Python: Add overlay annotations to AST classes

... and everything else that it depends on.

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 {
     /**