diff --git a/cice.setup b/cice.setup
index 43fdd836c..3efe94827 100755
--- a/cice.setup
+++ b/cice.setup
@@ -40,6 +40,7 @@ set suitebuild  = true
 set suitereuse  = true
 set suiterun    = false
 set suitesubmit = true
+set ignoreuserset = false
 
 if ($#argv < 1) then
   set helpheader = 1
@@ -98,6 +99,7 @@ DESCRIPTION
     --acct     : account number for the batch submission
     --grid, -g : grid, grid (default = ${grid})
     --set,  -s : case option setting(s), comma separated (default = " ")
+    --ignore-user-set: ignore ~/.cice_set if it exists
     --queue    : queue for the batch submission
 
     For testing
@@ -112,7 +114,7 @@ DESCRIPTION
     --diff     : generate comparison against another case
     --report   : automatically post results when tests are complete
     --coverage : generate and report test coverage metrics when tests are complete,
-                 requires GNU compiler (ie. normally ``--env gnu``)
+                 requires GNU compiler (ie. normally --env gnu)
     --setup-only         : for suite, setup testcases, no build, no submission
     --setup-build        : for suite, setup and build testcases, no submission
     --setup-build-run    : for suite, setup, build, and run interactively
@@ -263,6 +265,10 @@ while (1)
     set suitesubmit = true
     shift argv
 
+  else if ("$option" == "--ignore-user-set") then
+    set ignoreuserset = true
+    shift argv
+
 # arguments with settings
   else
     shift argv
@@ -412,6 +418,17 @@ set vers = ${ICE_VERSION}
 set shhash = `echo ${hash} | cut -c 1-10`
 
 if ( ${dosuite} == 0 ) then
+  # grab user defined default sets
+  if ("${ignoreuserset}" == "false" && -e ~/.cice_set) then
+    set setsu1 = `cat ~/.cice_set`
+    # get rid of spaces if they exist!
+    set setsuser = `echo ${setsu1} | sed 's/ //g'`
+    if ( ${sets} == "" ) then
+      set sets = "${setsuser}"
+    else
+      set sets = "${setsuser},${sets}"
+    endif
+  endif
   set teststring = "${test} ${grid} ${pesx} ${sets}"
   if ( $bfbcomp != ${spval} ) then
     if ( ${sets} == "" ) then
diff --git a/cicecore/cicedynB/general/ice_init.F90 b/cicecore/cicedynB/general/ice_init.F90
index c0f7a4eaa..66c725834 100644
--- a/cicecore/cicedynB/general/ice_init.F90
+++ b/cicecore/cicedynB/general/ice_init.F90
@@ -1290,12 +1290,12 @@ subroutine input_data
          write(nu_diag,1012) ' calc_strair      = ', calc_strair,' calculate wind stress and speed'
          write(nu_diag,1012) ' rotate_wind      = ', rotate_wind,' rotate wind/stress to computational grid'
          write(nu_diag,1012) ' formdrag         = ', formdrag,' use form drag parameterization'
-         if (trim(atmbndy) == 'constant') then
+         if (trim(atmbndy) == 'default') then
             tmpstr2 = ': stability-based boundary layer'
             write(nu_diag,1012) ' highfreq         = ', highfreq,' high-frequency atmospheric coupling'
             write(nu_diag,1022) ' natmiter         = ', natmiter,' number of atmo boundary layer iterations'
             write(nu_diag,1006) ' atmiter_conv     = ', atmiter_conv,' convergence criterion for ustar'
-         elseif (trim(atmbndy) == 'default') then
+         elseif (trim(atmbndy) == 'constant') then
             tmpstr2 = ': boundary layer uses bulk transfer coefficients'
          endif
          write(nu_diag,*) 'atmbndy          = ', trim(atmbndy),trim(tmpstr2)
diff --git a/configuration/scripts/parse_namelist.sh b/configuration/scripts/parse_namelist.sh
index c94420f6e..ea539a2d0 100755
--- a/configuration/scripts/parse_namelist.sh
+++ b/configuration/scripts/parse_namelist.sh
@@ -5,12 +5,15 @@ if [[ "$#" -ne 2 ]]; then
   exit -1
 fi
 
+scriptname=`basename "$0"`
 filename=$1
 filemods=$2
 
 #echo "$0 $1 $2" 
 echo "running parse_namelist.sh"
 foundstring="FoundSTRING"
+vnamearray=()
+valuearray=()
 
 while read -r line
 do
@@ -24,17 +27,39 @@ do
     value=`echo $line | sed "s|^[[:space:]]*\([^[:space:]]*\)[[:space:]]*=[[:space:]]*\([^[:space:]]*\).*$|\2|g"`
 #    echo "$line $vname $value"
 
