From 292b23a651068ec39f9cc3001197a39d8ca7327b Mon Sep 17 00:00:00 2001
From: idrissrio <idrissrio@github.com>
Date: Thu, 26 Feb 2026 15:47:50 +0100
Subject: [PATCH] C/C++ overlay: exclude pulled in headers

---
 cpp/ql/lib/semmle/code/cpp/internal/Overlay.qll | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/cpp/ql/lib/semmle/code/cpp/internal/Overlay.qll b/cpp/ql/lib/semmle/code/cpp/internal/Overlay.qll
index 3dea144bbf67..28253e70098e 100644
--- a/cpp/ql/lib/semmle/code/cpp/internal/Overlay.qll
+++ b/cpp/ql/lib/semmle/code/cpp/internal/Overlay.qll
@@ -97,13 +97,18 @@ overlay[local]
 private predicate isBase() { not isOverlay() }
 
 /**
- * Holds if `path` was extracted in the overlay database.
+ * Holds if `path` is a file whose entities should be discarded from the base.
+ * This covers explicitly changed files and source files compiled by the
+ * overlay, but not headers pulled in only as transitive includes.
  */
 overlay[local]
 private predicate overlayHasFile(string path) {
   isOverlay() and
-  files(_, path) and
-  path != ""
+  (
+    overlayChangedFiles(path)
+    or
+    exists(@file f | compilation_compiling_files(_, _, f) and files(f, path))
+  )
 }
 
 /**