Merge branch 'main' into redsun82/update-rules_java

2025-12-16 16:53:25 +01:00 · 2025-11-14 12:35:09 +01:00
parent 82435218dc 96f57b207d
commit da12d73f25
178 changed files with 21810 additions and 5559 deletions
--- a/.github/workflows/build-ripunzip.yml
+++ b/.github/workflows/build-ripunzip.yml
@@ -4,20 +4,45 @@ on:
  workflow_dispatch:
    inputs:
      ripunzip-version:
-        description: "what reference to checktout from google/runzip"
+        description: What reference to checkout from google/ripunzip. Latest by default
        required: false
      openssl-version:
-        description: "what reference to checkout from openssl/openssl for Linux"
+        description: What reference to checkout from openssl/openssl for Linux. Latest by default
        required: false
+      open-pr:
+        description: Open a pull request updating the ripunzip versions committed to lfs
+        required: false
+        default: true  # will be false on PRs
  pull_request:
    paths:
      - .github/workflows/build-ripunzip.yml
-env:
-  RIPUNZIP_DEFAULT: v2.0.3
-  OPENSSL_DEFAULT: openssl-3.6.0

+permissions: {}
+  
 jobs:
+  versions:
+    runs-on: ubuntu-slim
+    outputs:
+      ripunzip-version: ${{ inputs.ripunzip-version || steps.fetch-ripunzip-version.outputs.version }}
+      openssl-version: ${{ inputs.openssl-version || steps.fetch-openssl-version.outputs.version }}
+    steps:
+      - name: Fetch latest ripunzip version
+        id: fetch-ripunzip-version
+        if: "!inputs.ripunzip-version"
+        run: &fetch-version
+          echo "version=$(gh release view --repo $REPO --json tagName --jq .tagName)" | tee -a $GITHUB_OUTPUT
+        env:
+          REPO: "google/ripunzip"
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      - name: Fetch latest openssl version
+        id: fetch-openssl-version
+        if: "!inputs.openssl-version"
+        run: *fetch-version
+        env:
+          REPO: "openssl/openssl"
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
  build:
+    needs: versions
    strategy:
      fail-fast: false
      matrix:
@@ -27,7 +52,7 @@ jobs:
      - uses: actions/checkout@v5
        with:
          repository: google/ripunzip
-          ref: ${{ inputs.ripunzip-version || env.RIPUNZIP_DEFAULT }}
+          ref: ${{ needs.versions.outputs.ripunzip-version }}
      # we need to avoid ripunzip dynamically linking into libssl
      # see https://github.com/sfackler/rust-openssl/issues/183
      - if: runner.os == 'Linux'
@@ -36,7 +61,7 @@ jobs:
        with:
          repository: openssl/openssl
          path: openssl
-          ref: ${{ inputs.openssl-version || env.OPENSSL_DEFAULT }}
+          ref: ${{ needs.versions.outputs.openssl-version }}
      - if: runner.os == 'Linux'
        name: build and install openssl with fPIC
        shell: bash
@@ -68,11 +93,74 @@ jobs:
          lipo -create -output ripunzip-macos \
            -arch x86_64 target/x86_64-apple-darwin/release/ripunzip \
            -arch arm64 target/aarch64-apple-darwin/release/ripunzip
-      - uses: actions/upload-artifact@v4
+      - name: Archive
+        shell: bash
+        run: |
+          tar acf ripunzip-$RUNNER_OS.tar.zst ripunzip-$(echo $RUNNER_OS | tr '[:upper:]' '[:lower:]')
+      - name: Upload built binary
+        uses: actions/upload-artifact@v4
        with:
          name: ripunzip-${{ runner.os }}
-          path: ripunzip-*
+          path: ripunzip-${{ runner.os }}.tar.zst
+          retention-days: 5
+          compression: 0
      - name: Check built binary
        shell: bash
        run: |
+          rm -f ripunzip-*.tar.zst
          ./ripunzip-* --version
+  publish:
+    needs: [versions, build]
+    if: inputs.open-pr == 'true'
+    permissions:
+      contents: write
+      pull-requests: write
+    runs-on: ubuntu-slim
+    steps:
+      # workaround for git-lfs not being installed yet on ubuntu-slim runners
+      - name: Ensure git-lfs is installed
+        shell: bash
+        run: |
+          if which git-lfs &>/dev/null; then
+            echo "git-lfs is already installed"
+            exit 0
+          fi
+          cd $TMP
+          gh release download --repo git-lfs/git-lfs --pattern "git-lfs-linux-amd64-*.tar.gz" --clobber
+          tar xzf git-lfs-linux-amd64-*.tar.gz
+          rm git-lfs-linux-amd64-*.tar.gz
+          cd git-lfs-*
+          pwd | tee -a $GITHUB_PATH
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      - uses: actions/checkout@v5
+        with:
+          sparse-checkout: |
+            .github
+            misc/ripunzip
+          lfs: true
+      - name: Download built binaries
+        uses: actions/download-artifact@v4
+        with:
+          merge-multiple: true
+          path: misc/ripunzip
+      - name: Open PR
+        shell: bash
+        run: |
+          git config --global user.name "github-actions[bot]"
+          git config --global user.email "github-actions[bot]@users.noreply.github.com"
+          git switch -c update-ripunzip
+          git add misc/ripunzip
+          git commit -m "Update ripunzip binaries to version $VERSION"
+          git push --set-upstream origin update-ripunzip --force
+          TITLE="Update ripunzip binaries to version $VERSION"
+          gh pr create \
+            --draft \
+            --title "$TITLE" \
+            --body "Automated update of ripunzip binaries." \
+            --assignee "$ACTOR" ||
+              (gh pr edit --title "$TITLE" --add-assignee "$ACTOR" && gh pr ready --undo)
+        env:
+          ACTOR: ${{ github.actor }}
+          VERSION: ${{ needs.versions.outputs.ripunzip-version }}
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
--- a/MODULE.bazel
+++ b/MODULE.bazel
@@ -273,19 +273,19 @@ lfs_archive = use_repo_rule("//misc/bazel:lfs.bzl", "lfs_archive")

 lfs_archive(
    name = "ripunzip-linux",
-    src = "//misc/ripunzip:ripunzip-Linux.zip",
+    src = "//misc/ripunzip:ripunzip-Linux.tar.zst",
    build_file = "//misc/ripunzip:BUILD.ripunzip.bazel",
 )

 lfs_archive(
    name = "ripunzip-windows",
-    src = "//misc/ripunzip:ripunzip-Windows.zip",
+    src = "//misc/ripunzip:ripunzip-Windows.tar.zst",
    build_file = "//misc/ripunzip:BUILD.ripunzip.bazel",
 )

 lfs_archive(
    name = "ripunzip-macos",
-    src = "//misc/ripunzip:ripunzip-macOS.zip",
+    src = "//misc/ripunzip:ripunzip-macOS.tar.zst",
    build_file = "//misc/ripunzip:BUILD.ripunzip.bazel",
 )

