Take some suggestions from Bill Sacks,change order of perl libraries …

…checking, and make some of the gitignore specific to directories, add a few more required path changes

.gitignore

@@ -28,11 +28,16 @@ CMakeFiles/
 !components/cism/**/build
 
 # configure / build files
-CESM_cppdefs
-Filepath
-config_cache.xml
-clm.input_data_list
-clm.input_data_list.previous
+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
@@ -43,6 +48,8 @@ test_driver_*.sh
 # mksurfdata output
 surfdata_*.log
 surfdata_*.namelist
+clm.input_data_list
+clm.input_data_list.previous
 
 
 # build output

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/";
 

bld/queryDefaultNamelist.pl

@@ -34,8 +34,8 @@
 
 #-----------------------------------------------------------------------------------------------
 # Add $cfgdir to the list of paths that Perl searches for modules
-my @dirs = ( $cfgdir, "$cfgdir/../../../cime/utils/perl5lib", 
-             "$cfgdir/../cime/utils/perl5lib" );
+my @dirs = ( "$cfgdir/../cime/utils/perl5lib", 
+             "$cfgdir/../../../cime/utils/perl5lib" );
 unshift @INC, @dirs;
 my $result = eval "require XML::Lite";
 if ( ! defined($result) ) {

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;

tools/mksurfdata_map/mksurfdata.pl

@@ -27,8 +27,8 @@
 
 #-----------------------------------------------------------------------------------------------
 # Add $scrdir to the list of paths that Perl searches for modules
-my @dirs = ( $scrdir, "$scrdir/../../../../cime/utils/perl5lib",
-             "$scrdir/../../cime/utils/perl5lib"
+my @dirs = ( "$scrdir/../../cime/utils/perl5lib",
+             "$scrdir/../../../../cime/utils/perl5lib"
            );
 unshift @INC, @dirs;
 my $result = eval "require XML::Lite";