+    found=${foundstring}
+    for i in "${!vnamearray[@]}"; do
+      if [[ "${found}" == "${foundstring}" ]]; then
+        vn=${vnamearray[$i]}
+        vv=${valuearray[$i]}
+#        echo "names/values $i ${vname} ${vn} ${value} ${vv}"
+        if [[ "$vname" == "$vn" ]]; then
+          found=$i
+          if [[ "$value" != "${vv}" ]]; then
+#            echo "names/values $i ${vname} ${vn} ${value} ${vv}"
+            echo "${scriptname} WARNING: re-overriding $vname from ${vv} to ${value}"
+          fi
+        fi
+      fi
+    done
+
     #sed -i 's|\(^\s*'"$vname"'\s*\=\s*\)\(.*$\)|\1'"$value"'|g' $filename
     cp ${filename} ${filename}.check
     sed -i.sedbak -e 's|\(^[[:space:]]*'"$vname"'[[:space:]]*=[[:space:]]*\)\(.*$\)|\1'"$foundstring"'|g' ${filename}.check
     grep -q ${foundstring} ${filename}.check
     if [ $? -eq 0 ]; then
       sed -i.sedbak -e 's|\(^[[:space:]]*'"$vname"'[[:space:]]*=[[:space:]]*\)\(.*$\)|\1'"$value"'|g' ${filename}
+      if [[ "${found}" == "${foundstring}" ]]; then
+        vnamearray+=($vname)
+        valuearray+=($value)
+      else
+        valuearray[$found]=${value}
+      fi
       if [[ -e "${filename}.sedbak" ]]; then
         rm ${filename}.sedbak
       fi
     else
-      echo "$0 ERROR: parsing error for ${vname}"
+      echo "${scriptname} ERROR: parsing error for ${vname}"
       exit -99
     fi
     rm ${filename}.check ${filename}.check.sedbak
diff --git a/configuration/scripts/parse_settings.sh b/configuration/scripts/parse_settings.sh
index f797dbebe..d6ed31c15 100755
--- a/configuration/scripts/parse_settings.sh
+++ b/configuration/scripts/parse_settings.sh
@@ -5,11 +5,15 @@ if [[ "$#" -ne 2 ]]; then
   exit -1
 fi
 
+scriptname=`basename "$0"`
 filename=$1
 filemods=$2
 
 #echo "$0 $1 $2" 
 echo "running parse_settings.sh"
+foundstring="FoundSTRING"
+vnamearray=()
+valuearray=()
 
 while read -r line
 do
@@ -23,8 +27,32 @@ do
     value=`echo $line | sed "s|\(^[[:space:]]*set[^[:space:]]*\)[[:space:]][[:space:]]*\([^[:space:]]*\)[[:space:]][[:space:]]*\([^[:space:]]*\).*$|\3|g"`
 #    echo "$line $vname $value"
 
+    found=${foundstring}
+    for i in "${!vnamearray[@]}"; do
+      if [[ "${found}" == "${foundstring}" ]]; then
+        vn=${vnamearray[$i]}
+        vv=${valuearray[$i]}
+#        echo "names/values $i ${vname} ${vn} ${value} ${vv}"
+        if [[ "$vname" == "$vn" ]]; then
+          found=$i
+          if [[ "$value" != "${vv}" ]]; then
+#            echo "names/values $i ${vname} ${vn} ${value} ${vv}"
+            echo "${scriptname} WARNING: re-overriding $vname from ${vv} to ${value}"
+          fi
+        fi
+      fi
+    done
+
     #sed -i 's|\(^\s*set.* '"$vname"' \)[^#]*\(#*.*$\)|\1 '"$value"'  \2|g' $filename
     sed -i.sedbak -e 's|\(^[[:space:]]*set.* '"$vname"' \)[^#]*\(#*.*$\)|\1 '"$value"'  \2|g' $filename
+
+    if [[ "${found}" == "${foundstring}" ]]; then
+      vnamearray+=($vname)
+      valuearray+=($value)
+    else
+      valuearray[$found]=${value}
+    fi
+
     if [[ -e "${filename}.sedbak" ]]; then
       rm ${filename}.sedbak
     fi
diff --git a/configuration/scripts/tests/cice.lcov.csh b/configuration/scripts/tests/cice.lcov.csh
index 8107778d9..5772833d1 100644
--- a/configuration/scripts/tests/cice.lcov.csh
+++ b/configuration/scripts/tests/cice.lcov.csh
@@ -9,7 +9,7 @@ set lcovhtmldir = lcov_cice_${report_name}
 genhtml -o ./${lcovhtmldir} --precision 2 -t "${report_name}" total.info
 
 rm -r -f ${lcovrepo}
-git clone https://github.com/apcraig/${lcovrepo}
+git clone --depth=1 https://github.com/apcraig/${lcovrepo}
 cp -p -r ${lcovhtmldir} ${lcovrepo}/
 