--- a/csharp/codeql-extractor.yml
+++ b/csharp/codeql-extractor.yml
@@ -4,6 +4,7 @@ aliases:
 display_name: "C#"
 version: 1.22.1
 column_kind: "utf16"
+overlay_support_version: 20250626
 extra_env_vars:
  DOTNET_GENERATE_ASPNET_CERTIFICATE: "false"
 build_modes:
--- a/csharp/downgrades/605f85053409cd72b4904df3f198ddc8324f3a83/old.dbscheme
+++ b/csharp/downgrades/605f85053409cd72b4904df3f198ddc8324f3a83/old.dbscheme
--- a/csharp/downgrades/605f85053409cd72b4904df3f198ddc8324f3a83/semmlecode.csharp.dbscheme
+++ b/csharp/downgrades/605f85053409cd72b4904df3f198ddc8324f3a83/semmlecode.csharp.dbscheme
--- a/csharp/downgrades/605f85053409cd72b4904df3f198ddc8324f3a83/upgrade.properties
+++ b/csharp/downgrades/605f85053409cd72b4904df3f198ddc8324f3a83/upgrade.properties
@@ -0,0 +1,4 @@
+description: Delete databaseMetadata and overlayChangedFiles relations
+compatibility: full
+databaseMetadata.rel: delete
+overlayChangedFiles.rel: delete
--- a/csharp/downgrades/68b5aec54e50fe7e375df3777b756a746ca3a37c/old.dbscheme
+++ b/csharp/downgrades/68b5aec54e50fe7e375df3777b756a746ca3a37c/old.dbscheme
--- a/csharp/downgrades/68b5aec54e50fe7e375df3777b756a746ca3a37c/semmlecode.csharp.dbscheme
+++ b/csharp/downgrades/68b5aec54e50fe7e375df3777b756a746ca3a37c/semmlecode.csharp.dbscheme
--- a/csharp/downgrades/68b5aec54e50fe7e375df3777b756a746ca3a37c/upgrade.properties
+++ b/csharp/downgrades/68b5aec54e50fe7e375df3777b756a746ca3a37c/upgrade.properties
@@ -0,0 +1,2 @@
+description: Remove @locatable type
+compatibility: full
--- a/csharp/extractor/Semmle.Extraction.CSharp.Standalone/Extractor.cs
+++ b/csharp/extractor/Semmle.Extraction.CSharp.Standalone/Extractor.cs
@@ -2,6 +2,7 @@ using System;
 using System.Collections.Concurrent;
 using System.Collections.Generic;
 using System.Diagnostics;
+using System.IO;
 using System.Linq;
 using Microsoft.CodeAnalysis;
 using Microsoft.CodeAnalysis.CSharp;
@@ -53,6 +54,20 @@ namespace Semmle.Extraction.CSharp.Standalone
                        }

                        progressMonitor.MissingSummary(analyser.ExtractionContext!.MissingTypes.Count(), analyser.ExtractionContext!.MissingNamespaces.Count());
+
+                        // If extracting a base database, we need to create an empty metadata file.
+                        if (EnvironmentVariables.GetBaseMetaDataOutPath() is string baseMetaDataOutPath)
+                        {
+                            try
+                            {
+                                analyser.Logger.LogInfo($"Creating base metadata file at {baseMetaDataOutPath}");
+                                File.WriteAllText(baseMetaDataOutPath, string.Empty);
+                            }
+                            catch (Exception ex)
+                            {
+                                analyser.Logger.LogError($"Failed to create base metadata file: {ex.Message}");
+                            }
+                        }
                    });
            }
            finally
@@ -143,7 +158,8 @@ namespace Semmle.Extraction.CSharp.Standalone
            var pathTransformer = new PathTransformer(canonicalPathCache);

            var progressMonitor = new ExtractionProgress(logger);
-            using var analyser = new StandaloneAnalyser(progressMonitor, fileLogger, pathTransformer, canonicalPathCache, false);
+            var overlayInfo = OverlayInfoFactory.Make(logger, options.SrcDir);
+            using var analyser = new StandaloneAnalyser(progressMonitor, fileLogger, pathTransformer, canonicalPathCache, overlayInfo, false);
            try
            {
                var extractionInput = new ExtractionInput(dependencyManager.AllSourceFiles, dependencyManager.ReferenceFiles, dependencyManager.CompilationInfos);
--- a/csharp/extractor/Semmle.Extraction.CSharp/Entities/Attribute.cs
+++ b/csharp/extractor/Semmle.Extraction.CSharp/Entities/Attribute.cs
@@ -57,8 +57,21 @@ namespace Semmle.Extraction.CSharp.Entities

        public override void Populate(TextWriter trapFile)
        {
+            // In this case, we don't extract the attribute again, as it was extracted using * ID
+            // originally and we re-use that.
+            if (Context.OnlyScaffold && (ReportingLocation is null || !ReportingLocation.IsInSource))
+            {
+                return;
+            }
+
            var type = Type.Create(Context, Symbol.AttributeClass);
            trapFile.attributes(this, kind, type.TypeRef, entity);
+
+            if (Context.OnlyScaffold)
+            {
+                return;
+            }
+
            WriteLocationToTrap(trapFile.attribute_location, this, Location);

            if (attributeSyntax is not null)
--- a/csharp/extractor/Semmle.Extraction.CSharp/Entities/CommentBlock.cs
+++ b/csharp/extractor/Semmle.Extraction.CSharp/Entities/CommentBlock.cs
@@ -10,9 +10,13 @@ namespace Semmle.Extraction.CSharp.Entities

        public override void Populate(TextWriter trapFile)
        {
+            if (Context.OnlyScaffold)
+            {
+                return;
+            }
            trapFile.commentblock(this);
-            WriteLocationToTrap(trapFile.commentblock_location, this, Context.CreateLocation(Symbol.Location));
            Symbol.CommentLines.ForEach((l, child) => trapFile.commentblock_child(this, l, child));
+            WriteLocationToTrap(trapFile.commentblock_location, this, Context.CreateLocation(Symbol.Location));
        }

        public override bool NeedsPopulation => true;
@@ -27,6 +31,10 @@ namespace Semmle.Extraction.CSharp.Entities

        public void BindTo(Label entity, CommentBinding binding)
        {
+            if (Context.OnlyScaffold)
+            {
+                return;
+            }
            Context.TrapWriter.Writer.commentblock_binding(this, entity, binding);
        }

--- a/csharp/extractor/Semmle.Extraction.CSharp/Entities/CommentLine.cs
+++ b/csharp/extractor/Semmle.Extraction.CSharp/Entities/CommentLine.cs
@@ -21,9 +21,14 @@ namespace Semmle.Extraction.CSharp.Entities

        public override void Populate(TextWriter trapFile)
        {
-            location = Context.CreateLocation(Location);
+            if (Context.OnlyScaffold)
+            {
+                return;
+            }
            trapFile.commentline(this, Type == CommentLineType.MultilineContinuation ? CommentLineType.Multiline : Type, Text, RawText);
+            location = Context.CreateLocation(Location);
            WriteLocationToTrap(trapFile.commentline_location, this, location);
+
        }

        public override Microsoft.CodeAnalysis.Location? ReportingLocation => location?.Symbol;
--- a/csharp/extractor/Semmle.Extraction.CSharp/Entities/Compilations/CompilerDiagnostic.cs
+++ b/csharp/extractor/Semmle.Extraction.CSharp/Entities/Compilations/CompilerDiagnostic.cs
@@ -21,6 +21,11 @@ namespace Semmle.Extraction.CSharp.Entities

        protected override void Populate(TextWriter trapFile)
        {
+            if (Context.OnlyScaffold)
+            {
+                return;
+            }
+
            var key = diagnostic.Id;
            var messageCount = compilation.messageCounts.AddOrUpdate(key, 1, (_, c) => c + 1);
            if (messageCount > limit)
--- a/csharp/extractor/Semmle.Extraction.CSharp/Entities/Constructor.cs
+++ b/csharp/extractor/Semmle.Extraction.CSharp/Entities/Constructor.cs
@@ -29,9 +29,17 @@ namespace Semmle.Extraction.CSharp.Entities
            ContainingType!.PopulateGenerics();

            trapFile.constructors(this, Symbol.ContainingType.Name, ContainingType, (Constructor)OriginalDefinition);
-            if (Context.ExtractLocation(Symbol) && (!IsDefault || IsBestSourceLocation))
+
+            if (Symbol.IsImplicitlyDeclared)
            {
-                WriteLocationToTrap(trapFile.constructor_location, this, Location);
+                var lineCounts = new LineCounts() { Total = 2, Code = 1, Comment = 0 };
+                trapFile.numlines(this, lineCounts);
+            }
+            ExtractCompilerGenerated(trapFile);
+
+            if (Context.OnlyScaffold)
+            {
+                return;
            }

            if (MakeSynthetic)
@@ -40,12 +48,11 @@ namespace Semmle.Extraction.CSharp.Entities
                Statements.SyntheticEmptyBlock.Create(Context, this, 0, Location);
            }

