diff --git a/ql/ql/src/codeql/Locations.qll b/ql/ql/src/codeql/Locations.qll
index ae8058c916d..e03c84f98fa 100644
--- a/ql/ql/src/codeql/Locations.qll
+++ b/ql/ql/src/codeql/Locations.qll
@@ -1,4 +1,6 @@
 /** Provides classes for working with locations. */
+overlay[local]
+module;
 
 import files.FileSystem
 
diff --git a/ql/ql/src/codeql/files/FileSystem.qll b/ql/ql/src/codeql/files/FileSystem.qll
index 5a219f3b7f0..52174250af0 100644
--- a/ql/ql/src/codeql/files/FileSystem.qll
+++ b/ql/ql/src/codeql/files/FileSystem.qll
@@ -1,4 +1,6 @@
 /** Provides classes for working with files and folders. */
+overlay[local?]
+module;
 
 private import codeql_ql.ast.internal.TreeSitter
 private import codeql.Locations
diff --git a/ql/ql/src/codeql_ql/StructuredLogs.qll b/ql/ql/src/codeql_ql/StructuredLogs.qll
index 4c0ef69fd55..87527eae1d2 100644
--- a/ql/ql/src/codeql_ql/StructuredLogs.qll
+++ b/ql/ql/src/codeql_ql/StructuredLogs.qll
@@ -1,3 +1,6 @@
+overlay[local]
+module;
+
 private import ql
 private import codeql_ql.ast.internal.TreeSitter
 private import experimental.RA
@@ -23,6 +26,7 @@ private float stringToTimestamp(string str) {
 }
 
 bindingset[s]
+overlay[global]
 private Predicate getPredicateFromPosition(string s) {
   exists(string r, string filepath, int startline | r = "(.*):(\\d+),(\\d+)-(\\d+),(\\d+)" |
     filepath = s.regexpCapture(r, 1) and
@@ -397,6 +401,7 @@ module KindPredicatesLog {
 
     string getPosition() { result = this.getString("position") }
 
+    overlay[global]
     Predicate getPredicate() { result = getPredicateFromPosition(this.getPosition()) }
 
     /**
diff --git a/ql/ql/src/codeql_ql/ast/internal/TreeSitter.qll b/ql/ql/src/codeql_ql/ast/internal/TreeSitter.qll
index 2d4a9d65465..c81830e1d59 100644
--- a/ql/ql/src/codeql_ql/ast/internal/TreeSitter.qll
+++ b/ql/ql/src/codeql_ql/ast/internal/TreeSitter.qll
@@ -23,6 +23,7 @@ private predicate discardLocation(@location_default loc) {
   )
 }
 
+overlay[local]
 module QL {
   /** The base class for all AST nodes */
   class AstNode extends @ql_ast_node {
@@ -67,7 +68,6 @@ module QL {
   }
 
   /** Gets the file containing the given `node`. */
-  overlay[local]
   private @file getNodeFile(@ql_ast_node node) {
     exists(@location_default loc | ql_ast_node_location(node, loc) |
       locations_default(loc, result, _, _, _, _)
@@ -75,7 +75,6 @@ module QL {
   }
 
   /** Holds if `node` is in the `file` and is part of the overlay base database. */
-  overlay[local]
   private predicate discardableAstNode(@file file, @ql_ast_node node) {
     not isOverlay() and file = getNodeFile(node)
   }
@@ -1315,6 +1314,7 @@ module QL {
   }
 }
 
+overlay[local]
 module Dbscheme {
   /** The base class for all AST nodes */
   class AstNode extends @dbscheme_ast_node {
@@ -1359,7 +1359,6 @@ module Dbscheme {
   }
 
   /** Gets the file containing the given `node`. */
-  overlay[local]
   private @file getNodeFile(@dbscheme_ast_node node) {
     exists(@location_default loc | dbscheme_ast_node_location(node, loc) |
       locations_default(loc, result, _, _, _, _)
@@ -1367,7 +1366,6 @@ module Dbscheme {
   }
 
   /** Holds if `node` is in the `file` and is part of the overlay base database. */
-  overlay[local]
   private predicate discardableAstNode(@file file, @dbscheme_ast_node node) {
     not isOverlay() and file = getNodeFile(node)
   }
@@ -1673,6 +1671,7 @@ module Dbscheme {
   }
 }
 
+overlay[local]
 module Blame {
   /** The base class for all AST nodes */
   class AstNode extends @blame_ast_node {
@@ -1717,7 +1716,6 @@ module Blame {
   }
 
   /** Gets the file containing the given `node`. */
-  overlay[local]
   private @file getNodeFile(@blame_ast_node node) {
     exists(@location_default loc | blame_ast_node_location(node, loc) |
       locations_default(loc, result, _, _, _, _)
@@ -1725,7 +1723,6 @@ module Blame {
   }
 
