All languages: account for paths and paths-ignore in XML and other ancillary extraction

ql/tools/pre-finalize.cmd

@@ -3,6 +3,7 @@
 type NUL && "%CODEQL_DIST%\codeql" database index-files ^
     --include=**/qlpack.yml ^
     --include-extension=.qlref ^
+    --also-match-lgtm-index-filters ^
     --size-limit=5m ^
     --language yaml ^
     -- ^

ql/tools/pre-finalize.sh

@@ -5,6 +5,7 @@ set -eu
 "$CODEQL_DIST/codeql" database index-files \
     "--include=**/qlpack.yml" \
     --include-extension=.qlref \
+    --also-match-lgtm-index-filters \
     --size-limit=5m \
     --language yaml \
     -- \