… & FV3_HRRR_gf (NOAA-EMC#692)

* fix fortran coding error in dynamical core
* use clm lake in fv3_hrrr_c3
* initialize arrays after allocation
* ressurect FV3_HRRR_gf suite and give it the clm lake model
* bug fix from Dusan to use the correct type kind when reading lan & lon in quilt server

…A-EMC#595)

* Change the format of domain restart files to netcdf4 and set chunksizes

* Remove nc_format="netcdf4" argument when opening restart files

* Set chunksize of zaxis and time axis to 1

* Update clm_lake and rrfs_sd modules to support chunksizes

* Make quilting restart files identical to fms files

* 2D advection of cellular automata

* update missing value

* adding timing information

* add write_runtimelog option

* update upp and not include dycore updates that change results

* add SPP support to G-F deep convection

…PR98