From fd7b123ee38957e99ac0cedf83fee8cd0e5cc2f7 Mon Sep 17 00:00:00 2001
From: Taus <tausbn@github.com>
Date: Fri, 5 Dec 2025 13:23:11 +0000
Subject: [PATCH] Python: Add overlay annotations to AST classes

... and everything else that it depends on.
---
 python/ql/lib/semmle/python/AstExtended.qll           | 3 +++
 python/ql/lib/semmle/python/AstGenerated.qll          | 2 ++
 python/ql/lib/semmle/python/Class.qll                 | 2 ++
 python/ql/lib/semmle/python/Comment.qll               | 2 ++
 python/ql/lib/semmle/python/Comprehensions.qll        | 3 +++
 python/ql/lib/semmle/python/Constants.qll             | 2 ++
 python/ql/lib/semmle/python/Exprs.qll                 | 3 +++
 python/ql/lib/semmle/python/Files.qll                 | 3 +++
 python/ql/lib/semmle/python/Flow.qll                  | 3 +++
 python/ql/lib/semmle/python/Function.qll              | 3 +++
 python/ql/lib/semmle/python/GuardedControlFlow.qll    | 3 +++
 python/ql/lib/semmle/python/Import.qll                | 3 +++
 python/ql/lib/semmle/python/Keywords.qll              | 3 +++
 python/ql/lib/semmle/python/Module.qll                | 3 +++
 python/ql/lib/semmle/python/Operations.qll            | 3 +++
 python/ql/lib/semmle/python/Patterns.qll              | 2 ++
 python/ql/lib/semmle/python/SSA.qll                   | 2 ++
 python/ql/lib/semmle/python/Scope.qll                 | 5 +++++
 python/ql/lib/semmle/python/Stmts.qll                 | 3 +++
 python/ql/lib/semmle/python/Variables.qll             | 3 +++
 python/ql/lib/semmle/python/essa/Definitions.qll      | 3 +++
 python/ql/lib/semmle/python/essa/Essa.qll             | 2 ++
 python/ql/lib/semmle/python/essa/SsaCompute.qll       | 2 ++
 python/ql/lib/semmle/python/essa/SsaDefinitions.qll   | 2 ++
 python/ql/lib/semmle/python/internal/CachedStages.qll | 1 +
 python/ql/lib/semmle/python/types/Builtins.qll        | 3 +++
 python/ql/lib/semmle/python/types/ImportTime.qll      | 3 +++
 27 files changed, 72 insertions(+)

diff --git a/python/ql/lib/semmle/python/AstExtended.qll b/python/ql/lib/semmle/python/AstExtended.qll
index 73292b85c3a..13da4e899a7 100644
--- a/python/ql/lib/semmle/python/AstExtended.qll
+++ b/python/ql/lib/semmle/python/AstExtended.qll
@@ -1,3 +1,6 @@
+overlay[local]
+module;
+
 import python
 private import semmle.python.internal.CachedStages
 
diff --git a/python/ql/lib/semmle/python/AstGenerated.qll b/python/ql/lib/semmle/python/AstGenerated.qll
index 12f86832387..8805a43bec3 100644
--- a/python/ql/lib/semmle/python/AstGenerated.qll
+++ b/python/ql/lib/semmle/python/AstGenerated.qll
@@ -3,6 +3,8 @@
  *      WARNING: Any modifications to this file will be lost.
  *      Relations can be changed by modifying master.py.
  */
+overlay[local]
+module;
 
 import python
 
diff --git a/python/ql/lib/semmle/python/Class.qll b/python/ql/lib/semmle/python/Class.qll
index 19b81e86a12..cee0e730cb4 100644
--- a/python/ql/lib/semmle/python/Class.qll
+++ b/python/ql/lib/semmle/python/Class.qll
@@ -1,6 +1,8 @@
 /**
  * Provides classes representing Python classes.
  */
+overlay[local]
+module;
 
