diff --git a/.gitignore b/.gitignore
index 7ec31341da..26dc864032 100644
--- a/.gitignore
+++ b/.gitignore
@@ -27,6 +27,31 @@ CMakeFiles/
 # don't ignore cism build utilities directory
 !components/cism/**/build
 
+# configure / build files
+bld/*CESM_cppdefs
+bld/*Filepath
+bld/*config_cache.xml
+
+# build-naemlist testing
+bld/unit_testers/lnd_in*
+bld/unit_testers/drv_flds_in*
+bld/unit_testers/temp_file.txt*
+bld/unit_testers/user_nl_clm_real_parameters*
+bld/unit_testers/env_run.xml
+
+# tools testing output
+td.*.status
+td.*.log
+td.*.status.xFail
+test_driver_*.sh
+
+# mksurfdata output
+surfdata_*.log
+surfdata_*.namelist
+clm.input_data_list
+clm.input_data_list.previous
+
+
 # build output
 *.o
 *.mod
diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index 45431c9323..16882b0e50 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -350,6 +350,19 @@ sub check_for_perl_utils {
 
   # Determine CIME root directory and perl5lib root directory
   my $cimeroot = $opts_ref->{'cimeroot'};
+  if ( ! defined($cimeroot) ) {
+    $cimeroot = "$cfgdir/../cime";
+    if (      -d $cimeroot ) {
+    } elsif ( -d "$cfgdir/../../../cime" ) {
+      $cimeroot = "$cfgdir/../../../cime";
+    } else {
+      die <<"EOF";
+** Cannot find the root of the cime directory  enter it using the -cimeroot option
+   Did you run the checkout_externals scripts?
+EOF
+    }
+  }
+
   my $perl5lib_dir = "$cimeroot/utils/perl5lib";
 
   #-----------------------------------------------------------------------------
diff --git a/bld/configure b/bld/configure
index b333259a98..fb5fe9bf7f 100755
--- a/bld/configure
+++ b/bld/configure
@@ -180,6 +180,18 @@ my %cfg = ();           # build configuration
 # Look for them in the directory that contains the configure script.
 
 my $cimeroot   = $opts{'cimeroot'};
+if ( ! defined($cimeroot) ) {
+  $cimeroot = "$cfgdir/../cime";
+  if (      -d $cimeroot ) {
+  } elsif ( -d "$cfgdir/../../../cime" ) {
+    $cimeroot = "$cfgdir/../../../cime";
+  } else {
+    die <<"EOF";
+** Cannot find the root of the cime directory  enter it using the -cimeroot option
+   Did you run the checkout_externals scripts?
+EOF
+  }
+}
 my $casecfgdir = "$cimeroot/scripts/Tools";
 my $perl5lib   = "$cimeroot/utils/perl5lib/";
 
diff --git a/bld/queryDefaultNamelist.pl b/bld/queryDefaultNamelist.pl
index 97cd3d4394..eab81301d0 100755
--- a/bld/queryDefaultNamelist.pl
+++ b/bld/queryDefaultNamelist.pl
@@ -34,7 +34,8 @@
 
 #-----------------------------------------------------------------------------------------------
 # Add $cfgdir to the list of paths that Perl searches for modules
-my @dirs = ( $cfgdir, "$cfgdir/../../../cime/utils/perl5lib" );
+my @dirs = ( "$cfgdir/../cime/utils/perl5lib", 
+             "$cfgdir/../../../cime/utils/perl5lib" );
 unshift @INC, @dirs;
 my $result = eval "require XML::Lite";
 if ( ! defined($result) ) {
diff --git a/bld/unit_testers/xFail/expectedFail.pm b/bld/unit_testers/xFail/expectedFail.pm
index 04fc32726f..3e072f57bf 100755
--- a/bld/unit_testers/xFail/expectedFail.pm
+++ b/bld/unit_testers/xFail/expectedFail.pm
@@ -427,6 +427,7 @@ sub _readXml
    #-----------------------------------------------------------------------------------------------
    # Add $cfgdir to the list of paths that Perl searches for modules
    my @dirs = ( $cfgdir, "$cfgdir/perl5lib",
+               "$cfgdir/../../../cime/utils/perl5lib",
                "$cfgdir/../../../../cime/utils/perl5lib"
        );
    unshift @INC, @dirs;
diff --git a/test/tools/TBLCFGtools.sh b/test/tools/TBLCFGtools.sh
index e519ccdab1..6276c885e2 100755
--- a/test/tools/TBLCFGtools.sh
+++ b/test/tools/TBLCFGtools.sh
@@ -64,7 +64,7 @@ if [ -n "${BL_ROOT}" ]; then
     echo "TBLCFGtools.sh: generating baseline data from root $BL_ROOT - results in $BL_TESTDIR"
 
