shellcheck ignore array references for now (SC2039) and run everywhere

Tools/run-shellcheck.sh

@@ -24,12 +24,14 @@ echo "Running shellcheck in '$search_directory'."
 # SC2086: double quote to prevent globbing and word splitting
 # SC2166: allow the form [ $OUTPUT_MODE == fmu -o $OUTPUT_MODE == io ]
 # SC2148: allow files w/o shebang
+# SC2039: In POSIX sh, array references are undefined. TODO: fix this
 shellcheck -x \
 	-e SC1008 \
 	-e SC2086 \
 	-e SC2121 \
 	-e SC2148 \
 	-e SC2166 \
+	-e SC2039 \
 	$scripts
 ret=$?
 if [ $ret -ne 0 ]; then