diff --git a/.gitignore b/.gitignore
index f83211291ef..1ab98a5adcc 100644
--- a/.gitignore
+++ b/.gitignore
@@ -80,6 +80,7 @@ parm/post/post_tag_gfs128
 parm/post/gfs
 parm/post/gefs
 parm/post/sfs
+parm/post/gcafs
 parm/post/ocean.csv
 parm/post/ocean_gefs.csv
 parm/post/ocean_gfs.csv
@@ -96,9 +97,11 @@ parm/ufs/MOM6_data_table.IN
 parm/ufs/ice_in.IN
 parm/ufs/ufs.configure.*.IN
 parm/ufs/post_itag_gfs
+parm/ufs/post_itag_gcafs
 parm/ufs/ww3_shel.nml.IN
 parm/ufs/global_control.nml.IN
 parm/regrid_sfc
+parm/chem/nexus
 
 # Ignore sorc and logs folders from externals
 #--------------------------------------------
diff --git a/.shellcheckrc b/.shellcheckrc
index 67fabfe1576..fc9aa26124b 100644
--- a/.shellcheckrc
+++ b/.shellcheckrc
@@ -17,3 +17,6 @@ disable=SC2174
 
 # Disable warning of functions in test statements
 disable=SC2310
+
+# Disable masking of return codes from chained commands.  Use `set -o pipefail` to trap them.
+disable=SC2312
diff --git a/dev/ci/scripts/run_check_ci.sh b/dev/ci/scripts/run_check_ci.sh
index f1be7b92de4..f310cc7d059 100755
--- a/dev/ci/scripts/run_check_ci.sh
+++ b/dev/ci/scripts/run_check_ci.sh
@@ -71,7 +71,6 @@ while true; do
 
     # Get job statistics
     echo "Gather Rocoto statistics"
-    # shellcheck disable=SC2312 # We want to use the exit code of the command
     full_state=$("${HOMEgfs}/dev/ci/scripts/utils/rocotostat.py" -w "${xml}" -d "${db}" -v)
     error_stat=$?
 
diff --git a/dev/ci/scripts/utils/ci_utils.sh b/dev/ci/scripts/utils/ci_utils.sh
index 41a61ad2271..ca59cd30251 100755
--- a/dev/ci/scripts/utils/ci_utils.sh
+++ b/dev/ci/scripts/utils/ci_utils.sh
@@ -253,7 +253,6 @@ function delete_dataroot() {
     _runtests="${1}"
     _pslot="${2}"
 
-    # shellcheck disable=SC2312
     eval "$(
         PDY=0 cyc=0 source "${_runtests}/EXPDIR/${_pslot}/config.base" >&/dev/null
         echo _dataroot="${STMP}/RUNDIRS/${_pslot}"
diff --git a/dev/job_cards/rocoto/prep.sh b/dev/job_cards/rocoto/prep.sh
index 59df45e563e..578b5bbf0f6 100755
--- a/dev/job_cards/rocoto/prep.sh
+++ b/dev/job_cards/rocoto/prep.sh
@@ -74,11 +74,9 @@ if [[ ! -s "${COMINobsproc_PREV}/${GDUMP}.t${gcyc}z.updated.status.tm00.bufr_d"
     fi
 fi
 # exception handling to ensure no dead link
-# shellcheck disable=SC2312
 if [[ $(find "${COMOUT_OBS}" -xtype l | wc -l) -ge 1 ]]; then
     exit 9
 fi
-# shellcheck disable=SC2312
 if [[ $(find "${COMINobsproc_PREV}" -xtype l | wc -l) -ge 1 ]]; then
     exit 9
 fi
@@ -155,9 +153,10 @@ export COMSP=${COMSP:-"${COMIN_OBS}/${RUN_local}.t${cyc}z."}
 # Create or Copy prepbufr, prepbufr.acft_profiles, nsstbufr files
 # Do not fail on external errors
 if [[ ${MAKE_PREPBUFR:-"YES"} == "YES" ]]; then
-    set +eu
+    unset_strict
     "${HOMEobsproc}/jobs/JOBSPROC_GLOBAL_PREP" && true
     export err=$?
+    set_strict
     if [[ ${err} -ne 0 ]]; then
         err_exit "JOBSPROC_GLOBAL_PREP job failed, ABORT!"
     fi
diff --git a/dev/jobs/JGFS_ATMOS_CYCLONE_GENESIS b/dev/jobs/JGFS_ATMOS_CYCLONE_GENESIS
index 8b6e87a3477..c5cddebce08 100755
--- a/dev/jobs/JGFS_ATMOS_CYCLONE_GENESIS
+++ b/dev/jobs/JGFS_ATMOS_CYCLONE_GENESIS
@@ -34,15 +34,14 @@ export JYYYY=${PDY:0:4}
 ##############################################
 
 # Do not fail on errors or unassigned variables in external code
-set +eu
+unset_strict
 "${SCRIPTens_tracker}/exgfs_tc_genesis.sh" && true
 export err=$?
+set_strict
 if [[ ${err} -ne 0 ]]; then
     err_exit
 fi
 
-set_strict
-
 ##############################################
 # Final processing
 ##############################################
diff --git a/dev/jobs/JGFS_ATMOS_VERIFICATION b/dev/jobs/JGFS_ATMOS_VERIFICATION
index e15020e2aec..e15eac2f83e 100755
--- a/dev/jobs/JGFS_ATMOS_VERIFICATION
+++ b/dev/jobs/JGFS_ATMOS_VERIFICATION
@@ -29,13 +29,16 @@ done
 if [[ "${RUN_GRID2GRID_STEP1}" == "YES" || "${RUN_GRID2OBS_STEP1}" == "YES" || "${RUN_PRECIP_STEP1}" == "YES" ]]; then
     # Override the -e in VERIF_GLOBALSH's shebang and un-export SHELLOPTS
     # TODO: clean up the verif-global script so it does not raise false-positive errors
-    set +eu
+    unset_strict
     export -n SHELLOPTS
     bash -x "${VERIF_GLOBALSH}"
     err=$?
+    set_strict
     if [[ ${err} -ne 0 ]]; then
         exit "${err}"
     fi
 fi
 
-if [[ ${KEEPDATA:-"NO"} == "NO" ]]; then rm -rf "${DATAROOT}"; fi # TODO: This should be $DATA
+if [[ ${KEEPDATA:-"NO"} == "NO" ]]; then
+    rm -rf "${DATAROOT}" # TODO: This should be $DATA
+fi
diff --git a/dev/jobs/JGLOBAL_ARCHIVE_TARS b/dev/jobs/JGLOBAL_ARCHIVE_TARS
index 67b45b993ab..4b059b930d2 100755
--- a/dev/jobs/JGLOBAL_ARCHIVE_TARS
+++ b/dev/jobs/JGLOBAL_ARCHIVE_TARS
@@ -80,17 +80,15 @@ fi
 # Run archive script
 ###############################################################
 
-set +eu
 # Do not export shell opts to the bash scripts in the htar/hsi wrappers
 export -n SHELLOPTS
+unset_strict
 ${GLOBALARCHIVESH:-${SCRgfs}/exglobal_archive_tars.py}
 export err=$?
-set +x
+set_strict
 if [[ ${err} -ne 0 ]]; then
     err_exit "failed to archive the COM structure"
 fi
-set_trace
-set_strict
 
 ##############################################
 # End JOB SPECIFIC work
@@ -106,10 +104,7 @@ fi
 ##########################################
 # Remove the Temporary working directory
 ##########################################
-cd "${DATAROOT}" || (
-    echo "${DATAROOT} does not exist. ABORT!"
-    exit 1
-)
+cd "${DATAROOT}" || true
 if [[ "${KEEPDATA}" == "NO" ]]; then
     rm -rf "${DATA}"
 fi
diff --git a/dev/jobs/JGLOBAL_ATMENS_ANALYSIS_FINALIZE b/dev/jobs/JGLOBAL_ATMENS_ANALYSIS_FINALIZE
index 79ff131257a..6e39de57c88 100755
--- a/dev/jobs/JGLOBAL_ATMENS_ANALYSIS_FINALIZE
+++ b/dev/jobs/JGLOBAL_ATMENS_ANALYSIS_FINALIZE
@@ -45,13 +45,7 @@ fi
 ##########################################
 # Remove the Temporary working directory
 ##########################################
-cd "${DATAROOT}" && true
-export err=$?
-set +e
-if [[ ${err} -ne 0 ]]; then
-    err_exit "${DATAROOT} does not exist, ABORT!"
-fi
-set_trace
+cd "${DATAROOT}" || true
 if [[ "${KEEPDATA}" == "NO" ]]; then
     rm -rf "${DATA}"
 fi
diff --git a/dev/jobs/JGLOBAL_ATMOS_ANALYSIS_CALC_FV3JEDI b/dev/jobs/JGLOBAL_ATMOS_ANALYSIS_CALC_FV3JEDI
index e343fd235ca..1af6a422b3d 100755
--- a/dev/jobs/JGLOBAL_ATMOS_ANALYSIS_CALC_FV3JEDI
+++ b/dev/jobs/JGLOBAL_ATMOS_ANALYSIS_CALC_FV3JEDI
@@ -2,7 +2,6 @@
 