-            if (Symbol.IsImplicitlyDeclared)
+            if (Context.ExtractLocation(Symbol) && (!IsDefault || IsBestSourceLocation))
            {
-                var lineCounts = new LineCounts() { Total = 2, Code = 1, Comment = 0 };
-                trapFile.numlines(this, lineCounts);
+                WriteLocationToTrap(trapFile.constructor_location, this, Location);
            }
-            ExtractCompilerGenerated(trapFile);
+
        }

        protected override void ExtractInitializers(TextWriter trapFile)
@@ -53,7 +60,7 @@ namespace Semmle.Extraction.CSharp.Entities
            // Do not extract initializers for constructed types.
            // Extract initializers for constructors with a body, primary constructors
            // and default constructors for classes and structs declared in source code.
-            if (Block is null && ExpressionBody is null && !MakeSynthetic)
+            if (Block is null && ExpressionBody is null && !MakeSynthetic || Context.OnlyScaffold)
            {
                return;
            }
@@ -106,6 +113,7 @@ namespace Semmle.Extraction.CSharp.Entities
                }

                var baseConstructorTarget = Create(Context, baseConstructor);
+
                var info = new ExpressionInfo(Context,
                    AnnotatedTypeSymbol.CreateNotAnnotated(baseType),
                    Location,
@@ -179,7 +187,7 @@ namespace Semmle.Extraction.CSharp.Entities
        /// </summary>
        private bool IsBestSourceLocation => ReportingLocation is not null && Context.IsLocationInContext(ReportingLocation);

-        private bool MakeSynthetic => IsPrimary || (IsDefault && IsBestSourceLocation);
+        private bool MakeSynthetic => (IsPrimary || (IsDefault && IsBestSourceLocation)) && !Context.OnlyScaffold;

        [return: NotNullIfNotNull(nameof(constructor))]
        public static new Constructor? Create(Context cx, IMethodSymbol? constructor)
--- a/csharp/extractor/Semmle.Extraction.CSharp/Entities/Destructor.cs
+++ b/csharp/extractor/Semmle.Extraction.CSharp/Entities/Destructor.cs
@@ -15,6 +15,7 @@ namespace Semmle.Extraction.CSharp.Entities
            ContainingType!.PopulateGenerics();

            trapFile.destructors(this, $"~{Symbol.ContainingType.Name}", ContainingType, OriginalDefinition(Context, this, Symbol));
+
            if (Context.ExtractLocation(Symbol))
            {
                WriteLocationToTrap(trapFile.destructor_location, this, Location);
--- a/csharp/extractor/Semmle.Extraction.CSharp/Entities/Event.cs
+++ b/csharp/extractor/Semmle.Extraction.CSharp/Entities/Event.cs
@@ -37,7 +37,6 @@ namespace Semmle.Extraction.CSharp.Entities
                Method.Create(Context, remover);

            PopulateModifiers(trapFile);
-            BindComments();

            var declSyntaxReferences = IsSourceDeclaration
                ? Symbol.DeclaringSyntaxReferences.Select(d => d.GetSyntax()).ToArray()
@@ -51,6 +50,13 @@ namespace Semmle.Extraction.CSharp.Entities
                    TypeMention.Create(Context, syntax.ExplicitInterfaceSpecifier!.Name, this, explicitInterface);
            }

+            if (Context.OnlyScaffold)
+            {
+                return;
+            }
+
+            BindComments();
+
            if (Context.ExtractLocation(Symbol))
            {
                WriteLocationsToTrap(trapFile.event_location, this, Locations);
--- a/csharp/extractor/Semmle.Extraction.CSharp/Entities/ExtractionMessage.cs
+++ b/csharp/extractor/Semmle.Extraction.CSharp/Entities/ExtractionMessage.cs
@@ -28,6 +28,11 @@ namespace Semmle.Extraction.CSharp.Entities

        protected override void Populate(TextWriter trapFile)
        {
+            if (Context.OnlyScaffold)
+            {
+                return;
+            }
+
            // For the time being we're counting the number of messages per severity, we could introduce other groupings in the future
            var key = msg.Severity.ToString();
            groupedMessageCounts.AddOrUpdate(key, 1, (_, c) => c + 1);
--- a/csharp/extractor/Semmle.Extraction.CSharp/Entities/Field.cs
+++ b/csharp/extractor/Semmle.Extraction.CSharp/Entities/Field.cs
@@ -49,6 +49,11 @@ namespace Semmle.Extraction.CSharp.Entities
                }
            }

+            if (Context.OnlyScaffold)
+            {
+                return;
+            }
+
            if (Context.ExtractLocation(Symbol))
            {
                WriteLocationsToTrap(trapFile.field_location, this, Locations);
--- a/csharp/extractor/Semmle.Extraction.CSharp/Entities/Indexer.cs
+++ b/csharp/extractor/Semmle.Extraction.CSharp/Entities/Indexer.cs
@@ -19,10 +19,6 @@ namespace Semmle.Extraction.CSharp.Entities

            var type = Type.Create(Context, Symbol.Type);
            trapFile.indexers(this, Symbol.GetName(useMetadataName: true), ContainingType!, type.TypeRef, OriginalDefinition);
-            if (Context.ExtractLocation(Symbol))
-            {
-                WriteLocationsToTrap(trapFile.indexer_location, this, Locations);
-            }

            var getter = BodyDeclaringSymbol.GetMethod;
            var setter = BodyDeclaringSymbol.SetMethod;
@@ -42,20 +38,8 @@ namespace Semmle.Extraction.CSharp.Entities
                Parameter.Create(Context, Symbol.Parameters[i], this, original);
            }

-            if (IsSourceDeclaration)
-            {
-                var expressionBody = ExpressionBody;
-                if (expressionBody is not null)
-                {
-                    // The expression may need to reference parameters in the getter.
-                    // So we need to arrange that the expression is populated after the getter.
-                    Context.PopulateLater(() => Expression.CreateFromNode(new ExpressionNodeInfo(Context, expressionBody, this, 0).SetType(Symbol.GetAnnotatedType())));
-                }
-            }
-
            PopulateAttributes();
            PopulateModifiers(trapFile);
-            BindComments();

            var declSyntaxReferences = IsSourceDeclaration
                ? Symbol.DeclaringSyntaxReferences.
@@ -70,6 +54,28 @@ namespace Semmle.Extraction.CSharp.Entities
                    TypeMention.Create(Context, syntax.ExplicitInterfaceSpecifier!.Name, this, explicitInterface);
            }

+            if (Context.OnlyScaffold)
+            {
+                return;
+            }
+
+            if (Context.ExtractLocation(Symbol))
+            {
+                WriteLocationsToTrap(trapFile.indexer_location, this, Locations);
+            }
+
+            if (IsSourceDeclaration)
+            {
+                var expressionBody = ExpressionBody;
+                if (expressionBody is not null)
+                {
+                    // The expression may need to reference parameters in the getter.
+                    // So we need to arrange that the expression is populated after the getter.
+                    Context.PopulateLater(() => Expression.CreateFromNode(new ExpressionNodeInfo(Context, expressionBody, this, 0).SetType(Symbol.GetAnnotatedType())));
+                }
+            }
+
+            BindComments();

            foreach (var syntax in declSyntaxReferences)
                TypeMention.Create(Context, syntax.Type, this, type);
--- a/csharp/extractor/Semmle.Extraction.CSharp/Entities/LocalVariable.cs
+++ b/csharp/extractor/Semmle.Extraction.CSharp/Entities/LocalVariable.cs
@@ -41,6 +41,11 @@ namespace Semmle.Extraction.CSharp.Entities
                trapFile.localvars(this, Kinds.VariableKind.None, Symbol.Name, @var, Type.Create(Context, parent.Type).TypeRef, parent);
            }

+            if (Context.OnlyScaffold)
+            {
+                return;
+            }
+
            WriteLocationToTrap(trapFile.localvar_location, this, Location);