     echo "TBLCFGtools.sh: calling ****baseline**** TSMCFGtools.sh for smoke test"
-    bl_dir=`/bin/ls -1d ${BL_ROOT}/components/clm/test/tools`
+    bl_dir=`/bin/ls -1d ${BL_ROOT}/test/tools`
     env CLM_TESTDIR=${BL_TESTDIR} \
         CLM_ROOT=${BL_ROOT} \
         CLM_SCRIPTDIR=$bl_dir \
diff --git a/test/tools/TBLscript_tools.sh b/test/tools/TBLscript_tools.sh
index 2b5a4b26ea..ff7afb0cd7 100755
--- a/test/tools/TBLscript_tools.sh
+++ b/test/tools/TBLscript_tools.sh
@@ -63,7 +63,7 @@ if [ -n "${BL_ROOT}" ]; then
     echo "TBLscript_tools.sh: generating baseline data from root $BL_ROOT - results in $BL_TESTDIR"
 
     echo "TBLscript_tools.sh: calling ****baseline**** TSMtools.sh for smoke test"
-    bl_dir=`/bin/ls -1d ${BL_ROOT}/components/clm/test/tools`
+    bl_dir=`/bin/ls -1d ${BL_ROOT}/test/tools`
     env CLM_TESTDIR=${BL_TESTDIR} \
         CLM_SCRIPTDIR=$bl_dir \
         CLM_ROOT=$BL_ROOT \
diff --git a/test/tools/TBLtools.sh b/test/tools/TBLtools.sh
index 80826cff8f..555ea7d1be 100755
--- a/test/tools/TBLtools.sh
+++ b/test/tools/TBLtools.sh
@@ -63,7 +63,7 @@ if [ -n "${BL_ROOT}" ]; then
     echo "TBLtools.sh: generating baseline data from root $BL_ROOT - results in $BL_TESTDIR"
 
     echo "TBLtools.sh: calling ****baseline**** TSMtools.sh for smoke test"
-    bl_dir=`/bin/ls -1d ${BL_ROOT}/components/clm/test/tools`
+    bl_dir=`/bin/ls -1d ${BL_ROOT}/test/tools`
     env CLM_TESTDIR=${BL_TESTDIR} \
         CLM_ROOT=${BL_ROOT} \
         CLM_SCRIPTDIR=$bl_dir \
diff --git a/test/tools/TCBCFGtools.sh b/test/tools/TCBCFGtools.sh
index 26a2795138..3b7e6fc9d3 100755
--- a/test/tools/TCBCFGtools.sh
+++ b/test/tools/TCBCFGtools.sh
@@ -32,7 +32,7 @@ if [ -f ${CLM_TESTDIR}/${test_name}/TestStatus ]; then
     fi
 fi
 
-cfgdir=`ls -1d ${CLM_ROOT}/components/clm/tools/${1}*`
+cfgdir=`ls -1d ${CLM_ROOT}/tools/${1}*`
 blddir=${CLM_TESTDIR}/${test_name}/src
 if [ -d ${blddir} ]; then
     rm -r ${blddir}
diff --git a/test/tools/TCBscripttools.sh b/test/tools/TCBscripttools.sh
index df2389da9f..6153684e3d 100755
--- a/test/tools/TCBscripttools.sh
+++ b/test/tools/TCBscripttools.sh
@@ -31,7 +31,7 @@ if [ -f ${CLM_TESTDIR}/${test_name}/TestStatus ]; then
     fi
 fi
 