 # Ignore possible spelling error (nothing is misspelled)
 # shellcheck disable=SC2153
-# shellcheck disable=SC2312
 
 source "${HOMEgfs}/ush/jjob_header.sh" -e "analcalc_fv3jedi" -c "base analcalc_fv3jedi"
 
diff --git a/dev/jobs/JGLOBAL_ENKF_ARCHIVE_TARS b/dev/jobs/JGLOBAL_ENKF_ARCHIVE_TARS
index 2e22ada681b..bad4e6a9633 100755
--- a/dev/jobs/JGLOBAL_ENKF_ARCHIVE_TARS
+++ b/dev/jobs/JGLOBAL_ENKF_ARCHIVE_TARS
@@ -23,16 +23,14 @@ mkdir -p "${COMIN_CONF}"
 ###############################################################
 
 # Calls an external bash command; do not fail on unassigned/error
-set +eu
 export -n SHELLOPTS
+unset_strict
 "${SCRgfs}/exglobal_enkf_earc_tars.py"
 export err=$?
-set +x
+set_strict
 if [[ ${err} -ne 0 ]]; then
     err_exit "Failed to archive the ensemble COM structure"
 fi
-set_trace
-set_strict
 
 ###############################################################
 
@@ -50,10 +48,7 @@ fi
 ##########################################
 # Remove the Temporary working directory
 ##########################################
-cd "${DATAROOT}" || (
-    echo "${DATAROOT} does not exist. ABORT!"
-    exit 1
-)
+cd "${DATAROOT}" || true
 if [[ "${KEEPDATA}" == "NO" ]]; then
     rm -rf "${DATA}"
 fi
diff --git a/dev/parm/config/gefs/config.resources.AZUREPW b/dev/parm/config/gefs/config.resources.AZUREPW
index a3065bd017a..513699163b3 100644
--- a/dev/parm/config/gefs/config.resources.AZUREPW
+++ b/dev/parm/config/gefs/config.resources.AZUREPW
@@ -6,7 +6,6 @@
 export is_exclusive="True"
 unset memory
 
-# shellcheck disable=SC2312
 for mem_var in $(env | grep '^memory_' | cut -d= -f1); do
   unset "${mem_var}"
 done
diff --git a/dev/parm/config/gefs/config.resources.GOOGLEPW b/dev/parm/config/gefs/config.resources.GOOGLEPW
index 8a148965068..934e9a94a32 100644
--- a/dev/parm/config/gefs/config.resources.GOOGLEPW
+++ b/dev/parm/config/gefs/config.resources.GOOGLEPW
@@ -6,7 +6,6 @@
 export is_exclusive="True"
 unset memory
 
-# shellcheck disable=SC2312
 for mem_var in $(env | grep '^memory_' | cut -d= -f1); do
   unset "${mem_var}"
 done
diff --git a/dev/parm/config/gfs/config.ecen b/dev/parm/config/gfs/config.ecen
index 933ccbd9060..105f186b10a 100644
--- a/dev/parm/config/gfs/config.ecen
+++ b/dev/parm/config/gfs/config.ecen
@@ -13,7 +13,6 @@ source "${EXPDIR}/config.resources" ecen
 # below queries IAUFHRS_ENKF to determine NECENGRP
 export NECENGRP=1
 if [[ ${DOIAU_ENKF} = "YES" ]]; then
-   # shellcheck disable=SC2312
    ngrps=$(grep -o ',' <<<"${IAUFHRS_ENKF}" | grep -c .)
    ((ngrps++))
    export NECENGRP=${ngrps}
diff --git a/dev/parm/config/gfs/config.resources.AZUREPW b/dev/parm/config/gfs/config.resources.AZUREPW
index a3065bd017a..513699163b3 100644
--- a/dev/parm/config/gfs/config.resources.AZUREPW
+++ b/dev/parm/config/gfs/config.resources.AZUREPW
@@ -6,7 +6,6 @@
 export is_exclusive="True"
 unset memory
 
-# shellcheck disable=SC2312
 for mem_var in $(env | grep '^memory_' | cut -d= -f1); do
   unset "${mem_var}"
 done
diff --git a/dev/parm/config/gfs/config.resources.GOOGLEPW b/dev/parm/config/gfs/config.resources.GOOGLEPW
index 8a148965068..934e9a94a32 100644
--- a/dev/parm/config/gfs/config.resources.GOOGLEPW
+++ b/dev/parm/config/gfs/config.resources.GOOGLEPW
@@ -6,7 +6,6 @@
 export is_exclusive="True"
 unset memory
 
-# shellcheck disable=SC2312
 for mem_var in $(env | grep '^memory_' | cut -d= -f1); do
   unset "${mem_var}"
 done
diff --git a/dev/scripts/exgdas_atmos_verfrad.sh b/dev/scripts/exgdas_atmos_verfrad.sh
index 7fe7dbc0934..034d7067720 100755
--- a/dev/scripts/exgdas_atmos_verfrad.sh
+++ b/dev/scripts/exgdas_atmos_verfrad.sh
@@ -18,7 +18,7 @@
 ################################################################################
 
 # Do not exit on errors so that restricted data can be protected
-set +eu
+unset_strict
 
 if [[ ! -s "${radstat}" || ! -s "${biascr}" ]]; then
     export err=1
@@ -102,7 +102,6 @@ for type in ${SATYPE}; do
         netcdf=1
     fi
 
-    # shellcheck disable=SC2312
     if [[ $(find . -maxdepth 1 -type f -name "diag_${type}_ges.${PDY}${cyc}*.${Z}" | wc -l) -gt 0 ]]; then
         mv "diag_${type}_ges.${PDY}${cyc}"*".${Z}" "${type}.${Z}"
         ${UNCOMPRESS} "./${type}.${Z}"
@@ -111,7 +110,6 @@ for type in ${SATYPE}; do
     fi
 
     if [[ ${USE_ANL} -eq 1 ]]; then
-        # shellcheck disable=SC2312
         file_count=$(find . -maxdepth 1 -type f -name "diag_${type}_anl.${PDY}${cyc}*.${Z}" | wc -l)
         if [[ ${file_count} -gt 0 ]]; then
             mv "diag_${type}_anl.${PDY}${cyc}"*".${Z}" "${type}_anl.${Z}"
diff --git a/dev/scripts/exgfs_atmos_awips_20km_1p0deg.sh b/dev/scripts/exgfs_atmos_awips_20km_1p0deg.sh
index 267a0623791..9989b0db0b3 100755
--- a/dev/scripts/exgfs_atmos_awips_20km_1p0deg.sh
+++ b/dev/scripts/exgfs_atmos_awips_20km_1p0deg.sh
@@ -82,7 +82,6 @@ export opt28=' -new_grid_interpolation budget -fi '
 cpreq "${COMIN_ATMOS_GRIB_0p25}/gfs.t${cyc}z.pres_a.0p25.f${fcsthr}.grib2" "tmpfile2${fcsthr}"
 cpreq "${COMIN_ATMOS_GRIB_0p25}/gfs.t${cyc}z.pres_b.0p25.f${fcsthr}.grib2" "tmpfile2b${fcsthr}"
 cat "tmpfile2${fcsthr}" "tmpfile2b${fcsthr}" > "tmpfile${fcsthr}"
-# shellcheck disable=SC2312
 ${WGRIB2} "tmpfile${fcsthr}" | grep -F -f "${PARMgfs}/product/gfs_awips_parmlist_g2" |
     ${WGRIB2} -i -grib masterfile "tmpfile${fcsthr}" && true
 export err=$?
@@ -91,7 +90,6 @@ if [[ ${err} -ne 0 ]]; then
 fi
 
 ${WGRIB2} masterfile -match ":PWAT:entire atmosphere" -grib gfs_pwat.grb
-# shellcheck disable=SC2312
 ${WGRIB2} masterfile | grep -v ":PWAT:entire atmosphere" | ${WGRIB2} -i -grib temp_gfs masterfile
 ##################################################################
 #  Process to change PWAT from level 200 to 10 (Entire Atmosphere)
@@ -156,7 +154,6 @@ for GRID in conus ak prico pac 003; do
     # NOTE: numparm is the total of fields in grib2_awpgfs_20km_conusf000 file
     ###########################################################################
     numparm=247
-    # shellcheck disable=SC2312
     numrec=$(${WGRIB2} "awps_file_f${fcsthr}_${GRID}" | wc -l)
 
