MPAS_ATM #407

bug fix for perturb_single_instance

A model specific pert_model_copies is now required to run perturb_single_instance.

Previously the program perturb_single_instance would run but not perturb if a model_mod did not provide a pert_model_copies interface.

CAM-SE Manhattan

• CAM-SE interface for Manhattan
• Shared code for CAM-SE and CAM-FV model_mods in cam-common-code

ROMS model_mod improvement to enable perturb_single_instance

• Defines a pert_model_copies subroutine within the ROMS model_mod that randomly perturbs temperature and salinity with the ROMS model history files
• Adding this subroutine ensures perturb_single_instance works as expected

Bug fix for CLM CESM2.2 shell scripts

• Fixes dtlimit bug in cesm2.2 CLM shell scripts. Loads all CAM
  reanalysis files within datm data stream file regardless if it
  is single year or multi-year run.
• Fixes single instance bug in cems2.2 CLM shell scripts. Allows
  for freerun scripts to generate single instance simulations.

Bug fix for POP CESM2.1 shell scripts

• Fixes bug in POP CESM2.1 shell scripts in which inflation files were not being propagated properly.

Automated initial setup of new model interfaces

• Automated initial setup of new model interfaces to aid users developing
  model_mod code and documentation.

contributed by Benjamin Gunn

Bug-fixes for obs_utilities build and mpas_atm

• obs_utilities_mod no longer included by default for model/work builds because
  these utilities are for threed_sphere and threed_cartesian location_mods only.
• mpas_atm model_mod check for required quantities changed to handle multiple
  variables of the same quantity.

TIEGCM 2.0 Manhattan

TIEGCM model_mod updated to Manhattan and TIEGCM 2.0

• Supports 2.5-degree and 5-degree resolution grids.
• vtec extrapolation is done in model_mod::model_interpolate with 10 levels for 5 deg, 20 levels for 2.5 deg.
• Model_interpolate uses X rather than X_MN variable no matter the order of state
  variables in model_nml. Previously in Lanai the variable given first in the state was used.
  _MN variables are from the previous model time step.
• f10.7 can be added to the DART state. An example f10_7.cdl file is provided in the work directory.
• Added hyperslice subroutine to state_structure_mod to read only part of a netCDF variable into the state
• Separated functions for io_dim_length and dim_length in state_structure_mod to allow for hyperslice.
• Replaced stub get_expected_vtec with COMMON_CODE.
• direct_netcdf_mod reads/write the latest slice of the unlimited dimension in the restart file.

RTTOV v13

• RTTOV v13 forward operators for satellite radiance assimilation.

Contributed by Lukas Kugler