C/C++ overlay: exclude pulled in headers

Author: IdrissRio

cpp/ql/lib/semmle/code/cpp/internal/Overlay.qll

@@ -97,13 +97,20 @@ 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)
+    )
+  )
 }
 
 /**