     if [[ ${numrec} -lt ${numparm} ]]; then
diff --git a/dev/scripts/exgfs_atmos_fbwind.sh b/dev/scripts/exgfs_atmos_fbwind.sh
index 2c76bb097c4..33aa30c90c0 100755
--- a/dev/scripts/exgfs_atmos_fbwind.sh
+++ b/dev/scripts/exgfs_atmos_fbwind.sh
@@ -38,7 +38,6 @@ for fhr3 in 006 012 024; do
     cpreq "${COMIN_ATMOS_GRIB_0p25}/gfs.${cycle}.pres_a.0p25.f${fhr3}.grib2" "tmp_pgrb2_0p25${fhr3}"
     cpreq "${COMIN_ATMOS_GRIB_0p25}/gfs.${cycle}.pres_b.0p25.f${fhr3}.grib2" "tmp_pgrb2b_0p25${fhr3}"
     cat "tmp_pgrb2_0p25${fhr3}" "tmp_pgrb2b_0p25${fhr3}" > "tmp0p25filef${fhr3}"
-    # shellcheck disable=SC2312
     ${WGRIB2} "tmp0p25filef${fhr3}" | grep -F -f "${PARMgfs}/product/gfs_fbwnd_parmlist_g2" |
         ${WGRIB2} -i -grib "tmpfilef${fhr3}" "tmp0p25filef${fhr3}"
     ${CNVGRIB} -g21 "tmpfilef${fhr3}" "gfs.t${cyc}z.grbf${fhr3}_grb1"
diff --git a/dev/scripts/exgfs_atmos_gempak_meta.sh b/dev/scripts/exgfs_atmos_gempak_meta.sh
index 130913e918e..87f411d38b7 100755
--- a/dev/scripts/exgfs_atmos_gempak_meta.sh
+++ b/dev/scripts/exgfs_atmos_gempak_meta.sh
@@ -49,7 +49,6 @@ while [[ ${fhr} -le ${fhend} ]]; do
 
     if [[ ${do_all} -eq 1 ]]; then
         do_all=0
-        # shellcheck disable=SC2312
         awk '{print $1}' "${HOMEgfs}/gempak/fix/gfs_meta" | envsubst > "poescript"
     else
         #
@@ -57,7 +56,6 @@ while [[ ${fhr} -le ${fhend} ]]; do
         #    This will work as long as we don't need 12 fhr metafiles
         #
         if [[ ${fhr} -ne 12 ]]; then
-            # shellcheck disable=SC2312
             grep "${fhr}" "${HOMEgfs}/gempak/fix/gfs_meta" | awk -F" [0-9]" '{print $1}' | envsubst > "poescript"
         fi
     fi
diff --git a/dev/scripts/exgfs_atmos_goes_nawips.sh b/dev/scripts/exgfs_atmos_goes_nawips.sh
index da085ca4ce1..323f8f7701b 100755
--- a/dev/scripts/exgfs_atmos_goes_nawips.sh
+++ b/dev/scripts/exgfs_atmos_goes_nawips.sh
@@ -21,8 +21,7 @@ done
 NAGRIB_TABLE="${HOMEgfs}/gempak/fix/nagrib.tbl"
 NAGRIB="${GEMEXE}/nagrib2"
 
-# shellcheck disable=SC2312
-entry=$(grep "^${RUN2} " "${NAGRIB_TABLE}" | awk 'index($1,"#") != 1 {print $0}')
+entry=$(grep "^${RUN2} " "${NAGRIB_TABLE}" | awk 'index($1,"#") != 1 {print $0}' || echo "")
 
 if [[ "${entry}" != "" ]]; then
     cpyfil=$(echo "${entry}" | awk 'BEGIN {FS="|"} {print $2}')
@@ -61,7 +60,7 @@ startmsg
 
 ${NAGRIB} << EOF
 GBFILE   = grib${fhr3}
-INDXFL   = 
+INDXFL   =
 GDOUTF   = ${GEMGRD}
 PROJ     = ${proj}
 GRDAREA  = ${grdarea}
@@ -71,7 +70,7 @@ CPYFIL   = ${cpyfil}
 GAREA    = ${garea}
 OUTPUT   = ${output}
 GBTBLS   = ${gbtbls}
-GBDIAG   = 
+GBDIAG   =
 PDSEXT   = ${pdsext}
 l
 r
diff --git a/dev/scripts/exgfs_atmos_grib2_special_npoess.sh b/dev/scripts/exgfs_atmos_grib2_special_npoess.sh
index d1c37c56dd8..51ce9674539 100755
--- a/dev/scripts/exgfs_atmos_grib2_special_npoess.sh
+++ b/dev/scripts/exgfs_atmos_grib2_special_npoess.sh
@@ -110,7 +110,6 @@ for ((fhr = SHOUR; fhr <= FHOUR; fhr = fhr + FHINC)); do
     cpreq "${COMIN_ATMOS_GRIB_0p50}/gfs.t${cyc}z.pres_a.0p50.f${fhr3}.grib2" tmpfile2
     cpreq "${COMIN_ATMOS_GRIB_0p50}/gfs.t${cyc}z.pres_b.0p50.f${fhr3}.grib2" tmpfile2b
     cat tmpfile2 tmpfile2b > tmpfile
-    # shellcheck disable=SC2312
     ${WGRIB2} tmpfile | grep -F -f "${paramlist}" | ${WGRIB2} -i -grib pgb2file tmpfile && true
     export err=$?
     if [[ ${err} -ne 0 ]]; then
diff --git a/dev/scripts/exgfs_wave_post_pnt.sh b/dev/scripts/exgfs_wave_post_pnt.sh
index 6525a18339c..deea1f95123 100755
--- a/dev/scripts/exgfs_wave_post_pnt.sh
+++ b/dev/scripts/exgfs_wave_post_pnt.sh
@@ -86,7 +86,6 @@ if [[ -f "${PARMgfs}/wave/wave_${NET}.buoys" ]]; then
     cpreq -f "${PARMgfs}/wave/wave_${NET}.buoys" buoy.loc.temp
     if [[ "${DOBNDPNT_WAV}" == "YES" ]]; then
         #only do boundary points
-        # shellcheck disable=SC2312
         sed -n '/^\$.*/!p' buoy.loc.temp | grep IBP > buoy.loc || {
             echo "WARNING: No boundary points found in buoy file ${PARMgfs}/wave/wave_${NET}.buoys"
             echo "         Ending job without doing anything."
@@ -94,7 +93,6 @@ if [[ -f "${PARMgfs}/wave/wave_${NET}.buoys" ]]; then
         }
     else
         #exclude boundary points
-        # shellcheck disable=SC2312
         sed -n '/^\$.*/!p' buoy.loc.temp | grep -v IBP > buoy.loc
     fi
 fi
@@ -182,7 +180,6 @@ if [[ ${err} -ne 0 && ! -f buoy_log.ww3 ]]; then
 fi
 
 # Create new buoy_log.ww3
-# shellcheck disable=SC2312
 awk '{print $3}' buoy.loc | sed 's/'\''//g' > ibp_tags
 grep -F -f ibp_tags buoy_log.ww3 > buoy_log.tmp
 rm -f buoy_log.dat
@@ -199,7 +196,6 @@ fi
 
 # 1.f Data summary
 
-# shellcheck disable=SC2312
 cat << EOF
 
 Input files read and processed at : $(date)
@@ -219,11 +215,8 @@ EOF
 
 echo '   Making command file for wave post points '
 
-# shellcheck disable=SC2312
 grep -F -f ibp_tags buoy_log.dat | awk '{ print $2 }' > buoys
-# shellcheck disable=SC2312
 grep -F -f buoys buoy_log.ww3 | awk '{ print $1 }' > points
-# shellcheck disable=SC2312
 points=$(awk '{print $0 "\\n"}' points | tr -d '\n')
 rm -f buoys
 
diff --git a/dev/scripts/exgfs_wave_prdgen_bulls.sh b/dev/scripts/exgfs_wave_prdgen_bulls.sh
index e1f89b217da..9d6140979e5 100755
--- a/dev/scripts/exgfs_wave_prdgen_bulls.sh
+++ b/dev/scripts/exgfs_wave_prdgen_bulls.sh
@@ -57,7 +57,6 @@ else
 fi
 
 # 1.b Output locations from bulletin files
-# shellcheck disable=SC2312
 Nb=$(find . -type f -name "*.cbull" -printf '.' | wc -c)
 echo ' '
 echo "   Number of bulletin files :   ${Nb}"
@@ -79,7 +78,6 @@ source awipsbull.data
 
 # 2.c Generate list of bulletins to process
 echo '   Generating buoy list ...'
-# shellcheck disable=SC2312
 bulls=$(sed -e 's/export b//g' -e 's/=/ /' awipsbull.data | grep -v "#" | awk '{print $1}')
 
 # 2.d Looping over buoys running formbul
@@ -89,7 +87,6 @@ echo
 for bull in ${bulls}; do
     fname="${RUN}.${bull}.cbull"
     oname="awipsbull.${bull}.${cycle}.${RUN}.wave"
-    # shellcheck disable=SC2312
     headr=$(grep "b${bull}=" awipsbull.data | sed 's/=/ /g' | awk '{ print $3}')
     echo "Processing ${bull} (${headr} ${oname}) ..."
 