            DefineConstantValue(trapFile);
--- a/csharp/extractor/Semmle.Extraction.CSharp/Entities/Method.cs
+++ b/csharp/extractor/Semmle.Extraction.CSharp/Entities/Method.cs
@@ -48,7 +48,7 @@ namespace Semmle.Extraction.CSharp.Entities

        protected virtual void PopulateMethodBody(TextWriter trapFile)
        {
-            if (!IsSourceDeclaration)
+            if (!IsSourceDeclaration || Context.OnlyScaffold)
                return;

            var block = Block;
--- a/csharp/extractor/Semmle.Extraction.CSharp/Entities/NamespaceDeclaration.cs
+++ b/csharp/extractor/Semmle.Extraction.CSharp/Entities/NamespaceDeclaration.cs
@@ -35,7 +35,6 @@ namespace Semmle.Extraction.CSharp.Entities

            var ns = Namespace.Create(Context, @namespace);
            trapFile.namespace_declarations(this, ns);
-            WriteLocationToTrap(trapFile.namespace_declaration_location, this, Context.CreateLocation(node.Name.GetLocation()));

            var visitor = new Populators.TypeOrNamespaceVisitor(Context, trapFile, this);

@@ -48,6 +47,12 @@ namespace Semmle.Extraction.CSharp.Entities
            {
                trapFile.parent_namespace_declaration(this, parent);
            }
+
+            if (Context.OnlyScaffold)
+            {
+                return;
+            }
+            WriteLocationToTrap(trapFile.namespace_declaration_location, this, Context.CreateLocation(node.Name.GetLocation()));
        }

        public static NamespaceDeclaration Create(Context cx, BaseNamespaceDeclarationSyntax decl, NamespaceDeclaration parent)
--- a/csharp/extractor/Semmle.Extraction.CSharp/Entities/OrdinaryMethod.cs
+++ b/csharp/extractor/Semmle.Extraction.CSharp/Entities/OrdinaryMethod.cs
@@ -34,6 +34,16 @@ namespace Semmle.Extraction.CSharp.Entities
            var returnType = Type.Create(Context, Symbol.ReturnType);
            trapFile.methods(this, Name, ContainingType, returnType.TypeRef, OriginalDefinition);

+            PopulateGenerics(trapFile);
+            Overrides(trapFile);
+            ExtractRefReturn(trapFile, Symbol, this);
+            ExtractCompilerGenerated(trapFile);
+
+            if (Context.OnlyScaffold)
+            {
+                return;
+            }
+
            if (IsSourceDeclaration)
            {
                foreach (var declaration in Symbol.DeclaringSyntaxReferences.Select(s => s.GetSyntax()).OfType<MethodDeclarationSyntax>())
@@ -47,11 +57,6 @@ namespace Semmle.Extraction.CSharp.Entities
            {
                WriteLocationsToTrap(trapFile.method_location, this, Locations);
            }
-
-            PopulateGenerics(trapFile);
-            Overrides(trapFile);
-            ExtractRefReturn(trapFile, Symbol, this);
-            ExtractCompilerGenerated(trapFile);
        }

        private bool IsCompilerGeneratedDelegate() =>
--- a/csharp/extractor/Semmle.Extraction.CSharp/Entities/Parameter.cs
+++ b/csharp/extractor/Semmle.Extraction.CSharp/Entities/Parameter.cs
@@ -115,6 +115,11 @@ namespace Semmle.Extraction.CSharp.Entities
            var type = Type.Create(Context, Symbol.Type);
            trapFile.@params(this, Name, type.TypeRef, Ordinal, ParamKind, Parent!, Original);

+            if (Context.OnlyScaffold)
+            {
+                return;
+            }
+
            if (Context.ExtractLocation(Symbol))
            {
                var locations = Context.GetLocations(Symbol);
--- a/csharp/extractor/Semmle.Extraction.CSharp/Entities/PreprocessorDirectives/PreprocessorDirective.cs
+++ b/csharp/extractor/Semmle.Extraction.CSharp/Entities/PreprocessorDirectives/PreprocessorDirective.cs
@@ -13,10 +13,15 @@ namespace Semmle.Extraction.CSharp.Entities
            PopulatePreprocessor(trapFile);

            trapFile.preprocessor_directive_active(this, Symbol.IsActive);
-            WriteLocationToTrap(trapFile.preprocessor_directive_location, this, Context.CreateLocation(ReportingLocation));

            var compilation = Compilation.Create(Context);
            trapFile.preprocessor_directive_compilation(this, compilation);
+
+            if (Context.OnlyScaffold)
+            {
+                return;
+            }
+            WriteLocationToTrap(trapFile.preprocessor_directive_location, this, Context.CreateLocation(ReportingLocation));
        }

        protected abstract void PopulatePreprocessor(TextWriter trapFile);
--- a/csharp/extractor/Semmle.Extraction.CSharp/Entities/Property.cs
+++ b/csharp/extractor/Semmle.Extraction.CSharp/Entities/Property.cs
@@ -40,7 +40,6 @@ namespace Semmle.Extraction.CSharp.Entities
        {
            PopulateAttributes();
            PopulateModifiers(trapFile);
-            BindComments();
            PopulateNullability(trapFile, Symbol.GetAnnotatedType());
            PopulateRefKind(trapFile, Symbol.RefKind);

@@ -69,6 +68,13 @@ namespace Semmle.Extraction.CSharp.Entities
                    TypeMention.Create(Context, syntax.ExplicitInterfaceSpecifier!.Name, this, explicitInterface);
            }

+            if (Context.OnlyScaffold)
+            {
+                return;
+            }
+
+            BindComments();
+
            if (Context.ExtractLocation(Symbol))
            {
                WriteLocationsToTrap(trapFile.property_location, this, Locations);
--- a/csharp/extractor/Semmle.Extraction.CSharp/Entities/TypeMention.cs
+++ b/csharp/extractor/Semmle.Extraction.CSharp/Entities/TypeMention.cs
@@ -59,6 +59,11 @@ namespace Semmle.Extraction.CSharp.Entities

        protected override void Populate(TextWriter trapFile)
        {
+            if (Context.OnlyScaffold)
+            {
+                return;
+            }
+
            switch (syntax.Kind())
            {
                case SyntaxKind.ArrayType:
--- a/csharp/extractor/Semmle.Extraction.CSharp/Entities/Types/DynamicType.cs
+++ b/csharp/extractor/Semmle.Extraction.CSharp/Entities/Types/DynamicType.cs
@@ -16,10 +16,14 @@ namespace Semmle.Extraction.CSharp.Entities
        public override void Populate(TextWriter trapFile)
        {
            trapFile.types(this, Kinds.TypeKind.DYNAMIC, "dynamic");
-            WriteLocationToTrap(trapFile.type_location, this, Location);

            trapFile.has_modifiers(this, Modifier.Create(Context, "public"));
            trapFile.parent_namespace(this, Namespace.Create(Context, Context.Compilation.GlobalNamespace));
+            if (Context.OnlyScaffold)
+            {
+                return;
+            }
+            WriteLocationToTrap(trapFile.type_location, this, Location);
        }

        public override void WriteId(EscapingTextWriter trapFile)
--- a/csharp/extractor/Semmle.Extraction.CSharp/Entities/Types/NamedType.cs
+++ b/csharp/extractor/Semmle.Extraction.CSharp/Entities/Types/NamedType.cs
@@ -81,7 +81,7 @@ namespace Semmle.Extraction.CSharp.Entities
            }

            // Class location
-            if (!Symbol.IsGenericType || Symbol.IsReallyUnbound())
+            if ((!Symbol.IsGenericType || Symbol.IsReallyUnbound()) && !Context.OnlyScaffold)
            {
                WriteLocationsToTrap(trapFile.type_location, this, Locations);
            }
--- a/csharp/extractor/Semmle.Extraction.CSharp/Entities/Types/TupleType.cs
+++ b/csharp/extractor/Semmle.Extraction.CSharp/Entities/Types/TupleType.cs
@@ -51,6 +51,10 @@ namespace Semmle.Extraction.CSharp.Entities
                    trapFile.tuple_element(this, index++, element);
            }

