Build fixes (#277)

run.sh

@@ -75,8 +75,8 @@ if [ "$only_plotting" = true ]; then
     exit 0
 fi
 
-PATH=$(pwd)/src/scripts/merge_tools/:$PATH
-PATH=$(pwd)/src/scripts/merge_tools/merging/src/main/sh/:$PATH
+PATH=$(pwd)/src/scripts/merge_tools:$PATH
+PATH=$(pwd)/src/scripts/merge_tools/merging/src/main/sh:$PATH
 export PATH
 
 # Clone all submodules
@@ -101,7 +101,11 @@ if [ -z "${machine_id:+isset}" ] ; then machine_id=0; fi
 if [ -z "${num_machines:+isset}" ] ; then num_machines=1; fi
 
 export JAVA_HOME=$JAVA17_HOME
-./src/scripts/merge_tools/merging/gradlew -p src/scripts/merge_tools/merging shadowJar
+if [ ! -f ./src/scripts/merge_tools/merging/.git ] ; then
+    git submodule update --init --recursive
+fi
+git submodule update --recursive --remote
+(cd ./src/scripts/merge_tools/merging && ./gradlew shadowJar)
 
 echo "Machine ID: $machine_id"
 echo "Number of machines: $num_machines"

test/small-goal-files/merges_tested/mangstadt/ez-vcard.csv

@@ -1,2 +1,2 @@
 idx,branch_name,merge,left,right,notes,test merge,diff contains java file,left_tree_fingerprint,left parent test result,right_tree_fingerprint,right parent test result,parents pass,sampled for testing,gitmerge_ort,gitmerge_ort_merge_fingerprint,gitmerge_ort_ignorespace,gitmerge_ort_ignorespace_merge_fingerprint,gitmerge_recursive_histogram,gitmerge_recursive_histogram_merge_fingerprint,gitmerge_recursive_ignorespace,gitmerge_recursive_ignorespace_merge_fingerprint,gitmerge_recursive_minimal,gitmerge_recursive_minimal_merge_fingerprint,gitmerge_recursive_myers,gitmerge_recursive_myers_merge_fingerprint,gitmerge_recursive_patience,gitmerge_recursive_patience_merge_fingerprint,gitmerge_resolve,gitmerge_resolve_merge_fingerprint,gitmerge_ort_adjacent,gitmerge_ort_adjacent_merge_fingerprint,gitmerge_ort_imports,gitmerge_ort_imports_merge_fingerprint,gitmerge_ort_imports_ignorespace,gitmerge_ort_imports_ignorespace_merge_fingerprint,git_hires_merge,git_hires_merge_merge_fingerprint,spork,spork_merge_fingerprint,intellimerge,intellimerge_merge_fingerprint
-7,refs/heads/master,63ab6b841a7aa31372315a902b98fc5b2cc3b661,ea6026ee62cc184db68d841d50d58474fcdf4862,ab2032ca9769d452d4906f51cf56ca7d983a27c4,,True,True,aa82b49dd87edb07fbe37b7c2d6801fce8db7c437d1afe8a7b2723c81806286e,Tests_passed,66055b6c4498a64239ae0e49781e086ed06ec3e58be7d9651c23c53f8c6bab6a,Tests_passed,True,True,Tests_passed,da2456383ebd3cdf892ad5208d4f13c8184ddf492bc3e309d44553d43bd280f0,Tests_passed,3cba91122d229079d26dfa7ac449401fc3198521cdbc1013a722ad7a8a37ac6a,Tests_passed,da2456383ebd3cdf892ad5208d4f13c8184ddf492bc3e309d44553d43bd280f0,Tests_passed,3cba91122d229079d26dfa7ac449401fc3198521cdbc1013a722ad7a8a37ac6a,Tests_passed,da2456383ebd3cdf892ad5208d4f13c8184ddf492bc3e309d44553d43bd280f0,Tests_passed,da2456383ebd3cdf892ad5208d4f13c8184ddf492bc3e309d44553d43bd280f0,Tests_passed,da2456383ebd3cdf892ad5208d4f13c8184ddf492bc3e309d44553d43bd280f0,Tests_passed,da2456383ebd3cdf892ad5208d4f13c8184ddf492bc3e309d44553d43bd280f0,Tests_passed,da2456383ebd3cdf892ad5208d4f13c8184ddf492bc3e309d44553d43bd280f0,Tests_failed,3f37b0a2b5698f2b85676272803e2318a441d25a0e2152ac20f277a4dced33b0,Tests_failed,3f37b0a2b5698f2b85676272803e2318a441d25a0e2152ac20f277a4dced33b0,Tests_passed,da2456383ebd3cdf892ad5208d4f13c8184ddf492bc3e309d44553d43bd280f0,Tests_passed,2eb4722f282ab563c519ff9eaa07c7fe5bb4d008eaef5edb034f712791619ed7,Tests_passed,da2456383ebd3cdf892ad5208d4f13c8184ddf492bc3e309d44553d43bd280f0
+7,refs/heads/master,63ab6b841a7aa31372315a902b98fc5b2cc3b661,ea6026ee62cc184db68d841d50d58474fcdf4862,ab2032ca9769d452d4906f51cf56ca7d983a27c4,,True,True,aa82b49dd87edb07fbe37b7c2d6801fce8db7c437d1afe8a7b2723c81806286e,Tests_passed,66055b6c4498a64239ae0e49781e086ed06ec3e58be7d9651c23c53f8c6bab6a,Tests_passed,True,True,Tests_passed,da2456383ebd3cdf892ad5208d4f13c8184ddf492bc3e309d44553d43bd280f0,Tests_passed,3cba91122d229079d26dfa7ac449401fc3198521cdbc1013a722ad7a8a37ac6a,Tests_passed,da2456383ebd3cdf892ad5208d4f13c8184ddf492bc3e309d44553d43bd280f0,Tests_passed,3cba91122d229079d26dfa7ac449401fc3198521cdbc1013a722ad7a8a37ac6a,Tests_passed,da2456383ebd3cdf892ad5208d4f13c8184ddf492bc3e309d44553d43bd280f0,Tests_passed,da2456383ebd3cdf892ad5208d4f13c8184ddf492bc3e309d44553d43bd280f0,Tests_passed,da2456383ebd3cdf892ad5208d4f13c8184ddf492bc3e309d44553d43bd280f0,Tests_passed,da2456383ebd3cdf892ad5208d4f13c8184ddf492bc3e309d44553d43bd280f0,Tests_passed,da2456383ebd3cdf892ad5208d4f13c8184ddf492bc3e309d44553d43bd280f0,Tests_passed,da2456383ebd3cdf892ad5208d4f13c8184ddf492bc3e309d44553d43bd280f0,Tests_passed,da2456383ebd3cdf892ad5208d4f13c8184ddf492bc3e309d44553d43bd280f0,Tests_passed,da2456383ebd3cdf892ad5208d4f13c8184ddf492bc3e309d44553d43bd280f0,Tests_passed,2eb4722f282ab563c519ff9eaa07c7fe5bb4d008eaef5edb034f712791619ed7,Tests_passed,da2456383ebd3cdf892ad5208d4f13c8184ddf492bc3e309d44553d43bd280f0