diff --git a/dev/scripts/exgfs_wave_prdgen_gridded.sh b/dev/scripts/exgfs_wave_prdgen_gridded.sh
index 07ee67f5d49..22a6a506e06 100755
--- a/dev/scripts/exgfs_wave_prdgen_gridded.sh
+++ b/dev/scripts/exgfs_wave_prdgen_gridded.sh
@@ -98,12 +98,9 @@ while [[ "${fhcnt}" -le "${FHMAX_WAV}" ]]; do
             echo "${nip} ${prepar} ${paridx} ${npart}"
             rm -f temp.grib2
             if [[ ${npart} -eq 0 ]]; then
-                #shellcheck disable=SC2312
                 ${WGRIB2} "${GRIBIN}" -s | grep ":${nip}" | "${WGRIB2}" -i "${GRIBIN}" -grib temp.grib2 > wgrib.out 2>&1
-                #shellcheck disable=SC2312
                 ${WGRIB2} temp.grib2 -append -grib "${GRIBOUT}"
             else
-                #shellcheck disable=SC2312
                 ${WGRIB2} "${GRIBIN}" -s | grep ":${prepar}" | grep "${paridx} in sequence" |
                     ${WGRIB2} -i "${GRIBIN}" -grib temp.grib2 > wgrib.out 2>&1
                 ${WGRIB2} temp.grib2 -append -grib "${GRIBOUT}"
diff --git a/dev/scripts/exglobal_atmos_analysis.sh b/dev/scripts/exglobal_atmos_analysis.sh
index a53153d97e8..31506dc2365 100755
--- a/dev/scripts/exglobal_atmos_analysis.sh
+++ b/dev/scripts/exglobal_atmos_analysis.sh
@@ -383,7 +383,6 @@ ${NLN} "${FIXgfs}/gsi/IASI_CLDDET.NL" IASI_CLDDET.NL
 #If using correlated error, link to the covariance files
 if [[ "${USE_CORRELATED_OBERRS}" == "YES" ]]; then
     if grep -q "Rcov" "${ANAVINFO}"; then
-        # shellcheck disable=SC2312
         mapfile -t covfile_array < <(find "${FIXgfs}/gsi/" -name "Rcov*")
         if ((${#covfile_array[@]} > 0)); then
             for covfile in "${covfile_array[@]}"; do
@@ -413,7 +412,6 @@ fi
 ##############################################################
 # CRTM Spectral and Transmittance coefficients
 mkdir -p crtm_coeffs
-# shellcheck disable=SC2312
 for file in $(awk '{if($1!~"!"){print $1}}' satinfo | sort | uniq); do
     if [[ ${file:0:4} == "hirs" ]]; then
         ${NLN} "${HIRS_FIX}/${file}.SpcCoeff.bin" "./crtm_coeffs/${file}.SpcCoeff.bin"
@@ -528,10 +526,9 @@ fi
 
 ##############################################################
 # Required bias guess files
-${NLN} "${GBIAS}" satbias_in
-${NLN} "${GBIASPC}" satbias_pc
-${NLN} "${GBIASAIR}" aircftbias_in
-${NLN} "${GRADSTAT}" radstat.gdas
+cpreq "${GBIAS}" satbias_in
+cpreq "${GBIASPC}" satbias_pc
+cpreq "${GBIASAIR}" aircftbias_in
 
 ##############################################################
 # Required model guess files
@@ -645,7 +642,6 @@ fi
 # If requested, link (and if tarred, de-tar obsinput.tar) into obs_input.* files
 if [[ "${USE_SELECT}" == "YES" ]]; then
     rm -f obs_input.*
-    # shellcheck disable=SC2312
     nl=$(file "${SELECT_OBS}" | cut -d: -f2 | grep -c tar)
     if [[ ${nl} -eq 1 ]]; then
         rm -f obsinput.tar
@@ -663,8 +659,8 @@ fi
 ##############################################################
 # If requested, copy and de-tar guess radstat file
 if [[ "${USE_RADSTAT}" == "YES" ]]; then
-    rm -f "${DATA}/unzip_radstat.sh"
-    cat > "${DATA}/unzip_radstat.sh" << EOF
+    rm -f "${DATA}/unzip_diag.sh"
+    cat > "${DATA}/unzip_diag.sh" << EOF
 #!/bin/bash
 diag_file=\$1
 diag_suffix=\$2
@@ -674,20 +670,21 @@ ${UNCOMPRESS} \$diag_file
 fnameges=\$(echo \$fname | sed 's/_ges//g')
 ${NMV} \$fname.\$fdate\$diag_suffix \$fnameges
 EOF
-    chmod 755 "${DATA}/unzip_radstat.sh"
+    chmod 755 "${DATA}/unzip_diag.sh"
 
     rm -f "${DATA}/cmdfile"
-    #shellcheck disable=SC2312
-    listdiag=$(tar -xvf radstat.gdas | cut -d' ' -f2 | grep _ges)
+    cpreq "${GRADSTAT}" radstat.tar
+    tar -xvf radstat.tar
+    listdiag=$(find ./ -maxdepth 1 -path "./diag_*_ges.*" -type f)
     for type in ${listdiag}; do
-        diag_file=$(echo "${type}" | cut -d',' -f1)
-        echo "${DATA}/unzip_radstat.sh ${diag_file} ${DIAG_SUFFIX:-}.nc4" >> "${DATA}/cmdfile"
+        diag_file=$(basename "${type}")
+        echo "${DATA}/unzip_diag.sh ${diag_file} ${DIAG_SUFFIX:-}.nc4" >> "${DATA}/cmdfile"
     done
 
     "${USHgfs}/run_mpmd.sh" "${DATA}/cmdfile" && true
     export err=$?
     if [[ ${err} -ne 0 ]]; then
-        err_exit "Failed to unzip radstat.gdas file!"
+        err_exit "Failed to unzip rad diag file!"
     fi
 fi # if [[ $USE_RADSTAT == "YES" ]
 
@@ -860,7 +857,6 @@ cat fort.2* > "${GSISTAT}"
 
 # If requested, create obsinput tarball from obs_input.* files
 if [[ ${RUN_SELECT} == "YES" ]]; then
-    # shellcheck disable=SC2312
     echo "$(date) START tar obs_input" >&2
     if [[ -s obsinput.tar ]]; then
         rm -f obsinput.tar
@@ -871,7 +867,6 @@ if [[ ${RUN_SELECT} == "YES" ]]; then
     chmod 750 "${SELECT_OBS}"
     ${CHGRP_CMD} "${SELECT_OBS}"
     rm -f obsinput.tar
-    # shellcheck disable=SC2312
     echo "$(date) END tar obs_input" >&2
 fi
 
@@ -907,7 +902,6 @@ if [[ "${GENDIAG}" == "YES" ]]; then
     cpfs gsidiags.tar "${COMOUT_ATMOS_ANALYSIS}/${APREFIX}gsidiags${DIAG_SUFFIX:-}.tar"
 fi
 
-# shellcheck disable=SC2312
 echo "${rCDUMP} ${PDY}${cyc} atminc done at $(date)" > "${COMOUT_ATMOS_ANALYSIS}/${APREFIX}increment.done.txt"
 
 ################################################################################
diff --git a/dev/scripts/exglobal_atmos_analysis_calc.sh b/dev/scripts/exglobal_atmos_analysis_calc.sh
index 17f55fd75a6..3f3224c53b5 100755
--- a/dev/scripts/exglobal_atmos_analysis_calc.sh
+++ b/dev/scripts/exglobal_atmos_analysis_calc.sh
@@ -177,7 +177,6 @@ if [[ "${DOGAUSFCANL}" == "YES" ]]; then
     fi
 fi
 
-# shellcheck disable=SC2312
 echo "${rCDUMP} ${PDY}${cyc} atmanl and sfcanl done at $(date)" > "${COMOUT_ATMOS_ANALYSIS}/${APREFIX}analysis.done.txt"
 
 ################################################################################
diff --git a/dev/scripts/exglobal_atmos_products.sh b/dev/scripts/exglobal_atmos_products.sh
index 24f0b311fd4..8ba75e0c40e 100755
--- a/dev/scripts/exglobal_atmos_products.sh
+++ b/dev/scripts/exglobal_atmos_products.sh
@@ -58,7 +58,6 @@ for ((nset = 1; nset <= downset; nset++)); do
     paramlist="paramlist${grp}"
     parmfile="${!paramlist}"
 
-    # shellcheck disable=SC2312
     ${WGRIB2} "${MASTER_FILE}" | grep -F -f "${parmfile}" | ${WGRIB2} -i -grib "${tmpfile}" "${MASTER_FILE}" && true
     export err=$?
     if [[ ${err} -ne 0 ]]; then
@@ -68,7 +67,6 @@ for ((nset = 1; nset <= downset; nset++)); do
     # Number of processors available to process $nset
     nproc=${ntasks}
 
-    # shellcheck disable=SC2312
     ncount=$(${WGRIB2} "${tmpfile}" | wc -l)
     if [[ "${nproc}" -gt "${ncount}" ]]; then
         echo "WARNING: Total no. of available processors '${nproc}' exceeds no. of records '${ncount}' in ${tmpfile}"
@@ -89,8 +87,7 @@ for ((nset = 1; nset <= downset; nset++)); do
         # if final record of is u-component, add next record v-component
         # if final record is land, add next record icec
         # grep returns 1 if no match is found, so temporarily turn off exit on non-zero rc
-        set +e
-        # shellcheck disable=SC2312
+        unset_strict
         ${WGRIB2} -d "${last}" "${tmpfile}" | grep -E -i "ugrd|ustm|uflx|u-gwd|land|maxuw"
         rc=$?
         set_strict
diff --git a/dev/scripts/exglobal_atmos_sfcanl.sh b/dev/scripts/exglobal_atmos_sfcanl.sh
index 2a72a8c3ede..e02e5aae0ab 100755
--- a/dev/scripts/exglobal_atmos_sfcanl.sh
+++ b/dev/scripts/exglobal_atmos_sfcanl.sh
@@ -76,7 +76,6 @@ else
 fi
 
