Additional changes to source code:

(1) All variables updated in MPAS module mpas_atm_time_integration.F subroutines (assuming restart of MPAS model) are updated when updating the MPAS state from the GSI increments; the MPAS namelist flag 'config_DAcycling' may still be used, but it should have no effect since the MPAS diagnostic variables are recomputed by this routine.
(2) Cleaned up some minor details including initializing double precision variables correctly, etc.