 cd ${lcovrepo}
diff --git a/configuration/scripts/tests/cice_test_codecov.csh b/configuration/scripts/tests/cice_test_codecov.csh
index be9399f1b..d9a69e898 100755
--- a/configuration/scripts/tests/cice_test_codecov.csh
+++ b/configuration/scripts/tests/cice_test_codecov.csh
@@ -29,7 +29,7 @@ cd ${testdir}
 # Check out current cice master
 echo " "
 echo "*** checkout current cice master ***"
-git clone https://github.com/cice-consortium/cice cice.master.${date} --recursive
+git clone --depth=1 https://github.com/cice-consortium/cice cice.master.${date} --recursive
 cd cice.master.${date}
 set hash = `git rev-parse --short HEAD `
 cd ../
@@ -40,7 +40,7 @@ cd ../
 # This also copies in all dot file at the root that do not start with .g (ie. .git*)
 echo " "
 echo "*** checkout current test_cice_master ***"
-git clone https://github.com/apcraig/test_cice_icepack test_cice_icepack.${date}
+git clone --depth=1 https://github.com/apcraig/test_cice_icepack test_cice_icepack.${date}
 cd test_cice_icepack.${date}
 echo " "
 echo "*** remove current files and copy in cice master files ***"
diff --git a/configuration/scripts/tests/report_results.csh b/configuration/scripts/tests/report_results.csh
index e3f8eed70..2eb3731d5 100755
--- a/configuration/scripts/tests/report_results.csh
+++ b/configuration/scripts/tests/report_results.csh
@@ -25,7 +25,7 @@ set wikirepo = "https://github.com/CICE-Consortium/Test-Results.wiki.git"
 set wikiname = Test-Results.wiki
 
 rm -r -f ${wikiname}
-git clone ${wikirepo} ${wikiname}
+git clone --depth=1 ${wikirepo} ${wikiname}
 if ($status != 0) then
   echo " "
   echo "${0}: ERROR git clone failed"
diff --git a/doc/source/user_guide/ug_running.rst b/doc/source/user_guide/ug_running.rst
index 8befee9cb..96c3154f7 100644
--- a/doc/source/user_guide/ug_running.rst
+++ b/doc/source/user_guide/ug_running.rst
@@ -202,7 +202,10 @@ specifies the compilation environment associated with the machine.  This should
   specifies the grid.  This is a string and for the current CICE driver, gx1, gx3, and tx1 are supported. (default = gx3)
 
 ``--set``,  ``-s`` SET1,SET2,SET3
-  specifies the optional settings for the case.  The settings for ``--suite`` are defined in the suite file.  Multiple settings can be specified by providing a comma deliminated set of values without spaces between settings.  The available settings are in **configurations/scripts/options** and ``cice.setup --help`` will also list them.  These settings files can change either the namelist values or overall case settings (such as the debug flag).
+  specifies the optional settings for the case.  The settings for ``--suite`` are defined in the suite file.  Multiple settings can be specified by providing a comma deliminated set of values without spaces between settings.  The available settings are in **configurations/scripts/options** and ``cice.setup --help`` will also list them.  These settings files can change either the namelist values or overall case settings (such as the debug flag).  For cases and tests (not suites), settings defined in **~/.cice_set** will be included in the --set options.  This behaviour can be overridden with the `--ignore-user-set`` command line option.
+
+``--ignore-user-set``
+  ignores settings defined in **~/.cice.set** (if it exists) for cases and tests.  **~/.cice_set** is always ignored for test suites.
 
 For CICE, when setting up cases, the ``--case`` and ``--mach`` must be specified.  
 It's also recommended that ``--env`` be set explicitly as well.  
@@ -229,6 +232,8 @@ change the defaults.  This is done as part of the ``cice.setup`` and the
 modifications are resolved in the **cice.settings** and **ice_in** file placed in 
 the case directory.  If multiple options are chosen that conflict, then the last
 option chosen takes precedent.  Not all options are compatible with each other.
+Settings on the command line will take precedent over serttings defined in 
+**~/.cice_set**.
 
 Some of the options are
 
diff --git a/doc/source/user_guide/ug_testing.rst b/doc/source/user_guide/ug_testing.rst
index 8f8fe9441..afe7849bc 100644
--- a/doc/source/user_guide/ug_testing.rst
+++ b/doc/source/user_guide/ug_testing.rst
@@ -56,6 +56,8 @@ For individual tests, the following command line options can be set
 
 ``--set`` SET1,SET2,SET3 (see :ref:`case_options`)
 
+``--ignore-user-set`` (see :ref:`case_options`)
+
 ``--acct`` ACCOUNT (see :ref:`case_options`)
 
 ``--grid`` GRID (see :ref:`case_options`)