   /** Holds if `node` is in the `file` and is part of the overlay base database. */
-  overlay[local]
   private predicate discardableAstNode(@file file, @blame_ast_node node) {
     not isOverlay() and file = getNodeFile(node)
   }
@@ -1808,6 +1805,7 @@ module Blame {
   }
 }
 
+overlay[local]
 module JSON {
   /** The base class for all AST nodes */
   class AstNode extends @json_ast_node {
@@ -1852,7 +1850,6 @@ module JSON {
   }
 
   /** Gets the file containing the given `node`. */
-  overlay[local]
   private @file getNodeFile(@json_ast_node node) {
     exists(@location_default loc | json_ast_node_location(node, loc) |
       locations_default(loc, result, _, _, _, _)
@@ -1860,7 +1857,6 @@ module JSON {
   }
 
   /** Holds if `node` is in the `file` and is part of the overlay base database. */
-  overlay[local]
   private predicate discardableAstNode(@file file, @json_ast_node node) {
     not isOverlay() and file = getNodeFile(node)
   }
diff --git a/ql/ql/src/experimental/RA.qll b/ql/ql/src/experimental/RA.qll
index 7187ebfc8c7..5eb80455562 100644
--- a/ql/ql/src/experimental/RA.qll
+++ b/ql/ql/src/experimental/RA.qll
@@ -1,6 +1,5 @@
-/**
- * Parses RA expressions.
- */
+overlay[local]
+module;
 
 /**
  * A predicate that contains RA.
diff --git a/ql/ql/src/queries/performance/LargeTupleSum.ql b/ql/ql/src/queries/performance/LargeTupleSum.ql
index e5bbed79bbd..4e5ca6622e8 100644
--- a/ql/ql/src/queries/performance/LargeTupleSum.ql
+++ b/ql/ql/src/queries/performance/LargeTupleSum.ql
@@ -6,6 +6,7 @@ import ql
 import codeql_ql.StructuredLogs
 import KindPredicatesLog
 
+overlay[local]
 module SumCounts implements Fold<int> {
   int base(PipeLineRun run) { result = sum(int i | | run.getCount(i)) }
 
diff --git a/ql/ql/test/experimental/raparser.ql b/ql/ql/test/experimental/raparser.ql
index 29489e2a968..5704b0facdb 100644
--- a/ql/ql/test/experimental/raparser.ql
+++ b/ql/ql/test/experimental/raparser.ql
@@ -1,5 +1,6 @@
 import experimental.RA
 
+overlay[local]
 class TestPredicate extends string {
   TestPredicate() { this = "p1" }
 
diff --git a/ruby/ql/lib/codeql/Locations.qll b/ruby/ql/lib/codeql/Locations.qll
index 148c6b01f2d..df52d6822a2 100644
--- a/ruby/ql/lib/codeql/Locations.qll
+++ b/ruby/ql/lib/codeql/Locations.qll
@@ -1,4 +1,6 @@
 /** Provides classes for working with locations. */
+overlay[local]
+module;
 
 import files.FileSystem
 
diff --git a/ruby/ql/lib/codeql/files/FileSystem.qll b/ruby/ql/lib/codeql/files/FileSystem.qll
index 528dde52fd9..6cc771fad9d 100644
--- a/ruby/ql/lib/codeql/files/FileSystem.qll
+++ b/ruby/ql/lib/codeql/files/FileSystem.qll
@@ -1,4 +1,6 @@
 /** Provides classes for working with files and folders. */
+overlay[local]
+module;
 
 private import codeql.Locations
 private import codeql.util.FileSystem
diff --git a/ruby/ql/lib/codeql/ruby/AST.qll b/ruby/ql/lib/codeql/ruby/AST.qll
index bd42696a8db..2c2dbdfa532 100644
--- a/ruby/ql/lib/codeql/ruby/AST.qll
+++ b/ruby/ql/lib/codeql/ruby/AST.qll
@@ -1,3 +1,6 @@
+overlay[local]
+module;
+
 import codeql.Locations
 import ast.Call
 import ast.Control
diff --git a/ruby/ql/lib/codeql/ruby/Diagnostics.qll b/ruby/ql/lib/codeql/ruby/Diagnostics.qll
index 58de14b8fcf..5b55eec3809 100644
--- a/ruby/ql/lib/codeql/ruby/Diagnostics.qll
+++ b/ruby/ql/lib/codeql/ruby/Diagnostics.qll
@@ -1,4 +1,6 @@
 /** Provides classes relating to extraction diagnostics. */
+overlay[local]
+module;
 
 private import codeql.Locations
 
diff --git a/ruby/ql/lib/codeql/ruby/ast/Call.qll b/ruby/ql/lib/codeql/ruby/ast/Call.qll
index 8a69ebd36fb..3a82d0d39b3 100644
--- a/ruby/ql/lib/codeql/ruby/ast/Call.qll
+++ b/ruby/ql/lib/codeql/ruby/ast/Call.qll
@@ -1,3 +1,6 @@
+overlay[local]
+module;
+
 private import codeql.ruby.AST
 private import internal.AST
 private import internal.Call
@@ -52,6 +55,7 @@ class Call extends Expr instanceof CallImpl {
   final int getNumberOfArguments() { result = super.getNumberOfArgumentsImpl() }
 