+            if (Context.OnlyScaffold)
+            {
+                return;
+            }
            // Note: symbol.Locations seems to be very inconsistent
            // about what locations are available for a tuple type.
            // Sometimes it's the source code, and sometimes it's empty.
--- a/csharp/extractor/Semmle.Extraction.CSharp/Entities/Types/Type.cs
+++ b/csharp/extractor/Semmle.Extraction.CSharp/Entities/Types/Type.cs
@@ -222,7 +222,7 @@ namespace Semmle.Extraction.CSharp.Entities

        private IEnumerable<BaseTypeSyntax> GetBaseTypeDeclarations()
        {
-            if (!IsSourceDeclaration || !Symbol.FromSource())
+            if (!IsSourceDeclaration || !Symbol.FromSource() || Context.OnlyScaffold)
            {
                return Enumerable.Empty<BaseTypeSyntax>();
            }
--- a/csharp/extractor/Semmle.Extraction.CSharp/Entities/Types/TypeParameter.cs
+++ b/csharp/extractor/Semmle.Extraction.CSharp/Entities/Types/TypeParameter.cs
@@ -26,6 +26,11 @@ namespace Semmle.Extraction.CSharp.Entities
            var parentNs = Namespace.Create(Context, Symbol.TypeParameterKind == TypeParameterKind.Method ? Context.Compilation.GlobalNamespace : Symbol.ContainingNamespace);
            trapFile.parent_namespace(this, parentNs);

+            if (Context.OnlyScaffold)
+            {
+                return;
+            }
+
            if (Context.ExtractLocation(Symbol))
            {
                var locations = Context.GetLocations(Symbol);
--- a/csharp/extractor/Semmle.Extraction.CSharp/Entities/UserOperator.cs
+++ b/csharp/extractor/Semmle.Extraction.CSharp/Entities/UserOperator.cs
@@ -26,6 +26,14 @@ namespace Semmle.Extraction.CSharp.Entities
                returnType.TypeRef,
                (UserOperator)OriginalDefinition);

+            ContainingType.PopulateGenerics();
+            Overrides(trapFile);
+
+            if (Context.OnlyScaffold)
+            {
+                return;
+            }
+
            if (Context.ExtractLocation(Symbol))
            {
                WriteLocationsToTrap(trapFile.operator_location, this, Locations);
@@ -39,9 +47,6 @@ namespace Semmle.Extraction.CSharp.Entities
                foreach (var declaration in declSyntaxReferences.OfType<ConversionOperatorDeclarationSyntax>())
                    TypeMention.Create(Context, declaration.Type, this, returnType);
            }
-
-            ContainingType.PopulateGenerics();
-            Overrides(trapFile);
        }

        public override bool NeedsPopulation => Context.Defines(Symbol) || IsImplicitOperator(out _);
--- a/csharp/extractor/Semmle.Extraction.CSharp/Entities/UsingDirective.cs
+++ b/csharp/extractor/Semmle.Extraction.CSharp/Entities/UsingDirective.cs
@@ -20,6 +20,11 @@ namespace Semmle.Extraction.CSharp.Entities

        protected override void Populate(TextWriter trapFile)
        {
+            if (Context.OnlyScaffold)
+            {
+                return;
+            }
+
            // This is guaranteed to be non-null as we only deal with "using namespace" not "using X = Y"
            var name = node.Name!;

--- a/csharp/extractor/Semmle.Extraction.CSharp/Extractor/Analyser.cs
+++ b/csharp/extractor/Semmle.Extraction.CSharp/Extractor/Analyser.cs
@@ -41,16 +41,20 @@ namespace Semmle.Extraction.CSharp

        public IPathCache PathCache { get; }

+        public IOverlayInfo OverlayInfo { get; }
+
        protected Analyser(
            IProgressMonitor pm,
            ILogger logger,
            PathTransformer pathTransformer,
            IPathCache pathCache,
+            IOverlayInfo overlayInfo,
            bool addAssemblyTrapPrefix)
        {
            Logger = logger;
            PathTransformer = pathTransformer;
            PathCache = pathCache;
+            OverlayInfo = overlayInfo;
            this.addAssemblyTrapPrefix = addAssemblyTrapPrefix;
            this.progressMonitor = pm;

@@ -158,7 +162,7 @@ namespace Semmle.Extraction.CSharp

                    if (compilation.GetAssemblyOrModuleSymbol(r) is IAssemblySymbol assembly)
                    {
-                        var cx = new Context(ExtractionContext, compilation, trapWriter, new AssemblyScope(assembly, assemblyPath), addAssemblyTrapPrefix);
+                        var cx = new Context(ExtractionContext, compilation, trapWriter, new AssemblyScope(assembly, assemblyPath), OverlayInfo, addAssemblyTrapPrefix);

                        foreach (var module in assembly.Modules)
                        {
@@ -195,7 +199,7 @@ namespace Semmle.Extraction.CSharp
                var currentTaskId = IncrementTaskCount();
                ReportProgressTaskStarted(currentTaskId, sourcePath);

-                var cx = new Context(ExtractionContext, compilation, trapWriter, new SourceScope(tree), addAssemblyTrapPrefix);
+                var cx = new Context(ExtractionContext, compilation, trapWriter, new SourceScope(tree), OverlayInfo, addAssemblyTrapPrefix);
                // Ensure that the file itself is populated in case the source file is totally empty
                var root = tree.GetRoot();
                Entities.File.Create(cx, root.SyntaxTree.FilePath);
@@ -234,7 +238,7 @@ namespace Semmle.Extraction.CSharp
                var assembly = compilation.Assembly;
                var trapWriter = transformedAssemblyPath.CreateTrapWriter(Logger, options.TrapCompression, discardDuplicates: false);
                compilationTrapFile = trapWriter;  // Dispose later
-                var cx = new Context(ExtractionContext, compilation, trapWriter, new AssemblyScope(assembly, assemblyPath), addAssemblyTrapPrefix);
+                var cx = new Context(ExtractionContext, compilation, trapWriter, new AssemblyScope(assembly, assemblyPath), OverlayInfo, addAssemblyTrapPrefix);

                compilationEntity = Entities.Compilation.Create(cx);

--- a/csharp/extractor/Semmle.Extraction.CSharp/Extractor/BinaryLogAnalyser.cs
+++ b/csharp/extractor/Semmle.Extraction.CSharp/Extractor/BinaryLogAnalyser.cs
@@ -8,7 +8,7 @@ namespace Semmle.Extraction.CSharp
    public class BinaryLogAnalyser : Analyser
    {
        public BinaryLogAnalyser(IProgressMonitor pm, ILogger logger, PathTransformer pathTransformer, IPathCache pathCache, bool addAssemblyTrapPrefix)
-            : base(pm, logger, pathTransformer, pathCache, addAssemblyTrapPrefix)
+            : base(pm, logger, pathTransformer, pathCache, new TrivialOverlayInfo(), addAssemblyTrapPrefix)
        {
        }

--- a/csharp/extractor/Semmle.Extraction.CSharp/Extractor/Context.cs
+++ b/csharp/extractor/Semmle.Extraction.CSharp/Extractor/Context.cs
@@ -29,6 +29,12 @@ namespace Semmle.Extraction.CSharp
        /// </summary>
        public bool ShouldAddAssemblyTrapPrefix { get; }

+        /// <summary>
+        /// Holds if trap only should be created for types and member signatures (and not for expressions and statements).
+        /// This is the case for all unchanged files, when running in overlay mode.
+        /// </summary>
+        public bool OnlyScaffold { get; }
+
        public IList<object> TrapStackSuffix { get; } = new List<object>();

        private int GetNewId() => TrapWriter.IdCounter++;
@@ -523,13 +529,16 @@ namespace Semmle.Extraction.CSharp

        internal CommentProcessor CommentGenerator { get; } = new CommentProcessor();

