Delete checkout and update git ignore

Removes the checkout script that has been replaced by git submodules

Finishes the updates to the .gitignore since we don't want wildcards to
cover the new submodule directories.

.gitignore

@@ -31,6 +31,7 @@ fix/cice
 fix/cpl
 fix/datm
 fix/gldas
+fix/gdas
 fix/gsi
 fix/lut
 fix/mom6
@@ -40,7 +41,6 @@ fix/sfc_climo
 fix/ugwd
 fix/verif
 fix/wave
-fix/wafs
 
 # Ignore parm file symlinks
 #--------------------------
@@ -97,8 +97,42 @@ parm/wafs
 #--------------------------------------------
 sorc/*log
 sorc/logs
-# sorc/*.cd
-# sorc/*.fd
+sorc/calc_analysis.fd
+sorc/calc_increment_ens.fd
+sorc/calc_increment_ens_ncio.fd
+sorc/emcsfc_ice_blend.fd
+sorc/emcsfc_snow2mdl.fd
+sorc/enkf.fd
+sorc/enkf_chgres_recenter_nc.fd
+sorc/fbwndgfs.fd
+sorc/gaussian_sfcanl.fd
+sorc/getsfcensmeanp.fd
+sorc/getsigensmeanp_smooth.fd
+sorc/getsigensstatp.fd
+sorc/gfs_bufr.fd
+sorc/global_cycle.fd
+sorc/gsi.fd
+sorc/interp_inc.fd
+sorc/mkgfsawps.fd
+sorc/overgridid.fd
+sorc/oznmon_horiz.fd
+sorc/oznmon_time.fd
+sorc/radmon_angle.fd
+sorc/radmon_bcoef.fd
+sorc/radmon_bcor.fd
+sorc/radmon_time.fd
+sorc/rdbfmsua.fd
+sorc/recentersigp.fd
+sorc/reg2grb2.fd
+sorc/supvit.fd
+sorc/syndat_getjtbul.fd
+sorc/syndat_maksynrc.fd
+sorc/syndat_qctropcy.fd
+sorc/tave.fd
+sorc/tocsbufr.fd
+sorc/upp.fd
+sorc/vint.fd
+sorc/webtitle.fd
 
 # Ignore scripts from externals
 #------------------------------
@@ -121,6 +155,7 @@ scripts/exgfs_atmos_wafs_grib2_0p25.sh
 ush/chgres_cube.sh
 ush/emcsfc_ice_blend.sh
 ush/emcsfc_snow.sh
+ush/exglobal_prep_ocean_obs.py
 ush/fix_precip.sh
 ush/fv3gfs_driver_grid.sh
 ush/fv3gfs_filter_topo.sh