   /** Gets a potential target of this call, if any. */
+  overlay[global]
   final Callable getATarget() {
     exists(DataFlowCall c |
       this = c.asCall().getExpr() and
@@ -153,6 +157,7 @@ class MethodCall extends Call instanceof MethodCallImpl {
  * TODO: When API Graphs is able to resolve calls to methods like `Kernel.send`
  * this class is no longer necessary and should be removed.
  */
+overlay[global]
 class UnknownMethodCall extends MethodCall {
   UnknownMethodCall() { not exists(this.(Call).getATarget()) }
 }
diff --git a/ruby/ql/lib/codeql/ruby/ast/Constant.qll b/ruby/ql/lib/codeql/ruby/ast/Constant.qll
index fef057bc88e..9c7ac62e542 100644
--- a/ruby/ql/lib/codeql/ruby/ast/Constant.qll
+++ b/ruby/ql/lib/codeql/ruby/ast/Constant.qll
@@ -1,3 +1,6 @@
+overlay[local]
+module;
+
 private import codeql.ruby.AST
 private import internal.AST
 private import internal.Constant
diff --git a/ruby/ql/lib/codeql/ruby/ast/Control.qll b/ruby/ql/lib/codeql/ruby/ast/Control.qll
index 18182d8268a..5d83e7a62fd 100644
--- a/ruby/ql/lib/codeql/ruby/ast/Control.qll
+++ b/ruby/ql/lib/codeql/ruby/ast/Control.qll
@@ -1,3 +1,6 @@
+overlay[local]
+module;
+
 private import codeql.ruby.AST
 private import internal.AST
 private import internal.Control
diff --git a/ruby/ql/lib/codeql/ruby/ast/Erb.qll b/ruby/ql/lib/codeql/ruby/ast/Erb.qll
index 4dbcca73425..4def19f7ceb 100644
--- a/ruby/ql/lib/codeql/ruby/ast/Erb.qll
+++ b/ruby/ql/lib/codeql/ruby/ast/Erb.qll
@@ -1,3 +1,6 @@
+overlay[local]
+module;
+
 private import codeql.ruby.AST
 private import internal.Erb
 private import internal.TreeSitter
diff --git a/ruby/ql/lib/codeql/ruby/ast/Expr.qll b/ruby/ql/lib/codeql/ruby/ast/Expr.qll
index 5f916fbec5c..8ab203aed87 100644
--- a/ruby/ql/lib/codeql/ruby/ast/Expr.qll
+++ b/ruby/ql/lib/codeql/ruby/ast/Expr.qll
@@ -1,3 +1,6 @@
+overlay[local]
+module;
+
 private import codeql.ruby.AST
 private import codeql.ruby.CFG
 private import internal.AST
diff --git a/ruby/ql/lib/codeql/ruby/ast/Literal.qll b/ruby/ql/lib/codeql/ruby/ast/Literal.qll
index cdeae9e64a6..a32ca16e24c 100644
--- a/ruby/ql/lib/codeql/ruby/ast/Literal.qll
+++ b/ruby/ql/lib/codeql/ruby/ast/Literal.qll
@@ -1,3 +1,6 @@
+overlay[local]
+module;
+
 private import codeql.ruby.AST
 private import codeql.ruby.Regexp as RE
 private import internal.AST
@@ -387,6 +390,7 @@ class RegExpLiteral extends StringlikeLiteral instanceof RegExpLiteralImpl {
   final predicate hasFreeSpacingFlag() { this.getFlagString().charAt(_) = "x" }
 
   /** Returns the root node of the parse tree of this regular expression. */
+  overlay[global]
   final RE::RegExpTerm getParsed() { result = RE::getParsedRegExp(this) }
 }
 