-        public Context(ExtractionContext extractionContext, Compilation c, TrapWriter trapWriter, IExtractionScope scope, bool shouldAddAssemblyTrapPrefix = false)
+        public Context(ExtractionContext extractionContext, Compilation c, TrapWriter trapWriter, IExtractionScope scope, IOverlayInfo overlayInfo, bool shouldAddAssemblyTrapPrefix = false)
        {
            ExtractionContext = extractionContext;
            TrapWriter = trapWriter;
            ShouldAddAssemblyTrapPrefix = shouldAddAssemblyTrapPrefix;
            Compilation = c;
            this.scope = scope;
+            OnlyScaffold = overlayInfo.IsOverlayMode && (
+                IsAssemblyScope
+                || (scope is SourceScope ss && overlayInfo.OnlyMakeScaffold(ss.SourceTree.FilePath)));
        }

        public bool FromSource => scope is SourceScope;
@@ -552,7 +561,8 @@ namespace Semmle.Extraction.CSharp

        public bool ExtractLocation(ISymbol symbol) =>
            SymbolEqualityComparer.Default.Equals(symbol, symbol.OriginalDefinition) &&
-            scope.InScope(symbol);
+            scope.InScope(symbol) &&
+            !OnlyScaffold;

        /// <summary>
        /// Gets the locations of the symbol that are either
@@ -621,6 +631,10 @@ namespace Semmle.Extraction.CSharp
        /// <param name="l">Location of the entity.</param>
        public void BindComments(Entity entity, Microsoft.CodeAnalysis.Location? l)
        {
+            if (OnlyScaffold)
+            {
+                return;
+            }
            var duplicationGuardKey = GetCurrentTagStackKey();
            CommentGenerator.AddElement(entity.Label, duplicationGuardKey, l);
        }
--- a/csharp/extractor/Semmle.Extraction.CSharp/Extractor/OverlayInfo.cs
+++ b/csharp/extractor/Semmle.Extraction.CSharp/Extractor/OverlayInfo.cs
@@ -0,0 +1,124 @@
+using System.Collections.Generic;
+using System.IO;
+using System.Linq;
+using System.Text.Json;
+using Semmle.Util;
+using Semmle.Util.Logging;
+
+namespace Semmle.Extraction.CSharp
+{
+    public interface IOverlayInfo
+    {
+        /// <summary>
+        /// True, if the extractor is running in overlay mode.
+        /// </summary>
+        bool IsOverlayMode { get; }
+
+        /// <summary>
+        /// Returns true, if the given file is not in the set of changed files.
+        /// </summary>
+        /// <param name="filePath">A source file path</param>
+        bool OnlyMakeScaffold(string filePath);
+    }
+
+
+    /// <summary>
+    /// An instance of this class is used when overlay is not enabled.
+    /// </summary>
+    public class TrivialOverlayInfo : IOverlayInfo
+    {
+        public TrivialOverlayInfo() { }
+
+        public bool IsOverlayMode { get; } = false;
+
+        public bool OnlyMakeScaffold(string filePath) => false;
+    }
+
+    /// <summary>
+    /// An instance of this class is used for detecting
+    /// (1) Whether overlay is enabled.
+    /// (2) Fetch the changed files that should be fully extracted as a part
+    /// of the overlay extraction.
+    /// </summary>
+    public class OverlayInfo : IOverlayInfo
+    {
+        private readonly ILogger logger;
+        private readonly HashSet<string> changedFiles;
+        private readonly string srcDir;
+
+        public OverlayInfo(ILogger logger, string srcDir, string json)
+        {
+            this.logger = logger;
+            this.srcDir = srcDir;
+            changedFiles = ParseJson(json);
+        }
+
+        public bool IsOverlayMode { get; } = true;
+
+        public bool OnlyMakeScaffold(string filePath) => !changedFiles.Contains(filePath);
+
+        /// <summary>
+        /// Private type only used to parse overlay changes JSON files.
+        /// 
+        /// The content of such a file has the format
+        /// {
+        ///  "changes": [
+        ///    "app/controllers/about_controller.xyz",
+        ///    "app/models/about.xyz"
+        ///  ]
+        /// }
+        /// </summary>
+        private record ChangedFiles
+        {
+            public string[]? Changes { get; set; }
+        }
+
+        private HashSet<string> ParseJson(string json)
+        {
+            try
+            {
+                var options = new JsonSerializerOptions { PropertyNameCaseInsensitive = true };
+                var obj = JsonSerializer.Deserialize<ChangedFiles>(json, options);
+                return obj?.Changes is string[] changes
+                    ? changes.Select(change => Path.Join(srcDir, change)).ToHashSet()
+                    : [];
+            }
+            catch (JsonException)
+            {
+                logger.LogError("Overlay: Unable to parse the JSON content from the overlay changes file.");
+                return [];
+            }
+        }
+    }
+
+    public static class OverlayInfoFactory
+    {
+        /// <summary>
+        /// The returned object is used to decide, whether
+        /// (1) The extractor is running in overlay mode.
+        /// (2) Which files to only extract scaffolds for (unchanged files)
+        /// </summary>
+        /// <param name="logger">A logger</param>
+        /// <param name="srcDir">The (overlay) source directory</param>
+        /// <returns>An overlay information object.</returns>
+        public static IOverlayInfo Make(ILogger logger, string srcDir)
+        {
+            if (EnvironmentVariables.GetOverlayChangesFilePath() is string path)
+            {
+                logger.LogInfo($"Overlay: Reading overlay changes from file '{path}'.");
+                try
+                {
+                    var json = File.ReadAllText(path);
+                    return new OverlayInfo(logger, srcDir, json);
+                }
+                catch
+                {
+                    logger.LogError("Overlay: Unexpected error while reading the overlay changes file.");
+                }
+            }
+
+            logger.LogInfo("Overlay: Overlay mode not enabled.");
+            return new TrivialOverlayInfo();
+        }
+    }
+}
--- a/csharp/extractor/Semmle.Extraction.CSharp/Extractor/StandaloneAnalyser.cs
+++ b/csharp/extractor/Semmle.Extraction.CSharp/Extractor/StandaloneAnalyser.cs
@@ -8,8 +8,8 @@ namespace Semmle.Extraction.CSharp
 {
    public class StandaloneAnalyser : Analyser
    {
-        public StandaloneAnalyser(IProgressMonitor pm, ILogger logger, PathTransformer pathTransformer, IPathCache pathCache, bool addAssemblyTrapPrefix)
-            : base(pm, logger, pathTransformer, pathCache, addAssemblyTrapPrefix)
+        public StandaloneAnalyser(IProgressMonitor pm, ILogger logger, PathTransformer pathTransformer, IPathCache pathCache, IOverlayInfo overlayInfo, bool addAssemblyTrapPrefix)
+            : base(pm, logger, pathTransformer, pathCache, overlayInfo, addAssemblyTrapPrefix)
        {
        }

--- a/csharp/extractor/Semmle.Extraction.CSharp/Extractor/TracingAnalyser.cs
+++ b/csharp/extractor/Semmle.Extraction.CSharp/Extractor/TracingAnalyser.cs
@@ -14,7 +14,7 @@ namespace Semmle.Extraction.CSharp
        private bool init;

        public TracingAnalyser(IProgressMonitor pm, ILogger logger, PathTransformer pathTransformer, IPathCache pathCache, bool addAssemblyTrapPrefix)
-            : base(pm, logger, pathTransformer, pathCache, addAssemblyTrapPrefix)
+            : base(pm, logger, pathTransformer, pathCache, new TrivialOverlayInfo(), addAssemblyTrapPrefix)
        {
        }