 # If any snow files are missing, don't apply snow in the global_cycle step.
-# shellcheck disable=SC2312
 if [[ ! -f "${FNSNOA}" ]] || [[ ! -f "${FNSNOG}" ]]; then
     export FNSNOA=" "
     export CYCLVARS=FSNOL=99999.,FSNOS=99999.,
diff --git a/dev/scripts/exglobal_diag.sh b/dev/scripts/exglobal_diag.sh
index d5c79a4fd57..4d9aa5de94e 100755
--- a/dev/scripts/exglobal_diag.sh
+++ b/dev/scripts/exglobal_diag.sh
@@ -97,17 +97,17 @@ cat > "${DATA}/diag.sh" << EOF
 #!/bin/bash
 set -x
 
-type=\$1
+dtype=\$1
 loop=\$2
 string=\$3
 count=\$4
 suffix=\$5
 
 # Match files with this prefix
-diag_files=dir.*/\${type}_\${loop}
+diag_files=dir.*/\${dtype}_\${loop}
 
 # Name of combined diagnostic file from matched files
-out_diag_file=diag_\${type}_\${string}.${PDY}${cyc}\${suffix}
+out_diag_file=diag_\${dtype}_\${string}.${PDY}${cyc}\${suffix}
 
 # Combine diagnostic files
 if [[ \${count} -gt 1 ]]; then
@@ -149,19 +149,16 @@ for loop in ${loops}; do
     n=-1
     while [[ ${n} -lt ${ntype} ]]; do
         n=$((n + 1))
-        for type in ${diagtype[n]}; do
-            if [[ "${type}" == *"avhrr"* ]]; then
-                platform="${type##avhrr[23]}"
-                atype="avhrr${platform}"
-                type="${atype}"
+        for dtype in ${diagtype[n]}; do
+            if [[ "${dtype}" == *"avhrr"* ]]; then # recast dtype in avhrr form
+                dtype="avhrr${dtype##avhrr[23]}"
             fi
-            #shellcheck disable=SC2012,SC2312
-            count=$(ls dir.*/"${type}_${loop}"* 2> /dev/null | wc -l)
+            count=$(find ./ -path "./dir.*/${dtype}_${loop}*" -type f -printf "." | wc -c)
             if [[ ${count} -eq 0 ]]; then
                 continue
             fi
-            echo "${DATA}/diag.sh ${type} ${loop} ${string} ${count} ${DIAG_SUFFIX:-}.nc4" >> cmdfile
-            echo "diag_${type}_${string}.${PDY}${cyc}${DIAG_SUFFIX:-}.nc4${COMPRESS_SUFFIX:-}" >> "${diaglist[n]}"
+            echo "${DATA}/diag.sh ${dtype} ${loop} ${string} ${count} ${DIAG_SUFFIX:-}.nc4" >> cmdfile
+            echo "diag_${dtype}_${string}.${PDY}${cyc}${DIAG_SUFFIX:-}.nc4${COMPRESS_SUFFIX:-}" >> "${diaglist[n]}"
             numfile[n]=$((numfile[n] + 1))
         done
     done
diff --git a/dev/scripts/exglobal_enkf_sfc.sh b/dev/scripts/exglobal_enkf_sfc.sh
index 517b6cd40f6..514d453ff3d 100755
--- a/dev/scripts/exglobal_enkf_sfc.sh
+++ b/dev/scripts/exglobal_enkf_sfc.sh
@@ -113,9 +113,7 @@ if [[ ! -f "${FNSNOA}" || ! -f "${FNSNOG}" ]]; then
     export CYCLVARS="FSNOL=99999.,FSNOS=99999.,"
 else
     # Set CYCLVARS by checking grib date of current snogrb vs that of prev cycle
-    # shellcheck disable=SC2312
     snoa_count=$("${WGRIB}" -4yr "${FNSNOA}" 2> /dev/null | grep -i snowc | awk -F: '{print $3}' | awk -F= '{print $2}')
-    # shellcheck disable=SC2312
     snog_count=$("${WGRIB}" -4yr "${FNSNOG}" 2> /dev/null | grep -i snowc | awk -F: '{print $3}' | awk -F= '{print $2}')
     if [[ ${snoa_count} -le ${snog_count} ]]; then
         export FNSNOA=" "
diff --git a/dev/test/f90nmlcmp.sh b/dev/test/f90nmlcmp.sh
index 0350f17c32f..977eb2ce1a9 100755
--- a/dev/test/f90nmlcmp.sh
+++ b/dev/test/f90nmlcmp.sh
@@ -2,7 +2,7 @@
 
 # Compare two F90 namelists (forward and backward)
 
-# shellcheck disable=SC2155,SC2312
+# shellcheck disable=SC2155
 HOMEgfs=$(cd "$(dirname "$(readlink -f -n "${BASH_SOURCE[0]}")")/../.." && pwd -P)
 declare -rx HOMEgfs
 
diff --git a/dev/test/g2cmp.sh b/dev/test/g2cmp.sh
index 3a30350dd43..514f8bb163b 100755
--- a/dev/test/g2cmp.sh
+++ b/dev/test/g2cmp.sh
@@ -3,7 +3,7 @@
 # Compare two grib2 files with wgrib2
 # The files must have the same fields in the same order
 
-# shellcheck disable=SC2155,SC2312
+# shellcheck disable=SC2155
 HOMEgfs=$(cd "$(dirname "$(readlink -f -n "${BASH_SOURCE[0]}")")/../.." && pwd -P)
 declare -rx HOMEgfs
 
@@ -13,5 +13,4 @@ file2=${2:?}
 source "${HOMEgfs}/dev/ush/load_modules.sh" run
 
 # Use wgrib2 to compute correlations and print any record that does not have corr=1 for mismatch
-#shellcheck disable=SC2312
 wgrib2 "${file2}" -var -lev -rpn "sto_1" -import_grib "${file1}" -rpn "rcl_1:print_corr:print_rms" | grep -v "rpn_corr=1"
diff --git a/dev/test/nccmp.sh b/dev/test/nccmp.sh
index f7803fdf671..5c35dae0eca 100755
--- a/dev/test/nccmp.sh
+++ b/dev/test/nccmp.sh
@@ -1,6 +1,6 @@
 #! /usr/bin/env bash
 
-# shellcheck disable=SC2155,SC2312
+# shellcheck disable=SC2155
 HOMEgfs=$(cd "$(dirname "$(readlink -f -n "${BASH_SOURCE[0]}")")/../.." && pwd -P)
 declare -rx HOMEgfs
 
diff --git a/dev/test/netcdf_op_functions.sh b/dev/test/netcdf_op_functions.sh
index a9c5b8dc799..dbd7fab85ed 100644
--- a/dev/test/netcdf_op_functions.sh
+++ b/dev/test/netcdf_op_functions.sh
@@ -1,6 +1,5 @@
 #! /bin/env bash
 
-# shellcheck disable=SC2312
 # shellcheck disable=SC2317  # TODO: remove this when the script is corrected of errors
 
 if [[ -t 0 ]]; then
diff --git a/dev/ush/load_modules.sh b/dev/ush/load_modules.sh
index 263549f9f6c..673122d95d0 100755
--- a/dev/ush/load_modules.sh
+++ b/dev/ush/load_modules.sh
@@ -138,7 +138,6 @@ case "${MODULE_TYPE}" in
 
         # Detect the Python major.minor version
         _regex="[0-9]+\.[0-9]+"
-        # shellcheck disable=SC2312
         if [[ $(python --version) =~ ${_regex} ]]; then
             export PYTHON_VERSION="${BASH_REMATCH[0]}"
         else
diff --git a/dev/workflow/generate_workflows.sh b/dev/workflow/generate_workflows.sh
index f74a21bb3ea..8d9517370b9 100755
--- a/dev/workflow/generate_workflows.sh
+++ b/dev/workflow/generate_workflows.sh
@@ -540,7 +540,6 @@ for _case in "${_yaml_list[@]}"; do
     fi
 
     # Check if DATAROOT is already present; eval will return just DATAROOT from the sourcing
-    # shellcheck disable=SC2312
     eval "$(
         PDY=0 cyc=0 source "${_runtests}/EXPDIR/${_pslot}/config.base" >&/dev/null
         echo _dataroot="${STMP}/RUNDIRS/${_pslot}"
diff --git a/gempak/ush/gfs_meta_opc_na_ver.sh b/gempak/ush/gfs_meta_opc_na_ver.sh
index f3a8ed91074..956c5d72270 100755
--- a/gempak/ush/gfs_meta_opc_na_ver.sh
+++ b/gempak/ush/gfs_meta_opc_na_ver.sh
@@ -31,7 +31,7 @@ fcsthr="f00"
 
 # SET WHAT RUNS TO COMPARE AGAINST BASED ON MODEL CYCLE TIME.
 # seq won't give us any splitting problems, ignore warnings
-# shellcheck disable=SC2207,SC2312
+# shellcheck disable=SC2207
 case ${cyc} in
     00 | 12) lookbacks=($(IFS=$'\n' seq 6 6 84) $(IFS=$'\n' seq 96 12 120)) ;;
     06 | 18) lookbacks=($(IFS=$'\n' seq 6 6 84) $(IFS=$'\n' seq 90 12 126)) ;;
diff --git a/gempak/ush/gfs_meta_opc_np_ver.sh b/gempak/ush/gfs_meta_opc_np_ver.sh
index e6edfa90400..da95b6a0ba2 100755
--- a/gempak/ush/gfs_meta_opc_np_ver.sh
+++ b/gempak/ush/gfs_meta_opc_np_ver.sh
@@ -31,7 +31,7 @@ fcsthr="f00"
 
