The changes are:

 1, Modified for outer-loop with varying CV5 tuning factors:

 diff -r WRFDA/Registry/Registry.wrfvar WRFDA_release/Registry/  Registry.wrfvar

 diff -r WRFDA/var/da/da_main/da_solve.inc WRFDA_release/var/da/ da_main/da_solve.inc

 diff -r WRFDA/var/da/da_main/da_wrfvar_top.f90 WRFDA_release/var/da/da_main/da_wrfvar_top.f90

 diff -r WRFDA/var/da/da_minimisation/da_get_var_diagnostics.inc  WRFDA_release/var/da/da_minimisation/da_get_var_diagnostics.inc

 diff -r WRFDA/var/da/da_minimisation/da_minimisation.f90  WRFDA_release/var/da/da_minimisation/da_minimisation.f90

 diff -r WRFDA/var/da/da_setup_structures/da_rescale_background_errors.inc WRFDA_release/var/da/da_setup_structures/da_rescale_background_errors.inc

 Only in WRFDA/var/da/da_setup_structures:  da_scale_background_errors.inc

 diff -r WRFDA/var/da/da_setup_structures/da_setup_be_global.inc  WRFDA_release/var/da/da_setup_structures/da_setup_be_global.inc

 diff -r WRFDA/var/da/da_setup_structures/da_setup_be_nmm_regional.inc WRFDA_release/var/da/da_setup_structures/da_setup_be_nmm_regional.inc

 diff -r WRFDA/var/da/da_setup_structures/da_setup_be_regional.inc  WRFDA_release/var/da/da_setup_structures/da_setup_be_regional.inc

 diff -r WRFDA/var/da/da_setup_structures/da_setup_structures.f90  WRFDA_release/var/da/da_setup_structures/da_setup_structures.f90

 2, Bogus assimilation

 diff -r WRFDA/var/obsproc/src/module_diagnostics.F90 WRFDA_release/var/obsproc/src/module_diagnostics.F90

 diff -r WRFDA/var/obsproc/src/module_err_afwa.F90 WRFDA_release/var/obsproc/src/module_err_afwa.F90

 3, Intiate the values of factors for CV3 BE

 diff -r WRFDA/frame/module_configure.F WRFDA_release/frame/module_configure.F

 diff -r WRFDA/var/da/da_setup_structures/da_setup_be_ncep_gfs.inc  WRFDA_release/var/da/da_setup_structures/da_setup_be_ncep_gfs.inc

 4, GPSREF obs error tuning factor

 diff -r WRFDA/var/da/da_obs/da_use_obs_errfac.inc WRFDA_release/var/da/da_obs/da_use_obs_errfac.inc

 diff -r WRFDA/var/da/da_obs_io/da_write_noise_to_ob.inc  WRFDA_release/var/da/da_obs_io/da_write_noise_to_ob.inc

 5, Bug fix for surface assimilation (sfc=2)

 diff -r WRFDA/var/da/da_buoy/da_get_innov_vector_buoy.inc  WRFDA_release/var/da/da_buoy/da_get_innov_vector_buoy.inc

 diff -r WRFDA/var/da/da_metar/da_get_innov_vector_metar.inc  WRFDA_release/var/da/da_metar/da_get_innov_vector_metar.inc

 diff -r WRFDA/var/da/da_ships/da_get_innov_vector_ships.inc  WRFDA_release/var/da/da_ships/da_get_innov_vector_ships.inc

 diff -r WRFDA/var/da/da_sound/da_get_innov_vector_sonde_sfc.inc  WRFDA_release/var/da/da_sound/da_get_innov_vector_sonde_sfc.inc

 diff -r WRFDA/var/da/da_synop/da_get_innov_vector_synop.inc  WRFDA_release/var/da/da_synop/da_get_innov_vector_synop.inc

 diff -r WRFDA/var/da/da_tamdar/da_get_innov_vector_tamdar_sfc.inc  WRFDA_release/var/da/da_tamdar/da_get_innov_vector_tamdar_sfc.inc

 diff -r WRFDA/var/da/da_tools/da_convert_zk.inc WRFDA_release/var/da/da_tools/da_convert_zk.inc