Issue #1: clean up DA sections of link_fv3gfs.sh

sorc/link_fv3gfs.sh

@@ -116,7 +116,6 @@ cd ${pwd}/../jobs               ||exit 8
     $LINK ../sorc/gsi.fd/jobs/JGLOBAL_ANALDIAG           .
     $LINK ../sorc/gsi.fd/jobs/JGLOBAL_ENKF_SELECT_OBS    .
     $LINK ../sorc/gsi.fd/jobs/JGLOBAL_ENKF_ANALDIAG      .
-    $LINK ../sorc/gsi.fd/jobs/JGLOBAL_ENKF_INNOVATE_OBS  .
     $LINK ../sorc/gsi.fd/jobs/JGLOBAL_ENKF_UPDATE        .
     $LINK ../sorc/gsi.fd/jobs/JGDAS_ENKF_RECENTER        .
     $LINK ../sorc/gsi.fd/jobs/JGDAS_ENKF_SURFACE         .    
@@ -128,7 +127,6 @@ cd ${pwd}/../scripts            ||exit 8
     $LINK ../sorc/gsi.fd/scripts/exglobal_analcalc_fv3gfs.sh           .
     $LINK ../sorc/gsi.fd/scripts/exglobal_analdiag_fv3gfs.sh           .
     $LINK ../sorc/gsi.fd/scripts/exglobal_innovate_obs_fv3gfs.sh       .
-    $LINK ../sorc/gsi.fd/scripts/exglobal_enkf_innovate_obs_fv3gfs.sh  .
     $LINK ../sorc/gsi.fd/scripts/exglobal_enkf_update_fv3gfs.sh        .
     $LINK ../sorc/gsi.fd/scripts/exglobal_enkf_recenter_fv3gfs.sh      .
     $LINK ../sorc/gsi.fd/scripts/exglobal_enkf_surface_fv3gfs.sh       .
@@ -227,10 +225,10 @@ for ufs_utilsexe in \
     $LINK ../sorc/ufs_utils.fd/exec/$ufs_utilsexe .
 done
 
-for gsiexe in  global_gsi.x global_enkf.x calc_increment_ens.x  getsfcensmeanp.x  getsigensmeanp_smooth.x  \
-    calc_increment_ens_ncio.x calc_analysis.x interp_inc.x \
-    getsigensstatp.x  nc_diag_cat_serial.x nc_diag_cat.x recentersigp.x oznmon_horiz.x oznmon_time.x \
-    radmon_angle.x radmon_bcoef.x radmon_bcor.x radmon_time.x interp_inc.x;do
+for gsiexe in  calc_analysis.x calc_increment_ens_ncio.x calc_increment_ens.x \
+    getsfcensmeanp.x getsigensmeanp_smooth.x getsigensstatp.x global_enkf.x global_gsi.x \
+    interp_inc.x nc_diag_cat_serial.x oznmon_horiz.x oznmon_time.x radmon_angle.x \
+    radmon_bcoef.x radmon_bcor.x radmon_time.x recentersigp.x;do
     [[ -s $gsiexe ]] && rm -f $gsiexe
     $LINK ../sorc/gsi.fd/exec/$gsiexe .
 done
@@ -245,21 +243,55 @@ done
 #------------------------------
 
 cd ${pwd}/../sorc   ||   exit 8
+    [[ -d calc_analysis.fd ]] && rm -rf calc_analysis.fd
     $SLINK gsi.fd/util/netcdf_io/calc_analysis.fd                                          calc_analysis.fd
-    $SLINK gsi.fd/util/netcdf_io/interp_inc.fd                                             interp_inc.fd 
+
+    [[ -d calc_increment_ens.fd ]] && rm -rf calc_increment_ens.fd
     $SLINK gsi.fd/util/EnKF/gfs/src/calc_increment_ens.fd                                  calc_increment_ens.fd
+
+    [[ -d calc_increment_ens_ncio.fd ]] && rm -rf calc_increment_ens_ncio.fd
     $SLINK gsi.fd/util/EnKF/gfs/src/calc_increment_ens_ncio.fd                             calc_increment_ens_ncio.fd
+
+    [[ -d getsfcensmeanp.fd ]] && rm -rf getsfcensmeanp.fd
     $SLINK gsi.fd/util/EnKF/gfs/src/getsfcensmeanp.fd                                      getsfcensmeanp.fd
+
+    [[ -d getsigensmeanp_smooth.fd ]] && rm -rf getsigensmeanp_smooth.fd
     $SLINK gsi.fd/util/EnKF/gfs/src/getsigensmeanp_smooth.fd                               getsigensmeanp_smooth.fd
+
+    [[ -d getsigensstatp.fd ]] && rm -rf getsigensstatp.fd
     $SLINK gsi.fd/util/EnKF/gfs/src/getsigensstatp.fd                                      getsigensstatp.fd
-    $SLINK gsi.fd/src                                                                      global_enkf.fd
-    $SLINK gsi.fd/src                                                                      global_gsi.fd
+
+    [[ -d global_enkf.fd ]] && rm -rf global_enkf.fd
+    $SLINK gsi.fd/src/enkf                                                                 global_enkf.fd
+
+    [[ -d global_gsi.fd ]] && rm -rf global_gsi.fd
+    $SLINK gsi.fd/src/gsi                                                                  global_gsi.fd
+
+    [[ -d interp_inc.fd ]] && rm -rf interp_inc.fd
+    $SLINK gsi.fd/util/netcdf_io/interp_inc.fd                                             interp_inc.fd
+
+    [[ -d ncdiag.fd ]] && rm -rf ncdiag.fd
+    $SLINK gsi.fd/src/ncdiag                                                               ncdiag.fd
+
+    [[ -d oznmon_horiz.fd ]] && rm -rf oznmon_horiz.fd
     $SLINK gsi.fd/util/Ozone_Monitor/nwprod/oznmon_shared.v2.0.0/sorc/oznmon_horiz.fd      oznmon_horiz.fd
+
+    [[ -d oznmon_time.fd ]] && rm -rf oznmon_time.fd
     $SLINK gsi.fd/util/Ozone_Monitor/nwprod/oznmon_shared.v2.0.0/sorc/oznmon_time.fd       oznmon_time.fd
+
+    [[ -d radmon_angle.fd ]] && rm -rf radmon_angle.fd
     $SLINK gsi.fd/util/Radiance_Monitor/nwprod/radmon_shared.v3.0.0/sorc/verf_radang.fd    radmon_angle.fd
+
+    [[ -d radmon_bcoef.fd ]] && rm -rf radmon_bcoef.fd
     $SLINK gsi.fd/util/Radiance_Monitor/nwprod/radmon_shared.v3.0.0/sorc/verf_radbcoef.fd  radmon_bcoef.fd
+
+    [[ -d radmon_bcor.fd ]] && rm -rf radmon_bcor.fd
     $SLINK gsi.fd/util/Radiance_Monitor/nwprod/radmon_shared.v3.0.0/sorc/verf_radbcor.fd   radmon_bcor.fd 
+
+    [[ -d radmon_time.fd ]] && rm -rf radmon_time.fd
     $SLINK gsi.fd/util/Radiance_Monitor/nwprod/radmon_shared.v3.0.0/sorc/verf_radtime.fd   radmon_time.fd 
+
+    [[ -d recentersigp.fd ]] && rm -rf recentersigp.fd
     $SLINK gsi.fd/util/EnKF/gfs/src/recentersigp.fd                                        recentersigp.fd
 
     $SLINK gfs_post.fd/sorc/ncep_post.fd                                                   gfs_ncep_post.fd