 # SET WHAT RUNS TO COMPARE AGAINST BASED ON MODEL CYCLE TIME.
 # seq won't give us any splitting problems, ignore warnings
-# shellcheck disable=SC2207,SC2312
+# shellcheck disable=SC2207
 case ${cyc} in
     00 | 12) lookbacks=($(IFS=$'\n' seq 6 6 84) $(IFS=$'\n' seq 96 12 120)) ;;
     06 | 18) lookbacks=($(IFS=$'\n' seq 6 6 84) $(IFS=$'\n' seq 90 12 126)) ;;
diff --git a/gempak/ush/gfs_meta_ver.sh b/gempak/ush/gfs_meta_ver.sh
index 8b47f614dd6..7693bee68c4 100755
--- a/gempak/ush/gfs_meta_ver.sh
+++ b/gempak/ush/gfs_meta_ver.sh
@@ -31,7 +31,7 @@ fcsthr="f00"
 MDL2="GFSHPC"
 #GENERATING THE METAFILES.
 # seq won't give us any splitting problems, ignore warnings
-# shellcheck disable=SC2207,SC2312
+# shellcheck disable=SC2207
 lookbacks=($(IFS=$'\n' seq 6 6 180) $(IFS=$'\n' seq 192 12 216))
 for lookback in "${lookbacks[@]}"; do
     init_time="$(date --utc +%Y%m%d%H -d "${PDY} ${cyc} - ${lookback} hours")"
diff --git a/modulefiles/gw_gsi.wcoss2.lua b/modulefiles/gw_gsi.wcoss2.lua
index c3c11c92679..7d30ae3e792 100644
--- a/modulefiles/gw_gsi.wcoss2.lua
+++ b/modulefiles/gw_gsi.wcoss2.lua
@@ -18,6 +18,8 @@ load(pathJoin("hdf5-D", (os.getenv("hdf5_ver") or "None")))
 load(pathJoin("pnetcdf-D", (os.getenv("pnetcdf_ver") or "None")))
 load(pathJoin("netcdf-D", (os.getenv("netcdf_ver") or "None")))
 
+load(pathJoin("libjpeg", (os.getenv("libjpeg_ver") or "None")))
+load(pathJoin("grib_util", (os.getenv("grib_util_ver") or "None")))
 load(pathJoin("prod_util", (os.getenv("prod_util_ver") or "None")))
 load(pathJoin("ncdiag-A", (os.getenv("ncdiag_ver") or "None")))
 load(pathJoin("crtm", (os.getenv("crtm_ver") or "None")))
diff --git a/sorc/build_ww3prepost.sh b/sorc/build_ww3prepost.sh
index 6496f66b724..e76a32a5fbc 100755
--- a/sorc/build_ww3prepost.sh
+++ b/sorc/build_ww3prepost.sh
@@ -1,7 +1,7 @@
 #! /usr/bin/env bash
 set -x
 
-# shellcheck disable=SC2312,SC2155
+# shellcheck disable=SC2155
 readonly HOMEgfs_=$(cd "$(dirname "$(readlink -f -n "${BASH_SOURCE[0]}")")/.." && pwd -P)
 cd "${HOMEgfs_}/sorc" || exit 1
 
diff --git a/ush/atmos_extractvars.sh b/ush/atmos_extractvars.sh
index 31cd61087bd..4a085a1ea9e 100755
--- a/ush/atmos_extractvars.sh
+++ b/ush/atmos_extractvars.sh
@@ -71,7 +71,6 @@ for outtype in "f2d" "f3d"; do
                     echo "FATAL ERROR: Failed to copy ${infile} to ${new_infile}."
                     exit 1
                 fi
-                # shellcheck disable=SC2312
                 ${WGRIB2} "${new_infile}" | grep -F -f "${varlist}" | ${WGRIB2} -i "${new_infile}" -append -grib "${outfile}"
             else
                 echo "WARNING: ${infile} does not exist in ${com_dir}."
@@ -91,7 +90,6 @@ for outtype in "f2d" "f3d"; do
                         echo "FATAL ERROR: Failed to copy ${infile} to ${new_infile}."
                         exit 1
                     fi
-                    # shellcheck disable=SC2312
                     ${WGRIB2} "${new_infile}" | grep -F -f "${varlist_d}" | ${WGRIB2} -i "${new_infile}" -append -grib "${outfile}"
                 else
                     echo "WARNING: ${infile} does not exist in ${com_dir}."
diff --git a/ush/extractvars_tools.sh b/ush/extractvars_tools.sh
index fe7a4d34a43..ead740aad5e 100644
--- a/ush/extractvars_tools.sh
+++ b/ush/extractvars_tools.sh
@@ -12,7 +12,6 @@ check_atmos() {
     touch "${requestedvar_in_allgrb2file}"
     for infilep in "${infile1p}" "${infile2p}"; do
         # It is permitted for an empty string to return if no parmlist vars are in infilep, therefore do not return exit 1 error
-        # shellcheck disable=SC2312
         ${WGRIB2} "${infilep}" | grep -F -f "${varlist}" >> "${requestedvar_in_allgrb2file}" || true
     done
     mapfile -t requestedvar_in_allgrb2file_arr < "${requestedvar_in_allgrb2file}"
@@ -35,9 +34,7 @@ daily_avg_atmos() {
     vcnt=1 #count variables in varlist_d
     while read -r vari; do
         davgtmp=${subdata}/atmos_tmp.ldy${fnd}.${vcnt}
-        # shellcheck disable=SC2312
         ${WGRIB2} "${outfile_p}" | grep "${vari}" | ${WGRIB2} -i "${outfile_p}" -fcst_ave 6hr "${davgtmp}"
-        # shellcheck disable=SC2312
         ${WGRIB2} "${davgtmp}" | ${WGRIB2} -i "${davgtmp}" -append -grib "${davg_file}"
         rm -f "${davgtmp}"
         vcnt=$((vcnt + 1))
diff --git a/ush/forecast_det.sh b/ush/forecast_det.sh
index 602e7d473fb..558c10ad8e3 100755
--- a/ush/forecast_det.sh
+++ b/ush/forecast_det.sh
@@ -43,7 +43,6 @@ UFS_det() {
 
     # However, if this was run before, a DATArestart/FV3_RESTART must exist with data in it.
     local file_array nrestarts
-    # shellcheck disable=SC2312
     mapfile -t file_array < <(find "${DATArestart}/FV3_RESTART" -name "????????.??0000.coupler.res" | sort)
     nrestarts=${#file_array[@]}
     if [[ ${nrestarts} -eq 0 ]]; then
diff --git a/ush/forecast_predet.sh b/ush/forecast_predet.sh
index 102ae65a5a4..00bb2b43aa3 100755
--- a/ush/forecast_predet.sh
+++ b/ush/forecast_predet.sh
@@ -676,7 +676,6 @@ CICE_predet() {
 
     # CICE does not have a concept of high frequency output like FV3
     # Convert output settings into an explicit list for CICE
-    # shellcheck disable=SC2312
     mapfile -t CICE_OUTPUT_FH < <(seq "${FHMIN}" "${FHOUT_ICE}" "${FHMAX}") || exit 10
 
     # Fix files
diff --git a/ush/interp_atmos_master.sh b/ush/interp_atmos_master.sh
index b43b05c889b..d592fbfb18a 100755
--- a/ush/interp_atmos_master.sh
+++ b/ush/interp_atmos_master.sh
@@ -58,7 +58,6 @@ for grid in "${grids[@]}"; do
         echo "FATAL ERROR: Failed during the execution of trim_rh"
         exit "${err}"
     fi
-    # shellcheck disable=SC2312
     var_count=$(${WGRIB2} "${output_file_prefix}_${grid}" -match "LAND|ICEC" | wc -l)
     if [[ "${var_count}" -eq 2 ]]; then
         mod_icec "${output_file_prefix}_${grid}"
diff --git a/ush/parsing_namelists_FV3.sh b/ush/parsing_namelists_FV3.sh
index dfdfecacb52..0d871ccbe17 100755
--- a/ush/parsing_namelists_FV3.sh
+++ b/ush/parsing_namelists_FV3.sh
@@ -52,7 +52,6 @@ FV3_namelists() {
         nrec=$(wc -l < "${FIELD_TABLE}")
         prec=${nrec}
         if ((dnats > 0)); then
-            # shellcheck disable=SC2312
             prec=$(grep -F -n TRACER "${FIELD_TABLE}" 2> /dev/null | tail -n "${dnats}" | head -1 | cut -d: -f1)
             prec=${prec:-0}
             prec=$((prec > 0 ? prec - 1 : prec))
diff --git a/ush/parsing_namelists_FV3_nest.sh b/ush/parsing_namelists_FV3_nest.sh
index 89e16efca30..268c600516a 100755
--- a/ush/parsing_namelists_FV3_nest.sh
+++ b/ush/parsing_namelists_FV3_nest.sh
@@ -4,7 +4,6 @@
 
