From 3cd737e40d43fe5108a2f5710bb733e2c37ce454 Mon Sep 17 00:00:00 2001
From: Kasper Svendsen <kaspersv@github.com>
Date: Thu, 18 Sep 2025 10:32:20 +0200
Subject: [PATCH 1/2] Overlay: Future-proof Java config discarding

---
 java/ql/lib/semmle/code/java/Overlay.qll | 20 +++++++++++---------
 1 file changed, 11 insertions(+), 9 deletions(-)

diff --git a/java/ql/lib/semmle/code/java/Overlay.qll b/java/ql/lib/semmle/code/java/Overlay.qll
index 1d1a3896ba71..27e8badc2336 100644
--- a/java/ql/lib/semmle/code/java/Overlay.qll
+++ b/java/ql/lib/semmle/code/java/Overlay.qll
@@ -73,22 +73,24 @@ private predicate discardReferableLocatable(@locatable el) {
   )
 }
 
+/** Gets the raw file for a configLocatable. */
 overlay[local]
-private predicate baseConfigLocatable(@configLocatable l) { not isOverlay() and exists(l) }
+private string getRawFileForConfig(@configLocatable el) {
+  exists(@location loc, @file file |
+    configLocations(el, loc) and
+    locations_default(loc, file, _, _, _, _) and
+    files(file, result)
+  )
+}
 
 overlay[local]
-private predicate overlayHasConfigLocatables() {
-  isOverlay() and
-  exists(@configLocatable el)
+private string baseConfigLocatable(@configLocatable el) {
+  not isOverlay() and result = getRawFileForConfig(el)
 }
 
 overlay[discard_entity]
 private predicate discardBaseConfigLocatable(@configLocatable el) {
-  // The properties extractor is currently not incremental, so if
-  // the overlay contains any config locatables, the overlay should
-  // contain a full extraction and all config locatables from base
-  // should be discarded.
-  baseConfigLocatable(el) and overlayHasConfigLocatables()
+  overlayChangedFiles(baseConfigLocatable(el))
 }
 
 overlay[local]

From dbb9a26f78938a5ddd4763d56e9c7cdb54f204c5 Mon Sep 17 00:00:00 2001
From: Kasper Svendsen <kaspersv@github.com>
Date: Thu, 18 Sep 2025 10:35:11 +0200
Subject: [PATCH 2/2] Overlay: Future-proof Java XML discarding

---
 java/ql/lib/semmle/code/java/Overlay.qll | 22 +---------------------
 java/ql/lib/semmle/code/xml/XML.qll      | 11 +++++++++++
 2 files changed, 12 insertions(+), 21 deletions(-)

diff --git a/java/ql/lib/semmle/code/java/Overlay.qll b/java/ql/lib/semmle/code/java/Overlay.qll
index 27e8badc2336..0f6033d87b3d 100644
--- a/java/ql/lib/semmle/code/java/Overlay.qll
+++ b/java/ql/lib/semmle/code/java/Overlay.qll
@@ -18,7 +18,7 @@ predicate isOverlay() { databaseMetadata("isOverlay", "true") }
 overlay[local]
 string getRawFile(@locatable el) {
   exists(@location loc, @file file |
-    hasLocation(el, loc) and
+    (hasLocation(el, loc) or xmllocations(el, loc)) and
     locations_default(loc, file, _, _, _, _) and
     files(file, result)
   )
@@ -92,23 +92,3 @@ overlay[discard_entity]
 private predicate discardBaseConfigLocatable(@configLocatable el) {
   overlayChangedFiles(baseConfigLocatable(el))
 }
-
-overlay[local]
-private predicate baseXmlLocatable(@xmllocatable l) {
-  not isOverlay() and not files(l, _) and not xmlNs(l, _, _, _)
-}
-
-overlay[local]
-private predicate overlayHasXmlLocatable() {
-  isOverlay() and
-  exists(@xmllocatable l | not files(l, _) and not xmlNs(l, _, _, _))
-}
-
-overlay[discard_entity]
-private predicate discardBaseXmlLocatable(@xmllocatable el) {
-  // The XML extractor is currently not incremental, so if
-  // the overlay contains any XML locatables, the overlay should
-  // contain a full extraction and all XML locatables from base
-  // should be discarded.
-  baseXmlLocatable(el) and overlayHasXmlLocatable()
-}
diff --git a/java/ql/lib/semmle/code/xml/XML.qll b/java/ql/lib/semmle/code/xml/XML.qll
index e4073362fc6f..cd00991eb65c 100644
--- a/java/ql/lib/semmle/code/xml/XML.qll
+++ b/java/ql/lib/semmle/code/xml/XML.qll
@@ -6,6 +6,7 @@ module;
 
 import semmle.files.FileSystem
 private import codeql.xml.Xml
+private import semmle.code.java.Overlay
 
 private module Input implements InputSig<File, Location> {
   class XmlLocatableBase = @xmllocatable or @xmlnamespaceable;
@@ -69,3 +70,13 @@ private module Input implements InputSig<File, Location> {
 }
 
 import Make<File, Location, Input>
+
+private class DiscardableXmlAttribute extends DiscardableLocatable, @xmlattribute { }
+
+private class DiscardableXmlElement extends DiscardableLocatable, @xmlelement { }
+
+private class DiscardableXmlComment extends DiscardableLocatable, @xmlcomment { }
+
+private class DiscardableXmlCharacters extends DiscardableLocatable, @xmlcharacters { }
+
+private class DiscardableXmlDtd extends DiscardableLocatable, @xmldtd { }