diff --git a/ruby/ql/lib/codeql/ruby/ast/Method.qll b/ruby/ql/lib/codeql/ruby/ast/Method.qll
index 61ee58019d1..60c0c705b31 100644
--- a/ruby/ql/lib/codeql/ruby/ast/Method.qll
+++ b/ruby/ql/lib/codeql/ruby/ast/Method.qll
@@ -1,3 +1,6 @@
+overlay[local]
+module;
+
 private import codeql.ruby.AST
 private import codeql.ruby.controlflow.ControlFlowGraph
 private import internal.AST
diff --git a/ruby/ql/lib/codeql/ruby/ast/Module.qll b/ruby/ql/lib/codeql/ruby/ast/Module.qll
index 9e2ca31ee61..671910bfaef 100644
--- a/ruby/ql/lib/codeql/ruby/ast/Module.qll
+++ b/ruby/ql/lib/codeql/ruby/ast/Module.qll
@@ -1,3 +1,6 @@
+overlay[local]
+module;
+
 private import codeql.ruby.AST
 private import codeql.ruby.CFG
 private import internal.AST
diff --git a/ruby/ql/lib/codeql/ruby/ast/Operation.qll b/ruby/ql/lib/codeql/ruby/ast/Operation.qll
index 2e005a207e3..b9046a930b3 100644
--- a/ruby/ql/lib/codeql/ruby/ast/Operation.qll
+++ b/ruby/ql/lib/codeql/ruby/ast/Operation.qll
@@ -1,3 +1,6 @@
+overlay[local]
+module;
+
 private import codeql.ruby.AST
 private import internal.AST
 private import internal.TreeSitter
diff --git a/ruby/ql/lib/codeql/ruby/ast/Parameter.qll b/ruby/ql/lib/codeql/ruby/ast/Parameter.qll
index c4b233b62b6..5b3994378c1 100644
--- a/ruby/ql/lib/codeql/ruby/ast/Parameter.qll
+++ b/ruby/ql/lib/codeql/ruby/ast/Parameter.qll
@@ -1,3 +1,6 @@
+overlay[local]
+module;
+
 private import codeql.ruby.AST
 private import internal.AST
 private import internal.Variable
diff --git a/ruby/ql/lib/codeql/ruby/ast/Pattern.qll b/ruby/ql/lib/codeql/ruby/ast/Pattern.qll
index ef778664031..f705bf28301 100644
--- a/ruby/ql/lib/codeql/ruby/ast/Pattern.qll
+++ b/ruby/ql/lib/codeql/ruby/ast/Pattern.qll
@@ -1,3 +1,6 @@
+overlay[local]
+module;
+
 private import codeql.ruby.AST
 private import internal.AST
 private import internal.Pattern
diff --git a/ruby/ql/lib/codeql/ruby/ast/Scope.qll b/ruby/ql/lib/codeql/ruby/ast/Scope.qll
index 3e8437f79b3..334b36b583f 100644
--- a/ruby/ql/lib/codeql/ruby/ast/Scope.qll
+++ b/ruby/ql/lib/codeql/ruby/ast/Scope.qll
@@ -1,3 +1,6 @@
+overlay[local]
+module;
+
 private import codeql.ruby.AST
 private import internal.AST
 private import internal.Scope
diff --git a/ruby/ql/lib/codeql/ruby/ast/Statement.qll b/ruby/ql/lib/codeql/ruby/ast/Statement.qll
index 24e18fe4c36..dcd51dbb327 100644
--- a/ruby/ql/lib/codeql/ruby/ast/Statement.qll
+++ b/ruby/ql/lib/codeql/ruby/ast/Statement.qll
@@ -1,3 +1,6 @@
+overlay[local]
+module;
+
 private import codeql.ruby.AST
 private import codeql.ruby.CFG
 private import internal.AST
diff --git a/ruby/ql/lib/codeql/ruby/ast/Variable.qll b/ruby/ql/lib/codeql/ruby/ast/Variable.qll
index fa00cfb4cc7..f5fb4b60604 100644
--- a/ruby/ql/lib/codeql/ruby/ast/Variable.qll
+++ b/ruby/ql/lib/codeql/ruby/ast/Variable.qll
@@ -1,4 +1,6 @@
 /** Provides classes for modeling program variables. */
+overlay[local]
+module;
 