 import python
 
diff --git a/python/ql/lib/semmle/python/Comment.qll b/python/ql/lib/semmle/python/Comment.qll
index 839d700b8cd..c87ccc1521d 100644
--- a/python/ql/lib/semmle/python/Comment.qll
+++ b/python/ql/lib/semmle/python/Comment.qll
@@ -1,6 +1,8 @@
 /**
  * Provides classes representing comments in Python.
  */
+overlay[local]
+module;
 
 import python
 
diff --git a/python/ql/lib/semmle/python/Comprehensions.qll b/python/ql/lib/semmle/python/Comprehensions.qll
index 37f07614282..12e71e2d5d1 100644
--- a/python/ql/lib/semmle/python/Comprehensions.qll
+++ b/python/ql/lib/semmle/python/Comprehensions.qll
@@ -1,3 +1,6 @@
+overlay[local]
+module;
+
 import python
 
 /** The base class for list, set and dictionary comprehensions, and generator expressions. */
diff --git a/python/ql/lib/semmle/python/Constants.qll b/python/ql/lib/semmle/python/Constants.qll
index 03254a4bfd0..f86019c0256 100644
--- a/python/ql/lib/semmle/python/Constants.qll
+++ b/python/ql/lib/semmle/python/Constants.qll
@@ -1,4 +1,6 @@
 /** Standard builtin types and modules */
+overlay[local]
+module;
 
 import python
 
diff --git a/python/ql/lib/semmle/python/Exprs.qll b/python/ql/lib/semmle/python/Exprs.qll
index c374863d684..6ab9f8d8340 100644
--- a/python/ql/lib/semmle/python/Exprs.qll
+++ b/python/ql/lib/semmle/python/Exprs.qll
@@ -1,3 +1,6 @@
+overlay[local]
+module;
+
 private import python
 private import semmle.python.internal.CachedStages
 
diff --git a/python/ql/lib/semmle/python/Files.qll b/python/ql/lib/semmle/python/Files.qll
index 2da0dd61f88..bb3c504654e 100644
--- a/python/ql/lib/semmle/python/Files.qll
+++ b/python/ql/lib/semmle/python/Files.qll
@@ -1,4 +1,6 @@
 /** Provides classes for working with files and folders. */
+overlay[local]
+module;
 
 import python
 private import codeql.util.FileSystem
@@ -178,6 +180,7 @@ class Container extends Impl::Container {
 
   override Container getParentContainer() { result = super.getParentContainer() }
 
+  overlay[global]
   Container getChildContainer(string baseName) {
     result = this.getAChildContainer() and
     result.getBaseName() = baseName
diff --git a/python/ql/lib/semmle/python/Flow.qll b/python/ql/lib/semmle/python/Flow.qll
index 898cd566ab9..b29f9fd1383 100644
--- a/python/ql/lib/semmle/python/Flow.qll
+++ b/python/ql/lib/semmle/python/Flow.qll
@@ -1,3 +1,6 @@
+overlay[local]
+module;
+
 import python
 private import semmle.python.internal.CachedStages
 private import codeql.controlflow.BasicBlock as BB
diff --git a/python/ql/lib/semmle/python/Function.qll b/python/ql/lib/semmle/python/Function.qll
index e15d28d3a12..c133275b8b7 100644
--- a/python/ql/lib/semmle/python/Function.qll
+++ b/python/ql/lib/semmle/python/Function.qll
@@ -1,3 +1,6 @@
+overlay[local]
+module;
+
 import python
 
 /**
diff --git a/python/ql/lib/semmle/python/GuardedControlFlow.qll b/python/ql/lib/semmle/python/GuardedControlFlow.qll
index 73ea183850a..3169e4d0c1a 100644
--- a/python/ql/lib/semmle/python/GuardedControlFlow.qll
+++ b/python/ql/lib/semmle/python/GuardedControlFlow.qll
@@ -1,3 +1,6 @@
+overlay[local]
+module;
+
 import python
 
