From 718c0abdb6fe073349de892ddbbc383b404de607 Mon Sep 17 00:00:00 2001
From: Kasper Svendsen <kaspersv@github.com>
Date: Tue, 23 Sep 2025 10:31:28 +0200
Subject: [PATCH 1/2] Overlay: Discard base config entities in overlay
 extracted files

---
 java/ql/lib/semmle/code/java/Overlay.qll | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/java/ql/lib/semmle/code/java/Overlay.qll b/java/ql/lib/semmle/code/java/Overlay.qll
index 0f6033d87b3d..31a1518fc592 100644
--- a/java/ql/lib/semmle/code/java/Overlay.qll
+++ b/java/ql/lib/semmle/code/java/Overlay.qll
@@ -88,7 +88,17 @@ private string baseConfigLocatable(@configLocatable el) {
   not isOverlay() and result = getRawFileForConfig(el)
 }
 
+overlay[local]
+private predicate overlayConfigExtracted(string file) {
+  isOverlay() and
+  exists(@configLocatable el | file = getRawFileForConfig(el))
+}
+
 overlay[discard_entity]
 private predicate discardBaseConfigLocatable(@configLocatable el) {
   overlayChangedFiles(baseConfigLocatable(el))
+  or
+  // The config extractor is currently not incremental and may extract more
+  // property files than those included in overlayChangedFiles.
+  overlayConfigExtracted(baseConfigLocatable(el))
 }

From f02da68c55b450687aab8235b725f58139169fe5 Mon Sep 17 00:00:00 2001
From: Kasper Svendsen <kaspersv@github.com>
Date: Tue, 23 Sep 2025 10:34:49 +0200
Subject: [PATCH 2/2] Overlay: Discard base XML entities in overlay extracted
 files

---
 java/ql/lib/semmle/code/java/Overlay.qll | 28 ++++++++++++++++++++++++
 java/ql/lib/semmle/code/xml/XML.qll      | 10 ++++-----
 2 files changed, 33 insertions(+), 5 deletions(-)

diff --git a/java/ql/lib/semmle/code/java/Overlay.qll b/java/ql/lib/semmle/code/java/Overlay.qll
index 31a1518fc592..b5f7264eb3df 100644
--- a/java/ql/lib/semmle/code/java/Overlay.qll
+++ b/java/ql/lib/semmle/code/java/Overlay.qll
@@ -102,3 +102,31 @@ private predicate discardBaseConfigLocatable(@configLocatable el) {
   // property files than those included in overlayChangedFiles.
   overlayConfigExtracted(baseConfigLocatable(el))
 }
+
+/**
+ * An `@xmllocatable` that should be discarded in the base variant if its file is
+ * extracted in the overlay variant.
+ */
+overlay[local]
+abstract class DiscardableXmlLocatable extends @xmllocatable {
+  /** Gets the raw file for an xmllocatable in base. */
+  string getRawFileInBase() { not isOverlay() and result = getRawFile(this) }
+
+  /** Gets a textual representation of this discardable xmllocatable. */
+  string toString() { none() }
+}
+
+overlay[local]
+private predicate overlayXmlExtracted(string file) {
+  isOverlay() and
+  exists(@xmllocatable el | not files(el, _) and not xmlNs(el, _, _, _) and file = getRawFile(el))
+}
+
+overlay[discard_entity]
+private predicate discardXmlLocatable(@xmllocatable el) {
+  overlayChangedFiles(el.(DiscardableXmlLocatable).getRawFileInBase())
+  or
+  // The XML extractor is currently not incremental and may extract more
+  // XML files than those included in overlayChangedFiles.
+  overlayXmlExtracted(el.(DiscardableXmlLocatable).getRawFileInBase())
+}
diff --git a/java/ql/lib/semmle/code/xml/XML.qll b/java/ql/lib/semmle/code/xml/XML.qll
index cd00991eb65c..d13a83e77981 100644
--- a/java/ql/lib/semmle/code/xml/XML.qll
+++ b/java/ql/lib/semmle/code/xml/XML.qll
@@ -71,12 +71,12 @@ private module Input implements InputSig<File, Location> {
 
 import Make<File, Location, Input>
 
-private class DiscardableXmlAttribute extends DiscardableLocatable, @xmlattribute { }
+private class DiscardableXmlAttribute extends DiscardableXmlLocatable, @xmlattribute { }
 
-private class DiscardableXmlElement extends DiscardableLocatable, @xmlelement { }
+private class DiscardableXmlElement extends DiscardableXmlLocatable, @xmlelement { }
 
-private class DiscardableXmlComment extends DiscardableLocatable, @xmlcomment { }
+private class DiscardableXmlComment extends DiscardableXmlLocatable, @xmlcomment { }
 
-private class DiscardableXmlCharacters extends DiscardableLocatable, @xmlcharacters { }
+private class DiscardableXmlCharacters extends DiscardableXmlLocatable, @xmlcharacters { }
 
-private class DiscardableXmlDtd extends DiscardableLocatable, @xmldtd { }
+private class DiscardableXmlDtd extends DiscardableXmlLocatable, @xmldtd { }