 private import codeql.ruby.AST
 private import internal.AST
diff --git a/ruby/ql/lib/codeql/ruby/ast/internal/AST.qll b/ruby/ql/lib/codeql/ruby/ast/internal/AST.qll
index badcf1d6c6f..ee46fbe8b66 100644
--- a/ruby/ql/lib/codeql/ruby/ast/internal/AST.qll
+++ b/ruby/ql/lib/codeql/ruby/ast/internal/AST.qll
@@ -1,3 +1,6 @@
+overlay[local]
+module;
+
 import codeql.Locations
 private import TreeSitter
 private import codeql.ruby.ast.internal.Call
diff --git a/ruby/ql/lib/codeql/ruby/ast/internal/Call.qll b/ruby/ql/lib/codeql/ruby/ast/internal/Call.qll
index 5bb34989a90..4f3c236f102 100644
--- a/ruby/ql/lib/codeql/ruby/ast/internal/Call.qll
+++ b/ruby/ql/lib/codeql/ruby/ast/internal/Call.qll
@@ -1,3 +1,6 @@
+overlay[local]
+module;
+
 private import TreeSitter
 private import Variable
 private import codeql.ruby.AST
diff --git a/ruby/ql/lib/codeql/ruby/ast/internal/Constant.qll b/ruby/ql/lib/codeql/ruby/ast/internal/Constant.qll
index a04efc1ec94..133cea315c3 100644
--- a/ruby/ql/lib/codeql/ruby/ast/internal/Constant.qll
+++ b/ruby/ql/lib/codeql/ruby/ast/internal/Constant.qll
@@ -1,3 +1,6 @@
+overlay[local]
+module;
+
 private import codeql.ruby.AST
 private import codeql.ruby.ast.internal.AST
 private import codeql.ruby.ast.internal.Literal
diff --git a/ruby/ql/lib/codeql/ruby/ast/internal/Control.qll b/ruby/ql/lib/codeql/ruby/ast/internal/Control.qll
index 7b95d67efc4..dd57a0d197d 100644
--- a/ruby/ql/lib/codeql/ruby/ast/internal/Control.qll
+++ b/ruby/ql/lib/codeql/ruby/ast/internal/Control.qll
@@ -1,3 +1,6 @@
+overlay[local]
+module;
+
 private import TreeSitter
 private import codeql.ruby.AST
 private import codeql.ruby.ast.internal.AST
diff --git a/ruby/ql/lib/codeql/ruby/ast/internal/Erb.qll b/ruby/ql/lib/codeql/ruby/ast/internal/Erb.qll
index 7a69bf5b783..29960486907 100644
--- a/ruby/ql/lib/codeql/ruby/ast/internal/Erb.qll
+++ b/ruby/ql/lib/codeql/ruby/ast/internal/Erb.qll
@@ -1,3 +1,6 @@
+overlay[local]
+module;
+
 import codeql.Locations
 private import TreeSitter
 private import codeql.ruby.ast.Erb
diff --git a/ruby/ql/lib/codeql/ruby/ast/internal/Expr.qll b/ruby/ql/lib/codeql/ruby/ast/internal/Expr.qll
index ba4f9e51f4e..fdeec446a93 100644
--- a/ruby/ql/lib/codeql/ruby/ast/internal/Expr.qll
+++ b/ruby/ql/lib/codeql/ruby/ast/internal/Expr.qll
@@ -1,3 +1,6 @@
+overlay[local]
+module;
+
 private import codeql.ruby.AST
 private import codeql.ruby.CFG
 private import AST
diff --git a/ruby/ql/lib/codeql/ruby/ast/internal/Literal.qll b/ruby/ql/lib/codeql/ruby/ast/internal/Literal.qll
index 8af4673d916..6a2df06b349 100644
--- a/ruby/ql/lib/codeql/ruby/ast/internal/Literal.qll
+++ b/ruby/ql/lib/codeql/ruby/ast/internal/Literal.qll
@@ -1,3 +1,6 @@
+overlay[local]
+module;
+
 private import codeql.ruby.AST
 private import AST
 private import Constant
diff --git a/ruby/ql/lib/codeql/ruby/ast/internal/Method.qll b/ruby/ql/lib/codeql/ruby/ast/internal/Method.qll
index 075ac5fb8fa..c4dd1abbee0 100644
--- a/ruby/ql/lib/codeql/ruby/ast/internal/Method.qll
+++ b/ruby/ql/lib/codeql/ruby/ast/internal/Method.qll
@@ -1,3 +1,6 @@
+overlay[local]
+module;
+
 private import codeql.ruby.AST
 private import AST
 private import TreeSitter
diff --git a/ruby/ql/lib/codeql/ruby/ast/internal/Module.qll b/ruby/ql/lib/codeql/ruby/ast/internal/Module.qll
index 6905dd5ff2d..d222316bf26 100644
--- a/ruby/ql/lib/codeql/ruby/ast/internal/Module.qll
+++ b/ruby/ql/lib/codeql/ruby/ast/internal/Module.qll
@@ -1,3 +1,6 @@
+overlay[local]
+module;
+
 private import codeql.ruby.AST
 private import Scope as Scope
 
