Python: Add overlay annotations to AST classes

... and everything else that it depends on.

python/ql/lib/semmle/python/AstExtended.qll

@@ -1,3 +1,6 @@
+overlay[local]
+module;
+
 import python
 private import semmle.python.internal.CachedStages
 

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
 

python/ql/lib/semmle/python/Class.qll

@@ -1,6 +1,8 @@
 /**
  * Provides classes representing Python classes.
  */
+overlay[local]
+module;
 
 import python
 

python/ql/lib/semmle/python/Comment.qll

@@ -1,6 +1,8 @@
 /**
  * Provides classes representing comments in Python.
  */
+overlay[local]
+module;
 
 import python
 

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. */

python/ql/lib/semmle/python/Constants.qll

@@ -1,4 +1,6 @@
 /** Standard builtin types and modules */
+overlay[local]
+module;
 
 import python
 

python/ql/lib/semmle/python/Exprs.qll

@@ -1,3 +1,6 @@
+overlay[local]
+module;
+
 private import python
 private import semmle.python.internal.CachedStages
 

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

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

python/ql/lib/semmle/python/Function.qll

@@ -1,3 +1,6 @@
+overlay[local]
+module;
+
 import python
 
 /**

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 */

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

python/ql/lib/semmle/python/Keywords.qll

@@ -1,3 +1,6 @@
+overlay[local]
+module;
+
 import python
 
 class KeyValuePair extends KeyValuePair_, DictDisplayItem {

python/ql/lib/semmle/python/Module.qll

@@ -1,3 +1,6 @@
+overlay[local]
+module;
+
 import python
 private import semmle.python.internal.CachedStages
 

python/ql/lib/semmle/python/Operations.qll

@@ -1,3 +1,6 @@
+overlay[local]
+module;
+
 import python
 
 /** The base class for operators */

python/ql/lib/semmle/python/Patterns.qll

@@ -1,6 +1,8 @@
 /**
  * Wrapping generated AST classes: `Pattern_` and subclasses.
  */
+overlay[local]
+module;
 
 import python
 

python/ql/lib/semmle/python/SSA.qll

@@ -1,4 +1,6 @@
 /** SSA library */
+overlay[local]
+module;
 
 import python
 

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

python/ql/lib/semmle/python/Stmts.qll

@@ -1,3 +1,6 @@
+overlay[local]
+module;
+
 import python
 
 /** A statement */

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) */

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.

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

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

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

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 {
     /**

python/ql/lib/semmle/python/types/Builtins.qll

@@ -1,3 +1,6 @@
+overlay[local?]
+module;
+
 import python
 private import LegacyPointsTo
 

python/ql/lib/semmle/python/types/ImportTime.qll

@@ -1,3 +1,6 @@
+overlay[local]
+module;
+
 import python
 
 /**