filter_assim refactor

Refactoring filter assim:

• Each process calculates increments vs. previously only one process would do this for each observation. So more elements in the broadcast/send receive, and redundant (but simultaneous) calculation by each process. This is to allow future implementation of new assimilation algorithms

Code readability changes:

• removed timing variables
• get_close caching moved inside subroutine
• adaptive localization moved into subroutine
• cov_factor and adjust_obs_impact moved into subroutine
• Call new subroutines in adaptive_inflate_mod:
• update_single_state_space_inflation, update_varying_state_space_inflation

Bug fix for groups when used with posterior spatially-varying adaptive inflation

Removed the additional outlier threshold test for each group when using posterior spatially-varying adaptive inflation.
The outlier test is done for the entire ensemble when the posterior forward operators are computed.

CLM Snow Water Equivalent

Added snow repartitioning scheme to CLM-DART. Pre release version.

• Recommended for CLM only. If using other models, please checkout the latest version of DART.
• Uses CLM 5 and CESM 2.2. Not backwards compatible with older versions of CLM.

Improved observation converter documentation

• Improved radar observation converter documentation
• Fixed CHAMP converter links

bug fix for very large models

Bug fixes for models where the number of elements in the state exceeds 2^31-1:

• mpi_utilities_mod using correct check for message length > SNDRCV_MAXSIZE
• new developers test for large message sizes
• State vector IO updated to use i8 for state indexing
• WRF model_mod now using i8

bug fix for perfect_model_obs input.nml options

perfect_model_obs now exits cleanly if the user has not provided input_state_files or output_state_files.
Previously, blank entries (" ") for these namelist items could cause perfect_model_obs to hang.

Repository clean-up and DART registration form

removed obsolete code:

• cam-old
• restart_file_tool
• html boilerplate from pre-readthedocs documentation
• null versions of clamp_mod and vert_convert_mod
• io test harnesses
• jekyll website

removed experimental code:

• pnetcdf (for restart files)
• filter.separate_seq (split obs_seq across cores)

Registration info now on the GitHub README.md

NAG compiler fixes and updates to developer tests

• bug fix for fixsytem for the NAG compiler
• new developer test for mpi one-sided communication
• removed obsolete async 4 developer tests

WRF-Hydro diagnostics

Improved DART diagnostics for WRF-Hydro

Documentation and template update

• External forward operator documentation
• Typo fixes for GitHub templates