diff --git a/csharp/ql/lib/change-notes/2026-01-06-paths-directives-ancillary-data.md b/csharp/ql/lib/change-notes/2026-01-06-paths-directives-ancillary-data.md
new file mode 100644
index 000000000000..ac96e579147d
--- /dev/null
+++ b/csharp/ql/lib/change-notes/2026-01-06-paths-directives-ancillary-data.md
@@ -0,0 +1,4 @@
+---
+category: minorAnalysis
+---
+* When a code-scanning configuration specifies the `paths:` and/or `paths-ignore:` settings, these are now taken into account by the C# extractor's search for `.config`, `.props`, XML and project files.
diff --git a/csharp/tools/pre-finalize.cmd b/csharp/tools/pre-finalize.cmd
index 0ee982b65853..b20e2bf77d86 100644
--- a/csharp/tools/pre-finalize.cmd
+++ b/csharp/tools/pre-finalize.cmd
@@ -5,6 +5,7 @@ type NUL && "%CODEQL_DIST%\codeql" database index-files ^
     --include-extension=.csproj ^
     --include-extension=.props ^
     --include-extension=.xml ^
+    --also-match-lgtm-index-filters ^
     --size-limit 10m ^
     --language xml ^
     --working-dir=. ^
diff --git a/csharp/tools/pre-finalize.sh b/csharp/tools/pre-finalize.sh
index b0abd28f9eef..409fb252da3d 100755
--- a/csharp/tools/pre-finalize.sh
+++ b/csharp/tools/pre-finalize.sh
@@ -7,6 +7,7 @@ set -eu
     --include-extension=.csproj \
     --include-extension=.props \
     --include-extension=.xml \
+    --also-match-lgtm-index-filters \
     --size-limit 10m \
     --language xml \
     --working-dir=. \
diff --git a/go/codeql-tools/pre-finalize.cmd b/go/codeql-tools/pre-finalize.cmd
index 4abac2499336..66f6e80a69fc 100644
--- a/go/codeql-tools/pre-finalize.cmd
+++ b/go/codeql-tools/pre-finalize.cmd
@@ -9,6 +9,7 @@ if NOT "%CODEQL_EXTRACTOR_GO_EXTRACT_HTML%"=="no" (
                         --include-extension=.xhtm ^
                         --include-extension=.xhtml ^
                         --include-extension=.vue ^
+                        --also-match-lgtm-index-filters ^
                         --size-limit 10m ^
                         --language html ^
                         -- ^
diff --git a/go/codeql-tools/pre-finalize.sh b/go/codeql-tools/pre-finalize.sh
index 3a8b31c70a06..9cf0b7ae0b1b 100755
--- a/go/codeql-tools/pre-finalize.sh
+++ b/go/codeql-tools/pre-finalize.sh
@@ -10,6 +10,7 @@ if [ "${CODEQL_EXTRACTOR_GO_EXTRACT_HTML:-yes}" != "no" ]; then
                         --include-extension=.xhtm \
                         --include-extension=.xhtml \
                         --include-extension=.vue \
+                        --also-match-lgtm-index-filters \
                         --size-limit 10m \
                         --language html \
                         -- \
diff --git a/go/ql/lib/change-notes/2026-01-06-paths-directives-ancillary-data.md b/go/ql/lib/change-notes/2026-01-06-paths-directives-ancillary-data.md
new file mode 100644
index 000000000000..bf9c4553573a
--- /dev/null
+++ b/go/ql/lib/change-notes/2026-01-06-paths-directives-ancillary-data.md
@@ -0,0 +1,4 @@
+---
+category: minorAnalysis
+---
+* When a code-scanning configuration specifies the `paths:` and/or `paths-ignore:` settings, these are now taken into account by the Go extractor's search for `.vue` and HTML files.
diff --git a/python/ql/lib/change-notes/2026-01-06-paths-directives-ancillary-data.md b/python/ql/lib/change-notes/2026-01-06-paths-directives-ancillary-data.md
new file mode 100644
index 000000000000..ed16f8b6565d
--- /dev/null
+++ b/python/ql/lib/change-notes/2026-01-06-paths-directives-ancillary-data.md
@@ -0,0 +1,4 @@
+---
+category: minorAnalysis
+---
+* When a code-scanning configuration specifies the `paths:` and/or `paths-ignore:` settings, these are now taken into account by the Python extractor's search for YAML files.
diff --git a/python/tools/pre-finalize.cmd b/python/tools/pre-finalize.cmd
index 074546710627..235b79c77b0a 100644
--- a/python/tools/pre-finalize.cmd
+++ b/python/tools/pre-finalize.cmd
@@ -3,6 +3,7 @@
 type NUL && "%CODEQL_DIST%\codeql" database index-files ^
     --include-extension=.yaml ^
     --include-extension=.yml ^
+    --also-match-lgtm-index-filters ^
     --size-limit=5m ^
     --language yaml ^
     -- ^
diff --git a/python/tools/pre-finalize.sh b/python/tools/pre-finalize.sh
index 9fe5200a38f0..b938be75aa72 100755
--- a/python/tools/pre-finalize.sh
+++ b/python/tools/pre-finalize.sh
@@ -5,6 +5,7 @@ set -eu
 "$CODEQL_DIST/codeql" database index-files \
     --include-extension=.yaml \
     --include-extension=.yml \
+    --also-match-lgtm-index-filters \
     --size-limit=5m \
     --language yaml \
     -- \
diff --git a/ql/tools/pre-finalize.cmd b/ql/tools/pre-finalize.cmd
index 49d18f3d1974..19fa7b045237 100644
--- a/ql/tools/pre-finalize.cmd
+++ b/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 ^
     -- ^
diff --git a/ql/tools/pre-finalize.sh b/ql/tools/pre-finalize.sh
index 7003ad81c1b3..afae94ef83ad 100755
--- a/ql/tools/pre-finalize.sh
+++ b/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 \
     -- \