--- a/csharp/extractor/Semmle.Extraction.CSharp/Populators/CommentPopulator.cs
+++ b/csharp/extractor/Semmle.Extraction.CSharp/Populators/CommentPopulator.cs
@@ -12,6 +12,10 @@ namespace Semmle.Extraction.CSharp.Populators
    {
        public static void ExtractCommentBlocks(Context cx, CommentProcessor gen)
        {
+            if (cx.OnlyScaffold)
+            {
+                return;
+            }
            cx.Try(null, null, () =>
            {
                gen.GenerateBindings((entity, duplicationGuardKey, block, binding) =>
@@ -34,6 +38,10 @@ namespace Semmle.Extraction.CSharp.Populators

        public static void ExtractComment(Context cx, SyntaxTrivia trivia)
        {
+            if (cx.OnlyScaffold)
+            {
+                return;
+            }
            switch (trivia.Kind())
            {
                case SyntaxKind.SingleLineDocumentationCommentTrivia:
--- a/csharp/extractor/Semmle.Extraction.Tests/OverlayInfo.cs
+++ b/csharp/extractor/Semmle.Extraction.Tests/OverlayInfo.cs
@@ -0,0 +1,31 @@
+using Xunit;
+using Semmle.Extraction.CSharp;
+using System.IO;
+
+namespace Semmle.Extraction.Tests
+{
+    public class OverlayTests
+    {
+        [Fact]
+        public void TestOverlay()
+        {
+            var logger = new LoggerStub();
+            var json =
+                """
+                {
+                    "changes": [
+                        "app/controllers/about_controller.xyz",
+                        "app/models/about.xyz"
+                    ]
+                }
+                """;
+
+            var overlay = new OverlayInfo(logger, "overlay/source/path", json);
+
+            Assert.True(overlay.IsOverlayMode);
+            Assert.False(overlay.OnlyMakeScaffold("overlay/source/path" + Path.DirectorySeparatorChar + "app/controllers/about_controller.xyz"));
+            Assert.False(overlay.OnlyMakeScaffold("overlay/source/path" + Path.DirectorySeparatorChar + "app/models/about.xyz"));
+            Assert.True(overlay.OnlyMakeScaffold("overlay/source/path" + Path.DirectorySeparatorChar + "app/models/unchanged.xyz"));
+        }
+    }
+}
--- a/csharp/extractor/Semmle.Util/EnvironmentVariables.cs
+++ b/csharp/extractor/Semmle.Util/EnvironmentVariables.cs
@@ -53,5 +53,28 @@ namespace Semmle.Util
        {
            return Environment.GetEnvironmentVariable(name)?.Split(" ", StringSplitOptions.RemoveEmptyEntries) ?? [];
        }
+
+        /// <summary>
+        /// Used to
+        /// (1) Detect whether the extractor should run in overlay mode.
+        /// (2) Returns the path to the file containing a list of changed files
+        /// in JSON format.
+        ///
+        /// The environment variable is only set in case the extraction is supposed to be
+        /// performed in overlay mode. Furthermore, this only applies to buildless extraction.
+        /// </summary>
+        public static string? GetOverlayChangesFilePath()
+        {
+            return Environment.GetEnvironmentVariable("CODEQL_EXTRACTOR_CSHARP_OVERLAY_CHANGES");
+        }
+
+        /// <summary>
+        /// If the environment variable is set, the extractor is being called to extract a base database.
+        /// Its value will be a path, and the extractor must create either a file or directory at that location.
+        /// </summary>
+        public static string? GetBaseMetaDataOutPath()
+        {
+            return Environment.GetEnvironmentVariable("CODEQL_EXTRACTOR_CSHARP_OVERLAY_BASE_METADATA_OUT");
+        }
    }
 }
--- a/csharp/ql/lib/change-notes/2025-10-30-overlay-compilation-and-extraction.md
+++ b/csharp/ql/lib/change-notes/2025-10-30-overlay-compilation-and-extraction.md
@@ -0,0 +1,5 @@
+---
+category: feature
+---
+
+* Initial support for incremental C# databases via `codeql database create --overlay-base`/`--overlay-changes`.
--- a/csharp/ql/lib/csharp.qll
+++ b/csharp/ql/lib/csharp.qll
@@ -36,6 +36,7 @@ import semmle.code.csharp.controlflow.ControlFlowGraph
 import semmle.code.csharp.dataflow.DataFlow
 import semmle.code.csharp.dataflow.TaintTracking
 import semmle.code.csharp.dataflow.SSA
+private import semmle.code.csharp.internal.Overlay

 /** Whether the source was extracted without a build command. */
 predicate extractionIsStandalone() { exists(SourceFile f | f.extractedStandalone()) }
--- a/csharp/ql/lib/qlpack.yml
+++ b/csharp/ql/lib/qlpack.yml
@@ -18,3 +18,4 @@ dataExtensions:
  - ext/*.model.yml
  - ext/generated/*.model.yml
 warnOnImplicitThis: true
+compileForOverlayEval: true
--- a/csharp/ql/lib/semmle/code/csharp/Conversion.qll
+++ b/csharp/ql/lib/semmle/code/csharp/Conversion.qll
@@ -719,6 +719,15 @@ private Type convTypeParameterBase(TypeParameter tp) {
  result = getATypeParameterFromConstraints+(tp)
 }

+pragma[noinline]
+private Class typeConstraintToBaseType(TypeParameterConstraints tpc) {
+  tpc.hasValueTypeConstraint() and result instanceof SystemValueTypeClass
+  or
+  result = tpc.getATypeConstraint()
+  or
+  tpc.hasRefTypeConstraint() and result instanceof ObjectType
+}
+
 /**
 * 10.1.5: Candidates for the effective base class of type parameter `tp`.
 *
@@ -731,13 +740,9 @@ private Class effectiveBaseClassCandidate(TypeParameter tp) {
  not hasPrimaryConstraints(tp) and result instanceof ObjectType
  or
  exists(TypeParameterConstraints tpc | tpc = tp.getConstraints() |
-    tpc.hasValueTypeConstraint() and result instanceof SystemValueTypeClass
-    or
-    result = tpc.getATypeConstraint()
+    result = typeConstraintToBaseType(tpc)
    or
    result = effectiveBaseClassCandidate(tpc.getATypeConstraint())
-    or
-    tpc.hasRefTypeConstraint() and result instanceof ObjectType
  )
 }