 # Disable variable not used warnings and 'masking return value' warnings
 # shellcheck disable=SC2034
-# shellcheck disable=SC2312
 FV3_namelists_nest() {
 
     # First argument tells us which namelist we're writing:
diff --git a/ush/preamble.sh b/ush/preamble.sh
index df24338ac83..8e96496e911 100755
--- a/ush/preamble.sh
+++ b/ush/preamble.sh
@@ -34,11 +34,18 @@ declare -x PS4='+ $(basename ${BASH_SOURCE[0]:-${FUNCNAME[0]:-"Unknown"}})[${LIN
 set_strict() {
     if [[ ${STRICT:-"YES"} == "YES" ]]; then
         # Exit on error or undefined variable
-        # TODO: Also error in a pipeline (e.g. if and command in "cmd | cmd2" fails)
-        set -eu # -o pipefail
+        set -eu
+        # Exit on error in a pipeline (e.g. if and command in "cmd | cmd2" fails)
+        set -o pipefail
     fi
 }
 
+unset_strict() {
+    # Turn off strict mode
+    set +eu
+    set +o pipefail
+}
+
 set_trace() {
     # Print the script name and line number of each command as it is
     #   executed when using trace.
@@ -181,6 +188,7 @@ source "${HOMEgfs}/ush/bash_utils.sh"
 shopt -s nullglob # Allow null globs instead of treating * as literal
 export SHELLOPTS
 declare -xf set_strict
+declare -xf unset_strict
 declare -xf set_trace
 declare -xf postamble
 declare -xf err_exit
diff --git a/ush/radmon_diag_ck.sh b/ush/radmon_diag_ck.sh
index a8e65a57fe5..2f2d9122030 100755
--- a/ush/radmon_diag_ck.sh
+++ b/ush/radmon_diag_ck.sh
@@ -68,7 +68,6 @@ zero_len_diag=""
 #---------------------------------------------
 #  get list of diag files in the radstat file
 #
-# shellcheck disable=SC2312
 radstat_contents=$(tar -tf "${radstat_file}" | grep -Po '(?<=diag_).*(?=_ges.*)')
 
 #---------------------------------------------
@@ -112,7 +111,6 @@ declare -A file_sizes
 # Parse the filename and filesize from tar's verbose output and store in an associative array
 # Field $6 of verbose tar output is the filename, field $3 is the size
 # Caution: this method is not robust if the filename contains spaces
-# shellcheck disable=SC2312
 while IFS='|' read -r name size; do
     file_sizes[${name}]=${size}
 done < <(tar -vtf "${radstat_file}" --wildcards '*_ges*' | awk '$3 ~ /^[0-9]+$/ { print $6 "|" $3 }')
diff --git a/ush/run_mpmd.sh b/ush/run_mpmd.sh
index 89e65daaa97..36ddc4bc4cc 100755
--- a/ush/run_mpmd.sh
+++ b/ush/run_mpmd.sh
@@ -63,13 +63,12 @@ if [[ "${launcher:-}" =~ ^srun.* ]]; then #  srun-based system e.g. Hera, Orion,
     # Slurm requires a counter in front of each line in the script
     # Read the incoming cmdfile and create srun usable cmdfile
     nm=0
-    # shellcheck disable=SC2312
     while IFS= read -r line; do
         echo "${nm} ${line}" >> "${mpmd_cmdfile}"
         ((nm = nm + 1))
     done < "${cmdfile}"
 
-    set +e
+    unset_strict
     # shellcheck disable=SC2086
     ${launcher:-} ${mpmd_opt:-} -n ${nprocs} "${mpmd_cmdfile}"
     err=$?
@@ -81,7 +80,6 @@ elif [[ "${launcher:-}" =~ ^mpiexec.* ]]; then # mpiexec
     # Read the incoming cmdfile and create mpiexec usable cmdfile
     nm=0
     echo "#!/bin/bash" >> "${mpmd_cmdfile}"
-    # shellcheck disable=SC2312
     while IFS= read -r line; do
         echo "${line} > mpmd.${nm}.out" >> "${mpmd_cmdfile}"
         ((nm = nm + 1))
diff --git a/ush/syndat_getjtbul.sh b/ush/syndat_getjtbul.sh
index 0ce21ef7efd..78337be415c 100755
--- a/ush/syndat_getjtbul.sh
+++ b/ush/syndat_getjtbul.sh
@@ -66,7 +66,6 @@ find="${ymd} ${cyc}"
 echo "looking for string ${find} in ${jtwcdir}/tropcyc"
 
 rm -f jtwcbul
-# shellcheck disable=SC2312
 grep "${ymd} ${cyc}" "${jtwcdir}/tropcyc" | grep JTWC > jtwcbul
 if [[ -s jtwcbul ]]; then
     echo "String found: contents of JTWC bulletin are:"
@@ -76,7 +75,6 @@ else
 fi
 
 if [[ "${cyc}" == "00" ]]; then
-    # shellcheck disable=SC2312
     grep "${ymd} ${cyc}" "${jtwcdirm1}/tropcyc" | grep JTWC >> jtwcbul
     if [[ -s jtwcbul ]]; then
         echo "String found: contents of JTWC bulletin are:"
@@ -104,12 +102,12 @@ fi
 pgm=$(basename "${EXECgfs}/syndat_getjtbul.x")
 export pgm
 if [[ -s prep_step ]]; then
-    set +u
+    unset_strict
     source prep_step
-    set -u
+    set_strict
 else
     [[ -f errfile ]] && rm errfile
-    # shellcheck disable=SC2046,SC2312
+    #shellcheck disable=SC2046
     unset FORT00 $(env | grep "^FORT[0-9]\{1,\}=" | awk -F= '{print $1}')
 fi
 
@@ -117,7 +115,6 @@ rm -f fnoc
 
 export FORT11=jtwcbul
 export FORT51=fnoc
-# shellcheck disable=SC2312
 time -p "${EXECgfs}/${pgm}" 2> errfile
 errget=$?
 cat errfile
diff --git a/ush/syndat_qctropcy.sh b/ush/syndat_qctropcy.sh
index deef9ad515a..74db606b0a0 100755
--- a/ush/syndat_qctropcy.sh
+++ b/ush/syndat_qctropcy.sh
@@ -229,12 +229,12 @@ cpreq "${slmask}" slmask.126
 pgm=$(basename "${EXECgfs}/syndat_qctropcy.x")
 export pgm
 if [[ -s prep_step ]]; then
-    set +u
+    unset_strict
     source prep_step
-    set -u
+    set_strict
 else
     [[ -f errfile ]] && rm errfile
-    # shellcheck disable=SC2046,SC2312
+    # shellcheck disable=SC2046
     unset FORT00 $(env | grep "^FORT[0-9]\{1,\}=" | awk -F= '{print $1}')
 fi
 
diff --git a/ush/tropcy_relocate_extrkr.sh b/ush/tropcy_relocate_extrkr.sh
index 8427908ba6b..33539aee36f 100755
--- a/ush/tropcy_relocate_extrkr.sh
+++ b/ush/tropcy_relocate_extrkr.sh
@@ -299,9 +299,9 @@ case ${cmodel} in
         ;;
     other)
         cat << EOF
-Model selected by user is ${cmodel}, which is a 
+Model selected by user is ${cmodel}, which is a
 user-defined model, NOT operational....
- 
+
 EOF
         model=9
         ;;
@@ -417,7 +417,7 @@ EOF
 
 !!! FATAL ERROR in $(basename "$0"):
 !!! Input analysis file cannot be found.
-!!! The tracker is looking for this file in:  
+!!! The tracker is looking for this file in:
 !!! ---->  ${otherdir}/${fnamebeg}00${fnameend}
 !!! Please check the directory to make sure the file
 !!! is there and then submit this job again.
@@ -456,7 +456,6 @@ fi
 
 cpfs "${DATA}/tcvitals" "${vdir}/vitals.${symd}${dishh}"
 
-# shellcheck disable=SC2312
 grep -v TEST "${vdir}/vitals.${symd}${dishh}" |
     awk 'substr($0,6,1) !~ /[8-9]/ {print $0}' > "${vdir}/tempvit.nonameless"
 
@@ -558,7 +557,7 @@ if [[ -s "${DATA}/prep_step" ]]; then
 else
     [[ -f errfile ]] && rm errfile
     export XLFUNITS=0
-    # shellcheck disable=SC2046,SC2312
+    # shellcheck disable=SC2046
     unset $(env | grep XLFUNIT | awk -F= '{print $1}')
     export XLFRTEOPTS="${XLFRTEOPTS:+${XLFRTEOPTS}:}unit_vars=yes"
 fi
@@ -592,7 +591,7 @@ else
     msg=$(
         cat << EOF
 
-!!! FATAL ERROR: An error occurred while running supvitql, 
+!!! FATAL ERROR: An error occurred while running supvitql,
 !!! which is the program that updates the TC Vitals file.
 !!! Return code from supvitql = ${err}
 !!! model= ${cmodel}, forecast initial time = ${symd}${dishh}
@@ -614,18 +613,17 @@ fi
 numvitrecs=$(wc -l "${vdir}/vitals.upd.${cmodel}.${symd}${dishh}")
 if [[ "${numvitrecs}" -eq 0 ]]; then
     cat << EOF
- 
-!!! ERROR -- There are no vitals records for this time period 
+
+!!! ERROR -- There are no vitals records for this time period
 !!! in the UPDATED vitals file.
 !!! File ${vdir}/vitals.upd.${cmodel}.${symd}${dishh} is empty.
 !!! Please check the dates and submit this job again....
- 
+
 EOF
     err=8
     err_exit
 fi
 