diff --git a/ruby/ql/lib/codeql/ruby/ast/internal/Operation.qll b/ruby/ql/lib/codeql/ruby/ast/internal/Operation.qll
index 54c763e24d3..eeec2198b62 100644
--- a/ruby/ql/lib/codeql/ruby/ast/internal/Operation.qll
+++ b/ruby/ql/lib/codeql/ruby/ast/internal/Operation.qll
@@ -1,3 +1,6 @@
+overlay[local]
+module;
+
 private import codeql.ruby.AST
 private import AST
 private import TreeSitter
diff --git a/ruby/ql/lib/codeql/ruby/ast/internal/Parameter.qll b/ruby/ql/lib/codeql/ruby/ast/internal/Parameter.qll
index dc7fb8c7695..8f07554fb0c 100644
--- a/ruby/ql/lib/codeql/ruby/ast/internal/Parameter.qll
+++ b/ruby/ql/lib/codeql/ruby/ast/internal/Parameter.qll
@@ -1,3 +1,6 @@
+overlay[local]
+module;
+
 private import codeql.ruby.AST
 private import AST
 private import TreeSitter
diff --git a/ruby/ql/lib/codeql/ruby/ast/internal/Pattern.qll b/ruby/ql/lib/codeql/ruby/ast/internal/Pattern.qll
index c59898d88ee..a30cce32c7c 100644
--- a/ruby/ql/lib/codeql/ruby/ast/internal/Pattern.qll
+++ b/ruby/ql/lib/codeql/ruby/ast/internal/Pattern.qll
@@ -1,3 +1,6 @@
+overlay[local]
+module;
+
 private import codeql.ruby.AST
 private import codeql.ruby.ast.internal.Expr
 private import codeql.ruby.ast.internal.Parameter
diff --git a/ruby/ql/lib/codeql/ruby/ast/internal/Scope.qll b/ruby/ql/lib/codeql/ruby/ast/internal/Scope.qll
index 8f5bde5aeec..9ec237012bc 100644
--- a/ruby/ql/lib/codeql/ruby/ast/internal/Scope.qll
+++ b/ruby/ql/lib/codeql/ruby/ast/internal/Scope.qll
@@ -1,3 +1,6 @@
+overlay[local]
+module;
+
 private import TreeSitter
 private import codeql.ruby.AST
 private import codeql.ruby.ast.internal.AST
diff --git a/ruby/ql/lib/codeql/ruby/ast/internal/Synthesis.qll b/ruby/ql/lib/codeql/ruby/ast/internal/Synthesis.qll
index 5d1ee81c013..f2be91a63e5 100644
--- a/ruby/ql/lib/codeql/ruby/ast/internal/Synthesis.qll
+++ b/ruby/ql/lib/codeql/ruby/ast/internal/Synthesis.qll
@@ -1,4 +1,6 @@
 /** Provides predicates for synthesizing AST nodes. */
+overlay[local]
+module;
 
 private import AST
 private import TreeSitter
diff --git a/ruby/ql/lib/codeql/ruby/ast/internal/TreeSitter.qll b/ruby/ql/lib/codeql/ruby/ast/internal/TreeSitter.qll
index 4d9cd901f23..dbc7b38b84e 100644
--- a/ruby/ql/lib/codeql/ruby/ast/internal/TreeSitter.qll
+++ b/ruby/ql/lib/codeql/ruby/ast/internal/TreeSitter.qll
@@ -23,6 +23,7 @@ private predicate discardLocation(@location_default loc) {
   )
 }
 
+overlay[local]
 module Ruby {
   /** The base class for all AST nodes */
   class AstNode extends @ruby_ast_node {
@@ -67,7 +68,6 @@ module Ruby {
   }
 
   /** Gets the file containing the given `node`. */
-  overlay[local]
   private @file getNodeFile(@ruby_ast_node node) {
     exists(@location_default loc | ruby_ast_node_location(node, loc) |
       locations_default(loc, result, _, _, _, _)
@@ -75,7 +75,6 @@ module Ruby {
   }
 
   /** Holds if `node` is in the `file` and is part of the overlay base database. */
-  overlay[local]
   private predicate discardableAstNode(@file file, @ruby_ast_node node) {
     not isOverlay() and file = getNodeFile(node)
   }
@@ -1967,6 +1966,7 @@ module Ruby {
   }
 }
 
+overlay[local]
 module Erb {
   /** The base class for all AST nodes */
   class AstNode extends @erb_ast_node {
@@ -2011,7 +2011,6 @@ module Erb {
   }
 
   /** Gets the file containing the given `node`. */
-  overlay[local]
   private @file getNodeFile(@erb_ast_node node) {
     exists(@location_default loc | erb_ast_node_location(node, loc) |
       locations_default(loc, result, _, _, _, _)
@@ -2019,7 +2018,6 @@ module Erb {
   }
 
   /** Holds if `node` is in the `file` and is part of the overlay base database. */
-  overlay[local]
   private predicate discardableAstNode(@file file, @erb_ast_node node) {
     not isOverlay() and file = getNodeFile(node)
   }
diff --git a/ruby/ql/lib/codeql/ruby/ast/internal/Variable.qll b/ruby/ql/lib/codeql/ruby/ast/internal/Variable.qll
index bea1ddadbfb..7c130220a86 100644
--- a/ruby/ql/lib/codeql/ruby/ast/internal/Variable.qll
+++ b/ruby/ql/lib/codeql/ruby/ast/internal/Variable.qll
@@ -1,3 +1,6 @@
+overlay[local]
+module;
+
 private import TreeSitter
 private import codeql.ruby.AST
 private import codeql.ruby.CFG
diff --git a/ruby/ql/lib/codeql/ruby/controlflow/BasicBlocks.qll b/ruby/ql/lib/codeql/ruby/controlflow/BasicBlocks.qll
index f70062ad24f..93253371198 100644
--- a/ruby/ql/lib/codeql/ruby/controlflow/BasicBlocks.qll
+++ b/ruby/ql/lib/codeql/ruby/controlflow/BasicBlocks.qll
@@ -1,4 +1,6 @@
 /** Provides classes representing basic blocks. */
+overlay[local]
+module;
 