-cfgdir=`ls -1d ${CLM_ROOT}/components/clm/tools/$1`
+cfgdir=`ls -1d ${CLM_ROOT}/tools/$1`
 blddir=${CLM_TESTDIR}/${test_name}
 if [ -d ${blddir} ]; then
     rm -r ${blddir}
diff --git a/test/tools/TCBtools.sh b/test/tools/TCBtools.sh
index 63a01b4f91..b0ea9e4a87 100755
--- a/test/tools/TCBtools.sh
+++ b/test/tools/TCBtools.sh
@@ -31,7 +31,7 @@ if [ -f ${CLM_TESTDIR}/${test_name}/TestStatus ]; then
     fi
 fi
 
-cfgdir=`ls -1d ${CLM_ROOT}/components/clm/tools/$1`
+cfgdir=`ls -1d ${CLM_ROOT}/tools/$1`
 blddir=${CLM_TESTDIR}/${test_name}/src
 if [ -d ${blddir} ]; then
     rm -r ${blddir}
diff --git a/test/tools/TSMCFGtools.sh b/test/tools/TSMCFGtools.sh
index f65500a62d..b667a4c6ec 100755
--- a/test/tools/TSMCFGtools.sh
+++ b/test/tools/TSMCFGtools.sh
@@ -37,7 +37,7 @@ if [ "$CLM_RERUN" != "yes" ] && [ -f ${CLM_TESTDIR}/${test_name}/TestStatus ]; t
     fi
 fi
 
-cfgdir=`ls -1d ${CLM_ROOT}/components/clm/tools/${1}*`
+cfgdir=`ls -1d ${CLM_ROOT}/tools/${1}*`
 rundir=${CLM_TESTDIR}/${test_name}
 if [ -d ${rundir} ]; then
     rm -r ${rundir}
diff --git a/test/tools/TSMncl_tools.sh b/test/tools/TSMncl_tools.sh
index 8b921604c1..eb82142e4d 100755
--- a/test/tools/TSMncl_tools.sh
+++ b/test/tools/TSMncl_tools.sh
@@ -31,7 +31,7 @@ if [ -f ${CLM_TESTDIR}/${test_name}/TestStatus ]; then
     fi
 fi
 
-cfgdir=`ls -1d ${CLM_ROOT}/components/clm/tools/$1/ncl_scripts`
+cfgdir=`ls -1d ${CLM_ROOT}/tools/$1/ncl_scripts`
 rundir=${CLM_TESTDIR}/${test_name}
 if [ -d ${rundir} ]; then
     rm -r ${rundir}
diff --git a/test/tools/TSMscript_tools.sh b/test/tools/TSMscript_tools.sh
index 00aa7b434e..7cd94afde7 100755
--- a/test/tools/TSMscript_tools.sh
+++ b/test/tools/TSMscript_tools.sh
@@ -31,7 +31,7 @@ if [ -f ${CLM_TESTDIR}/${test_name}/TestStatus ]; then
     fi
 fi
 
-cfgdir=`ls -1d ${CLM_ROOT}/components/clm/tools/$1`
+cfgdir=`ls -1d ${CLM_ROOT}/tools/$1`
 rundir=${CLM_TESTDIR}/${test_name}
 if [ -d ${rundir} ]; then
     rm -r ${rundir}
diff --git a/test/tools/TSMtools.sh b/test/tools/TSMtools.sh
index cb82679997..33a2316973 100755
--- a/test/tools/TSMtools.sh
+++ b/test/tools/TSMtools.sh
@@ -35,7 +35,7 @@ if [ "$CLM_RERUN" != "yes" ] && [ -f ${CLM_TESTDIR}/${test_name}/TestStatus ]; t
     fi
 fi
 