-# shellcheck disable=SC2312
 cat << EOF | tee stormlist
 
 
@@ -634,7 +632,7 @@ cat << EOF | tee stormlist
 |        STORM SELECTION         |
 *--------------------------------*
 
-Below is a list of the storms to be processed: 
+Below is a list of the storms to be processed:
 
 $(cat "${vdir}/vitals.upd.${cmodel}.${symd}${dishh}")
 
@@ -680,8 +678,8 @@ done
 cat << EOF
 
 -----------------------------------------
-  NOW CUTTING APART INPUT GRIB FILES TO 
-  CREATE 1 BIG GRIB INPUT FILE 
+  NOW CUTTING APART INPUT GRIB FILES TO
+  CREATE 1 BIG GRIB INPUT FILE
 -----------------------------------------
 
 EOF
@@ -706,8 +704,8 @@ if [[ "${model}" -eq 5 ]]; then
 *******************************************************************
 !!! NGM model has been selected, but there are no storms in the
 !!! TC Vitals file that are from NHC.  Therefore, unless you have
-!!! entered your own auxiliary TC vitals file that has a storm 
-!!! within the NGM domain, the tracker will exit after reading 
+!!! entered your own auxiliary TC vitals file that has a storm
+!!! within the NGM domain, the tracker will exit after reading
 !!! in the analysis data.
 *******************************************************************
 
@@ -764,9 +762,9 @@ EOF
                 cat << EOF
 
 !!! FATAL ERROR using ${COPYGB} to interpolate ngm data.  We will stop execution because
-!!! some variables may have been copied okay, while some obviously have not, 
+!!! some variables may have been copied okay, while some obviously have not,
 !!! and that could lead to unreliable results from the tracker.  Check to make
-!!! sure you've allocated enough memory for this job (error 134 using ${COPYGB} is 
+!!! sure you've allocated enough memory for this job (error 134 using ${COPYGB} is
 !!! typically due to using more memory than you've allocated).  Exiting.....
 
 EOF
@@ -804,8 +802,8 @@ if [[ "${model}" -eq 6 ]]; then
 *******************************************************************
 !!! NAM model has been selected, but there are no storms in the
 !!! TC Vitals file that are from NHC.  Therefore, unless you have
-!!! entered your own auxiliary TC vitals file that has a storm 
-!!! within the NAM domain, the tracker will exit after reading 
+!!! entered your own auxiliary TC vitals file that has a storm
+!!! within the NAM domain, the tracker will exit after reading
 !!! in the analysis data.
 *******************************************************************
 
@@ -861,9 +859,9 @@ EOF
             cat << EOF
 
 !!! FATAL ERROR using ${COPYGB} to interpolate nam data.  We will stop execution because
-!!! some variables may have been copied okay, while some obviously have not, 
+!!! some variables may have been copied okay, while some obviously have not,
 !!! and that could lead to unreliable results from the tracker.  Check to make
-!!! sure you've allocated enough memory for this job (error 134 using ${COPYGB} is 
+!!! sure you've allocated enough memory for this job (error 134 using ${COPYGB} is
 !!! typically due to using more memory than you've allocated).  Exiting.....
 
 EOF
@@ -963,7 +961,6 @@ EOF
                 "SurfaceV") parm="VGRD:10 m" ;;
                 *) ;;
             esac
-            # shellcheck disable=SC2312
             grep "${parm}" "${TMPDIR}/gfs.ix" | ${WGRIB:?} -s "${gfile}" -i -grib -append \
                 -o "${vdir}/gfsgribfile.${symd}${dishh}"
         done
@@ -1025,7 +1022,6 @@ EOF
                     "SurfaceV") parm="VGRD:10 m" ;;
                     *) ;;
                 esac
-                # shellcheck disable=SC2312
                 grep "${parm}" "${TMPDIR}/gdas.ix" | ${WGRIB:?} -s "${gfile}" -i -grib -append \
                     -o "${vdir}/gdasgribfile.${symd}${dishh}"
             done
@@ -1067,7 +1063,6 @@ EOF
                     "SurfaceV") parm="VGRD:10 m" ;;
                     *) ;;
                 esac
-                # shellcheck disable=SC2312
                 grep "${parm}" "${TMPDIR}/gdas.ix" | ${WGRIB2:?} -i "${gfile}" -append -grib \
                     "${vdir}/gdasgribfile.${symd}${dishh}"
             done
@@ -1116,7 +1111,6 @@ EOF
                 "SurfaceV") parm="VGRD:10 m" ;;
                 *) ;;
             esac
-            # shellcheck disable=SC2312
             grep "${parm}" "${TMPDIR}/mrf.ix" | ${WGRIB:?} -s "${gfile}" -i -grib -append \
                 -o "${vdir}/mrfgribfile.${symd}${dishh}"
         done
@@ -1155,7 +1149,6 @@ EOF
         ${WGRIB:?} -s "${gfile}" > "${TMPDIR}/ukmet.ix"
 
         for parm in ${wgrib_parmlist}; do
-            # shellcheck disable=SC2312
             grep "${parm}" "${TMPDIR}/ukmet.ix" | ${WGRIB:?} -s "${gfile}" -i -grib -append \
                 -o "${vdir}/ukmetgribfile.${symd}${dishh}"
         done
@@ -1208,7 +1201,6 @@ EOF
                 "SurfaceV") parm="VGRD:19 m" ;;
                 *) ;;
             esac
-            # shellcheck disable=SC2312
             grep "${parm}" "${TMPDIR}/ngps.ix" | grep "${vtstring}" |
                 ${WGRIB:?} -s "${gfile}" -i -grib -append -o "${vdir}/ngpsgribfile.${symd}${dishh}"
         done
@@ -1235,7 +1227,6 @@ if [[ "${model}" -eq 9 ]]; then
 
     rm -f "${vdir}/otherlatlon.pgrb.${symdh}"
 
-    # shellcheck disable=SC2312
     gridtyp=$(${WGRIB:?} -GDS10 "${otherdir}/${fnamebeg}00${fnameend}" |
         awk -FGDS10= '{print $2}' | awk '{print $6}' | sed -n 1p)
 
@@ -1266,7 +1257,6 @@ EOF
                     "SurfaceV") parm="VGRD:10 m" ;;
                     *) ;;
                 esac
-                # shellcheck disable=SC2312
                 grep "${parm}" "${TMPDIR}/other.ix" | ${WGRIB:?} -s "${gfile}" -i -grib -append \
                     -o "${vdir}/otherlatlon.pgrb.${symdh}"
             done
@@ -1325,9 +1315,9 @@ EOF
                     cat << EOF
 
 !!! FATAL ERROR using ${COPYGB} to interpolate data.  We will stop execution because
-!!! some variables may have been copied okay, while some obviously have not, 
+!!! some variables may have been copied okay, while some obviously have not,
 !!! and that could lead to unreliable results from the tracker.  Check to make
-!!! sure you've allocated enough memory for this job (error 134 using ${COPYGB} is 
+!!! sure you've allocated enough memory for this job (error 134 using ${COPYGB} is
 !!! typically due to using more memory than you've allocated).  Exiting.....
 
 EOF
@@ -1425,7 +1415,7 @@ if [[ -s "${DATA}/prep_step" ]]; then
 else
     rm -f errfile
     export XLFUNITS=0
-    # shellcheck disable=SC2046,SC2312
+    # shellcheck disable=SC2046
     unset $(env | grep XLFUNIT | awk -F= '{print $1}')
     export XLFRTEOPTS="${XLFRTEOPTS:+${XLFRTEOPTS}:}unit_vars=yes"
 fi
diff --git a/ush/wave_extractvars.sh b/ush/wave_extractvars.sh
index dde21a2c690..2bef8368813 100755
--- a/ush/wave_extractvars.sh
+++ b/ush/wave_extractvars.sh
@@ -34,7 +34,6 @@ for ((nh = FHOUT_WAV_EXTRACT; nh <= FHMAX_WAV; nh = nh + FHOUT_WAV_EXTRACT)); do
             echo "FATAL ERROR: Failed to copy ${infile} to ${new_infile}."
             exit 1
         fi
-        # shellcheck disable=SC2312
         ${WGRIB2} "${new_infile}" | grep -F -f "${varlist_wav}" | ${WGRIB2} -i "${new_infile}" -append -grib "${outfile}"
     else
         echo "WARNING: ${infile} does not exist in ${com_dir}."
diff --git a/ush/wave_tar.sh b/ush/wave_tar.sh
index e24def1e11f..e23162dd47e 100755
--- a/ush/wave_tar.sh
+++ b/ush/wave_tar.sh
@@ -87,7 +87,6 @@ tardone='no'
 sleep_interval=10
 
 while [[ "${tardone}" == "no" ]]; do
-    # shellcheck disable=SC2312
     nf=$(find . -maxdepth 1 -type f -name "*.${filext}" -printf '.' | wc -c)
     nbm2=$((nb - 2))
     if [[ ${nf} -ge ${nbm2} ]]; then