 private import codeql.ruby.AST
 private import codeql.ruby.ast.internal.AST
diff --git a/ruby/ql/lib/codeql/ruby/controlflow/CfgNodes.qll b/ruby/ql/lib/codeql/ruby/controlflow/CfgNodes.qll
index c822450bf89..16d0a69fcc3 100644
--- a/ruby/ql/lib/codeql/ruby/controlflow/CfgNodes.qll
+++ b/ruby/ql/lib/codeql/ruby/controlflow/CfgNodes.qll
@@ -1,4 +1,6 @@
 /** Provides classes representing nodes in a control flow graph. */
+overlay[local]
+module;
 
 private import codeql.ruby.AST
 private import codeql.ruby.controlflow.BasicBlocks
diff --git a/ruby/ql/lib/codeql/ruby/controlflow/ControlFlowGraph.qll b/ruby/ql/lib/codeql/ruby/controlflow/ControlFlowGraph.qll
index dee31d8e901..f3c5dcd08f3 100644
--- a/ruby/ql/lib/codeql/ruby/controlflow/ControlFlowGraph.qll
+++ b/ruby/ql/lib/codeql/ruby/controlflow/ControlFlowGraph.qll
@@ -1,4 +1,6 @@
 /** Provides classes representing the control flow graph. */
+overlay[local]
+module;
 
 private import codeql.ruby.AST
 private import codeql.ruby.controlflow.BasicBlocks
diff --git a/ruby/ql/lib/codeql/ruby/controlflow/internal/Completion.qll b/ruby/ql/lib/codeql/ruby/controlflow/internal/Completion.qll
index 83ea11e9d23..b8edf83c20d 100644
--- a/ruby/ql/lib/codeql/ruby/controlflow/internal/Completion.qll
+++ b/ruby/ql/lib/codeql/ruby/controlflow/internal/Completion.qll
@@ -3,6 +3,8 @@
  *
  * A completion represents how a statement or expression terminates.
  */
+overlay[local]
+module;
 
 private import codeql.ruby.AST
 private import codeql.ruby.ast.internal.AST
diff --git a/ruby/ql/lib/codeql/ruby/controlflow/internal/ControlFlowGraphImpl.qll b/ruby/ql/lib/codeql/ruby/controlflow/internal/ControlFlowGraphImpl.qll
index dd672ba982d..d0d418a839f 100644
--- a/ruby/ql/lib/codeql/ruby/controlflow/internal/ControlFlowGraphImpl.qll
+++ b/ruby/ql/lib/codeql/ruby/controlflow/internal/ControlFlowGraphImpl.qll
@@ -2,6 +2,8 @@
  * Provides an implementation for constructing control-flow graphs (CFGs) from
  * abstract syntax trees (ASTs), using the shared library from `codeql.controlflow.Cfg`.
  */
+overlay[local]
+module;
 
 private import codeql.controlflow.Cfg as CfgShared
 private import codeql.ruby.AST
diff --git a/ruby/ql/lib/codeql/ruby/controlflow/internal/Guards.qll b/ruby/ql/lib/codeql/ruby/controlflow/internal/Guards.qll
index 1161a061581..a60102e017c 100644
--- a/ruby/ql/lib/codeql/ruby/controlflow/internal/Guards.qll
+++ b/ruby/ql/lib/codeql/ruby/controlflow/internal/Guards.qll
@@ -1,3 +1,6 @@
+overlay[local]
+module;
+
 private import codeql.ruby.CFG
 
 /** Holds if the guard `guard` controls block `bb` upon evaluating to `branch`. */
diff --git a/ruby/ql/lib/codeql/ruby/controlflow/internal/NonReturning.qll b/ruby/ql/lib/codeql/ruby/controlflow/internal/NonReturning.qll
index e1927a0b1c9..45b299a5d2b 100644
--- a/ruby/ql/lib/codeql/ruby/controlflow/internal/NonReturning.qll
+++ b/ruby/ql/lib/codeql/ruby/controlflow/internal/NonReturning.qll
@@ -1,4 +1,6 @@
 /** Provides a simple analysis for identifying calls that will not return. */
+overlay[local]
+module;
 
 private import codeql.ruby.AST
 private import Completion
diff --git a/ruby/ql/lib/codeql/ruby/controlflow/internal/Splitting.qll b/ruby/ql/lib/codeql/ruby/controlflow/internal/Splitting.qll
index 5331a3d26b6..146d5927479 100644
--- a/ruby/ql/lib/codeql/ruby/controlflow/internal/Splitting.qll
+++ b/ruby/ql/lib/codeql/ruby/controlflow/internal/Splitting.qll
@@ -1,6 +1,8 @@
 /**
  * Provides classes and predicates relevant for splitting the control flow graph.
  */
+overlay[local]
+module;
 