-cfgdir=`ls -1d ${CLM_ROOT}/components/clm/tools/$1`
+cfgdir=`ls -1d ${CLM_ROOT}/tools/$1`
 rundir=${CLM_TESTDIR}/${test_name}
 if [ -d ${rundir} ]; then
     rm -r ${rundir}
diff --git a/test/tools/input_tests_master b/test/tools/input_tests_master
index 304409c6b7..82564fc2f9 100644
--- a/test/tools/input_tests_master
+++ b/test/tools/input_tests_master
@@ -3,10 +3,10 @@
 smc#4 TSMscript_tools.sh mkprocdata_map mkprocdata_map_wrap mkprocdata_ne30_to_f19_I2000^tools__ds
 blc#4 TBLscript_tools.sh mkprocdata_map mkprocdata_map_wrap mkprocdata_ne30_to_f19_I2000^tools__ds
 
-sme14 TSMCFGtools.sh ../../../../cime/tools/mapping/gen_domain   CFGtools__ds T31.runoptions
-ble14 TBLCFGtools.sh ../../../../cime/tools/mapping/gen_domain   CFGtools__ds T31.runoptions
-sme@4 TSMCFGtools.sh ../../../../cime/tools/mapping/gen_domain   CFGtools__ds ne30.runoptions
-ble@4 TBLCFGtools.sh ../../../../cime/tools/mapping/gen_domain   CFGtools__ds ne30.runoptions
+sme14 TSMCFGtools.sh ../../cime/tools/mapping/gen_domain   CFGtools__ds T31.runoptions
+ble14 TBLCFGtools.sh ../../cime/tools/mapping/gen_domain   CFGtools__ds T31.runoptions
+sme@4 TSMCFGtools.sh ../../cime/tools/mapping/gen_domain   CFGtools__ds ne30.runoptions
+ble@4 TBLCFGtools.sh ../../cime/tools/mapping/gen_domain   CFGtools__ds ne30.runoptions
 
 smg54 TSMtools.sh mksurfdata_map   tools__s  namelist
 blg54 TBLtools.sh mksurfdata_map   tools__s  namelist
diff --git a/test/tools/test_driver.sh b/test/tools/test_driver.sh
index b37d7f8054..364c629579 100755
--- a/test/tools/test_driver.sh
+++ b/test/tools/test_driver.sh
@@ -254,15 +254,15 @@ fi
 ##establish script dir and clm_root
 if [ -f \${initdir}/test_driver.sh ]; then
     export CLM_SCRIPTDIR=\`cd \${initdir}; pwd \`
-    export CLM_ROOT=\`cd \${CLM_SCRIPTDIR}/../../../..; pwd \`
+    export CLM_ROOT=\`cd \${CLM_SCRIPTDIR}/../..; pwd \`
 else
-    if [ -n "\${CLM_ROOT}" ] && [ -f \${CLM_ROOT}/components/clm/test/tools/test_driver.sh ]; then
-	export CLM_SCRIPTDIR=\`cd \${CLM_ROOT}/components/clm/test/tools; pwd \`
+    if [ -n "\${CLM_ROOT}" ] && [ -f \${CLM_ROOT}/test/tools/test_driver.sh ]; then
+	export CLM_SCRIPTDIR=\`cd \${CLM_ROOT}/test/tools; pwd \`
     else
 	echo "ERROR: unable to determine script directory "
 	echo "       if initiating batch job from directory other than the one containing test_driver.sh, "
 	echo "       you must set the environment variable CLM_ROOT to the full path of directory containing "
-        echo "       <components> and <cime/scripts>. "
+        echo "       <cime/scripts>. "
 	exit 3
     fi
 fi
diff --git a/tools/mksurfdata_map/mksurfdata.pl b/tools/mksurfdata_map/mksurfdata.pl
index 422b614fed..9670bafc7e 100755
--- a/tools/mksurfdata_map/mksurfdata.pl
+++ b/tools/mksurfdata_map/mksurfdata.pl
@@ -27,7 +27,8 @@
 
 #-----------------------------------------------------------------------------------------------
 # Add $scrdir to the list of paths that Perl searches for modules
-my @dirs = ( $scrdir, "$scrdir/../../../../cime/utils/perl5lib",
+my @dirs = ( "$scrdir/../../cime/utils/perl5lib",
+             "$scrdir/../../../../cime/utils/perl5lib"
            );
 unshift @INC, @dirs;
 my $result = eval "require XML::Lite";