 /** A basic block which terminates in a condition, splitting the subsequent control flow */
diff --git a/python/ql/lib/semmle/python/Import.qll b/python/ql/lib/semmle/python/Import.qll
index c75ef9f0c91..e8a7facccad 100644
--- a/python/ql/lib/semmle/python/Import.qll
+++ b/python/ql/lib/semmle/python/Import.qll
@@ -1,3 +1,6 @@
+overlay[local]
+module;
+
 import python
 private import semmle.python.types.Builtins
 private import semmle.python.internal.CachedStages
diff --git a/python/ql/lib/semmle/python/Keywords.qll b/python/ql/lib/semmle/python/Keywords.qll
index b7ecca528bb..da7b582ef16 100644
--- a/python/ql/lib/semmle/python/Keywords.qll
+++ b/python/ql/lib/semmle/python/Keywords.qll
@@ -1,3 +1,6 @@
+overlay[local]
+module;
+
 import python
 
 class KeyValuePair extends KeyValuePair_, DictDisplayItem {
diff --git a/python/ql/lib/semmle/python/Module.qll b/python/ql/lib/semmle/python/Module.qll
index f22f0d6fe39..a30aab452c3 100644
--- a/python/ql/lib/semmle/python/Module.qll
+++ b/python/ql/lib/semmle/python/Module.qll
@@ -1,3 +1,6 @@
+overlay[local]
+module;
+
 import python
 private import semmle.python.internal.CachedStages
 
diff --git a/python/ql/lib/semmle/python/Operations.qll b/python/ql/lib/semmle/python/Operations.qll
index e8f5e4799a5..c6318af63e2 100644
--- a/python/ql/lib/semmle/python/Operations.qll
+++ b/python/ql/lib/semmle/python/Operations.qll
@@ -1,3 +1,6 @@
+overlay[local]
+module;
+
 import python
 
 /** The base class for operators */
diff --git a/python/ql/lib/semmle/python/Patterns.qll b/python/ql/lib/semmle/python/Patterns.qll
index 9b4760611d0..fb99a123584 100644
--- a/python/ql/lib/semmle/python/Patterns.qll
+++ b/python/ql/lib/semmle/python/Patterns.qll
@@ -1,6 +1,8 @@
 /**
  * Wrapping generated AST classes: `Pattern_` and subclasses.
  */
+overlay[local]
+module;
 
 import python
 
diff --git a/python/ql/lib/semmle/python/SSA.qll b/python/ql/lib/semmle/python/SSA.qll
index b71bd95de79..77779287734 100644
--- a/python/ql/lib/semmle/python/SSA.qll
+++ b/python/ql/lib/semmle/python/SSA.qll
@@ -1,4 +1,6 @@
 /** SSA library */
+overlay[local]
+module;
 
 import python
 
diff --git a/python/ql/lib/semmle/python/Scope.qll b/python/ql/lib/semmle/python/Scope.qll
index 4131455299c..66a7170aec7 100644
--- a/python/ql/lib/semmle/python/Scope.qll
+++ b/python/ql/lib/semmle/python/Scope.qll
@@ -1,3 +1,6 @@
+overlay[local]
+module;
+
 import python
 private import semmle.python.dataflow.new.internal.ImportResolution
 
@@ -6,6 +9,7 @@ private import semmle.python.dataflow.new.internal.ImportResolution
  *
  * This aims to be the same as m.getAnExport(), but without using the points-to machinery.
  */
+overlay[global]
 private string getAModuleExport(Module m) {
   py_exports(m, result)
   or
@@ -76,6 +80,7 @@ class Scope extends Scope_ {
   predicate isTopLevel() { this.getEnclosingModule() = this.getEnclosingScope() }
 
   /** Holds if this scope is deemed to be public */
+  overlay[global]
   predicate isPublic() {
     /* Not inside a function */
     not this.getEnclosingScope() instanceof Function and
diff --git a/python/ql/lib/semmle/python/Stmts.qll b/python/ql/lib/semmle/python/Stmts.qll
index ea309227af6..c0dfac10ee8 100644
--- a/python/ql/lib/semmle/python/Stmts.qll
+++ b/python/ql/lib/semmle/python/Stmts.qll
@@ -1,3 +1,6 @@
+overlay[local]
+module;
+
 import python
 