 private import codeql.ruby.AST as Ast
 private import Completion as Comp
diff --git a/ruby/ql/lib/codeql/ruby/dataflow/SSA.qll b/ruby/ql/lib/codeql/ruby/dataflow/SSA.qll
index 07721d33334..1478d9ed9d6 100644
--- a/ruby/ql/lib/codeql/ruby/dataflow/SSA.qll
+++ b/ruby/ql/lib/codeql/ruby/dataflow/SSA.qll
@@ -1,6 +1,8 @@
 /**
  * Provides the module `Ssa` for working with static single assignment (SSA) form.
  */
+overlay[local]
+module;
 
 /**
  * Provides classes for working with static single assignment (SSA) form.
diff --git a/ruby/ql/lib/codeql/ruby/dataflow/internal/SsaImpl.qll b/ruby/ql/lib/codeql/ruby/dataflow/internal/SsaImpl.qll
index adbec18be64..3e1d27a17ba 100644
--- a/ruby/ql/lib/codeql/ruby/dataflow/internal/SsaImpl.qll
+++ b/ruby/ql/lib/codeql/ruby/dataflow/internal/SsaImpl.qll
@@ -1,3 +1,6 @@
+overlay[local]
+module;
+
 private import codeql.ssa.Ssa as SsaImplCommon
 private import codeql.ruby.AST
 private import codeql.ruby.CFG as Cfg
@@ -393,6 +396,7 @@ private module Cached {
 
     signature predicate guardChecksSig(Cfg::CfgNodes::AstCfgNode g, Cfg::CfgNode e, boolean branch);
 
+    overlay[global]
     cached // nothing is actually cached
     module BarrierGuard<guardChecksSig/3 guardChecks> {
       private predicate guardChecksAdjTypes(
diff --git a/shared/tree-sitter-extractor/src/generator/mod.rs b/shared/tree-sitter-extractor/src/generator/mod.rs
index d9e6e00a121..5e58611092b 100644
--- a/shared/tree-sitter-extractor/src/generator/mod.rs
+++ b/shared/tree-sitter-extractor/src/generator/mod.rs
@@ -120,6 +120,7 @@ pub fn generate(
                 qldoc: None,
                 name: &language.name,
                 body,
+                overlay: Some(ql::OverlayAnnotation::Local),
             })],
         )?;
     }
diff --git a/shared/tree-sitter-extractor/src/generator/ql.rs b/shared/tree-sitter-extractor/src/generator/ql.rs
index e4c87b61bdb..b1e319afb1e 100644
--- a/shared/tree-sitter-extractor/src/generator/ql.rs
+++ b/shared/tree-sitter-extractor/src/generator/ql.rs
@@ -95,6 +95,7 @@ pub struct Module<'a> {
     pub qldoc: Option<String>,
     pub name: &'a str,
     pub body: Vec<TopLevel<'a>>,
+    pub overlay: Option<OverlayAnnotation>,
 }
 
 impl fmt::Display for Module<'_> {
@@ -102,6 +103,14 @@ impl fmt::Display for Module<'_> {
         if let Some(qldoc) = &self.qldoc {
             write!(f, "/** {} */", qldoc)?;
         }
+        if let Some(overlay_annotation) = &self.overlay {
+            write!(f, "overlay[")?;
+            match overlay_annotation {
+                OverlayAnnotation::Local => write!(f, "local")?,
+                OverlayAnnotation::DiscardEntity => write!(f, "discard_entity")?,
+            }
+            write!(f, "] ")?;
+        }
         writeln!(f, "module {} {{ ", self.name)?;
         for decl in &self.body {
             writeln!(f, "  {}", decl)?;
diff --git a/shared/tree-sitter-extractor/src/generator/ql_gen.rs b/shared/tree-sitter-extractor/src/generator/ql_gen.rs
index 8b6c9c18c6f..2cfaf5715ca 100644
--- a/shared/tree-sitter-extractor/src/generator/ql_gen.rs
+++ b/shared/tree-sitter-extractor/src/generator/ql_gen.rs
@@ -286,7 +286,7 @@ pub fn create_get_node_file_predicate<'a>(
         overridden: false,
         is_private: true,
         is_final: false,
-        overlay: Some(ql::OverlayAnnotation::Local),
+        overlay: None,
         return_type: Some(ql::Type::At("file")),
         formal_parameters: vec![ql::FormalParameter {
             name: "node",
@@ -327,7 +327,7 @@ pub fn create_discardable_ast_node_predicate(ast_node_name: &str) -> ql::Predica
         overridden: false,
         is_private: true,
         is_final: false,
-        overlay: Some(ql::OverlayAnnotation::Local),
+        overlay: None,
         return_type: None,
         formal_parameters: vec![
             ql::FormalParameter {