 /** A statement */
diff --git a/python/ql/lib/semmle/python/Variables.qll b/python/ql/lib/semmle/python/Variables.qll
index 1249fd020ca..d2baf04a5bf 100644
--- a/python/ql/lib/semmle/python/Variables.qll
+++ b/python/ql/lib/semmle/python/Variables.qll
@@ -1,3 +1,6 @@
+overlay[local]
+module;
+
 import python
 
 /** A variable, either a global or local variable (including parameters) */
diff --git a/python/ql/lib/semmle/python/essa/Definitions.qll b/python/ql/lib/semmle/python/essa/Definitions.qll
index aca6991b9f6..6e7b8d5b376 100644
--- a/python/ql/lib/semmle/python/essa/Definitions.qll
+++ b/python/ql/lib/semmle/python/essa/Definitions.qll
@@ -1,3 +1,6 @@
+overlay[local]
+module;
+
 import python
 /*
  * Classification of variables. These should be non-overlapping and complete.
diff --git a/python/ql/lib/semmle/python/essa/Essa.qll b/python/ql/lib/semmle/python/essa/Essa.qll
index 384bfd2f91f..ebc22beedf3 100644
--- a/python/ql/lib/semmle/python/essa/Essa.qll
+++ b/python/ql/lib/semmle/python/essa/Essa.qll
@@ -1,6 +1,8 @@
 /**
  * Library for SSA representation (Static Single Assignment form).
  */
+overlay[local]
+module;
 
 import python
 private import SsaCompute
diff --git a/python/ql/lib/semmle/python/essa/SsaCompute.qll b/python/ql/lib/semmle/python/essa/SsaCompute.qll
index d2512eecded..fb030b6250e 100644
--- a/python/ql/lib/semmle/python/essa/SsaCompute.qll
+++ b/python/ql/lib/semmle/python/essa/SsaCompute.qll
@@ -88,6 +88,8 @@
  * ```
  * and thus it falls out that `g3` must be `1`.
  */
+overlay[local]
+module;
 
 import python
 private import semmle.python.internal.CachedStages
diff --git a/python/ql/lib/semmle/python/essa/SsaDefinitions.qll b/python/ql/lib/semmle/python/essa/SsaDefinitions.qll
index 6c87af102fa..827bee34474 100644
--- a/python/ql/lib/semmle/python/essa/SsaDefinitions.qll
+++ b/python/ql/lib/semmle/python/essa/SsaDefinitions.qll
@@ -2,6 +2,8 @@
  * Provides classes and predicates for determining the uses and definitions of
  * variables for ESSA form.
  */
+overlay[local]
+module;
 
 import python
 private import semmle.python.internal.CachedStages
diff --git a/python/ql/lib/semmle/python/internal/CachedStages.qll b/python/ql/lib/semmle/python/internal/CachedStages.qll
index 687cabeceae..df96e849855 100644
--- a/python/ql/lib/semmle/python/internal/CachedStages.qll
+++ b/python/ql/lib/semmle/python/internal/CachedStages.qll
@@ -35,6 +35,7 @@ module Stages {
    * Computes predicates based on the AST.
    * These include SSA and basic-blocks.
    */
+  overlay[local]
   cached
   module AST {
     /**
diff --git a/python/ql/lib/semmle/python/types/Builtins.qll b/python/ql/lib/semmle/python/types/Builtins.qll
index 796397f72cd..371cf758d5c 100644
--- a/python/ql/lib/semmle/python/types/Builtins.qll
+++ b/python/ql/lib/semmle/python/types/Builtins.qll
@@ -1,3 +1,6 @@
+overlay[local?]
+module;
+
 import python
 private import LegacyPointsTo
 
diff --git a/python/ql/lib/semmle/python/types/ImportTime.qll b/python/ql/lib/semmle/python/types/ImportTime.qll
index 1604013d7ff..27f70b09aa4 100644
--- a/python/ql/lib/semmle/python/types/ImportTime.qll
+++ b/python/ql/lib/semmle/python/types/ImportTime.qll
@@ -1,3 +1,6 @@
+overlay[local]
+module;
+
 import python
 
 /**