--- a/csharp/ql/lib/semmle/code/csharp/internal/Overlay.qll
+++ b/csharp/ql/lib/semmle/code/csharp/internal/Overlay.qll
@@ -0,0 +1,166 @@
+/**
+ * Defines entity discard predicates for C# overlay analysis.
+ */
+
+/**
+ * Holds always for the overlay variant and never for the base variant.
+ * This local predicate is used to define local predicates that behave
+ * differently for the base and overlay variant.
+ */
+overlay[local]
+predicate isOverlay() { databaseMetadata("isOverlay", "true") }
+
+overlay[local]
+private string getLocationFilePath(@location_default loc) {
+  exists(@file file | locations_default(loc, file, _, _, _, _) | files(file, result))
+}
+
+overlay[local]
+private class DiscardableEntityBase extends @locatable {
+  /** Gets the path to the file in which this element occurs. */
+  abstract string getFilePath();
+
+  /** Holds if this element exists in the base variant. */
+  predicate existsInBase() { not isOverlay() }
+
+  /** Holds if this element exists in the overlay variant. */
+  predicate existsInOverlay() { isOverlay() }
+
+  /** Gets a textual representation of this discardable element. */
+  string toString() { none() }
+}
+
+/**
+ * A class of elements that can be discarded from the base.
+ */
+overlay[local]
+private class DiscardableEntity extends DiscardableEntityBase {
+  /** Gets the path to the file in which this element occurs. */
+  override string getFilePath() {
+    exists(@location_default loc | result = getLocationFilePath(loc) |
+      expr_location(this, loc) or
+      stmt_location(this, loc) or
+      using_directive_location(this, loc) or
+      namespace_declaration_location(this, loc) or
+      preprocessor_directive_location(this, loc) or
+      type_location(this, loc) or
+      attribute_location(this, loc) or
+      type_parameter_constraints_location(this, loc) or
+      property_location(this, loc) or
+      indexer_location(this, loc) or
+      accessor_location(this, loc) or
+      event_location(this, loc) or
+      event_accessor_location(this, loc) or
+      operator_location(this, loc) or
+      method_location(this, loc) or
+      constructor_location(this, loc) or
+      destructor_location(this, loc) or
+      field_location(this, loc) or
+      localvar_location(this, loc) or
+      param_location(this, loc) or
+      type_mention_location(this, loc) or
+      commentline_location(this, loc) or
+      commentblock_location(this, loc) or
+      diagnostics(this, _, _, _, _, loc) or
+      extractor_messages(this, _, _, _, _, loc, _)
+    )
+  }
+}
+
+/**
+ * A class of C# database entities that use `*` IDs.
+ * The rest use named TRAP IDs.
+ */
+overlay[local]
+private class StarEntity =
+  @expr or @stmt or @diagnostic or @extractor_message or @using_directive or @type_mention or
+      @local_variable;
+
+overlay[discard_entity]
+private predicate discardStarEntity(@locatable e) {
+  e instanceof StarEntity and
+  // Entities with *-ids can exist either in base or overlay, but not both.
+  e =
+    any(DiscardableEntity de |
+      overlayChangedFiles(de.getFilePath()) and
+      de.existsInBase()
+    )
+}
+
+overlay[discard_entity]
+private predicate discardNamedEntity(@locatable e) {
+  not e instanceof StarEntity and
+  // Entities with named IDs can exist both in base, overlay, or both.
+  e =
+    any(DiscardableEntity de |
+      overlayChangedFiles(de.getFilePath()) and
+      not de.existsInOverlay()
+    )
+}
+
+overlay[local]
+private predicate discardableLocation(@location_default loc, string path) {
+  not isOverlay() and
+  path = getLocationFilePath(loc)
+}
+
+// Discard locations that are in changed files from the base variant.
+overlay[discard_entity]
+private predicate discardLocation(@location_default loc) {
+  exists(string path | discardableLocation(loc, path) | overlayChangedFiles(path))
+}
+
+/**
+ * A class of Xml locatables that can be discarded from the base.
+ */
+overlay[local]
+private class DiscardableXmlEntity extends DiscardableEntityBase instanceof @xmllocatable {
+  /** Gets the path to the file in which this element occurs. */
+  override string getFilePath() {
+    exists(@location_default loc | result = getLocationFilePath(loc) | xmllocations(this, loc))
+  }
+}
+
+overlay[local]
+private predicate overlayXmlExtracted(string file) {
+  exists(DiscardableXmlEntity dxe |
+    dxe.existsInOverlay() and
+    file = dxe.getFilePath() and
+    not files(dxe, _) and
+    not xmlNs(dxe, _, _, _)
+  )
+}
+
+overlay[discard_entity]
+private predicate discardXmlEntity(@xmllocatable xml) {
+  overlayChangedFiles(xml.(DiscardableXmlEntity).getFilePath())
+  or
+  // The XML extractor is not incremental and may extract more
+  // XML files than those included in overlayChangedFiles.
+  overlayXmlExtracted(xml.(DiscardableXmlEntity).getFilePath())
+}
+
+overlay[local]
+private class DiscardableAspEntity extends DiscardableEntityBase instanceof @asp_element {
+  /** Gets the path to the file in which this element occurs. */
+  override string getFilePath() {
+    exists(@location_default loc | result = getLocationFilePath(loc) | asp_elements(this, _, loc))
+  }
+}
+
+overlay[local]
+private predicate overlayAspExtracted(string file) {
+  exists(DiscardableAspEntity dae |
+    dae.existsInOverlay() and
+    file = dae.getFilePath()
+  )
+}
+
+overlay[discard_entity]
+private predicate discardAspEntity(@asp_element asp) {
+  overlayChangedFiles(asp.(DiscardableAspEntity).getFilePath())
+  or
+  // The ASP extractor is not incremental and may extract more
+  // ASP files than those included in overlayChangedFiles.
+  overlayAspExtracted(asp.(DiscardableAspEntity).getFilePath())
+}
--- a/csharp/ql/lib/semmlecode.csharp.dbscheme
+++ b/csharp/ql/lib/semmlecode.csharp.dbscheme
@@ -194,6 +194,24 @@ externalData(
 sourceLocationPrefix(
  string prefix: string ref);

+/*
+ * Overlay support
+ */
+
+/**
+ * The CLI will automatically emit the tuple `databaseMetadata("isOverlay", "true")`,
+ * along with an `overlayChangedFiles` tuple for each new/modified/deleted file,
+ * when building an overlay database, and these can be used by the discard predicates.
+ */
+databaseMetadata(
+  string metadataKey : string ref,
+  string value : string ref
+);
+
+overlayChangedFiles(
+  string path : string ref
+);
+
 /*
 * C# dbscheme
 */
@@ -222,6 +240,12 @@ sourceLocationPrefix(

@location = @location_default | @assembly;

+@locatable = @declaration_with_accessors | @callable_accessor | @declaration_or_directive
+           | @diagnostic | @extractor_message | @preprocessor_directive | @attribute | @type_mention | @type_parameter_constraints
+           | @declaration_with_accessors | @callable_accessor | @operator | @method
+           | @constructor | @destructor | @field | @local_variable | @parameter | @stmt | @expr
+           | @xmllocatable | @commentline | @commentblock | @asp_element
+
 locations_default(
  unique int id: @location_default,
  int file: @file ref,
--- a/csharp/ql/lib/upgrades/605f85053409cd72b4904df3f198ddc8324f3a83/old.dbscheme
+++ b/csharp/ql/lib/upgrades/605f85053409cd72b4904df3f198ddc8324f3a83/old.dbscheme
--- a/csharp/ql/lib/upgrades/605f85053409cd72b4904df3f198ddc8324f3a83/semmlecode.csharp.dbscheme
+++ b/csharp/ql/lib/upgrades/605f85053409cd72b4904df3f198ddc8324f3a83/semmlecode.csharp.dbscheme
--- a/csharp/ql/lib/upgrades/605f85053409cd72b4904df3f198ddc8324f3a83/upgrade.properties
+++ b/csharp/ql/lib/upgrades/605f85053409cd72b4904df3f198ddc8324f3a83/upgrade.properties
@@ -0,0 +1,2 @@
+description: Add @locatable type
+compatibility: full
--- a/csharp/ql/lib/upgrades/66044cfa5bbf2ecfabd06ead25e91db2bdd79764/old.dbscheme
+++ b/csharp/ql/lib/upgrades/66044cfa5bbf2ecfabd06ead25e91db2bdd79764/old.dbscheme
--- a/csharp/ql/lib/upgrades/66044cfa5bbf2ecfabd06ead25e91db2bdd79764/semmlecode.csharp.dbscheme
+++ b/csharp/ql/lib/upgrades/66044cfa5bbf2ecfabd06ead25e91db2bdd79764/semmlecode.csharp.dbscheme
--- a/csharp/ql/lib/upgrades/66044cfa5bbf2ecfabd06ead25e91db2bdd79764/upgrade.properties
+++ b/csharp/ql/lib/upgrades/66044cfa5bbf2ecfabd06ead25e91db2bdd79764/upgrade.properties
@@ -0,0 +1,2 @@
+description: Add databaseMetadata and overlayChangedFiles relations
+compatibility: full
--- a/csharp/ql/test/library-tests/csharp11/PrintAst.expected
+++ b/csharp/ql/test/library-tests/csharp11/PrintAst.expected
@@ -1234,9 +1234,9 @@ StaticInterfaceMembers.cs:
 #   49|       1: [PropertyCall] access to property Real
 #   49|         -1: [ParameterAccess] access to parameter n
 #   51|   14: [Method] Inc
-#   51|     -1: [TypeMention] Complex
 #   51|     -1: [TypeMention] INumber<Complex>
 #   51|       1: [TypeMention] Complex
+#   51|     -1: [TypeMention] Complex
 #-----|     2: (Parameters)
 #   51|       0: [Parameter] other
 #   51|         -1: [TypeMention] Complex
@@ -1254,9 +1254,9 @@ StaticInterfaceMembers.cs:
 #   52|           1: [PropertyCall] access to property Imaginary
 #   52|             -1: [ParameterAccess] access to parameter other
 #   54|   15: [Method] Dec
-#   54|     -1: [TypeMention] Complex
 #   54|     -1: [TypeMention] INumber<Complex>
 #   54|       1: [TypeMention] Complex
+#   54|     -1: [TypeMention] Complex
 #-----|     2: (Parameters)
 #   54|       0: [Parameter] other
 #   54|         -1: [TypeMention] Complex
--- a/csharp/ql/test/library-tests/definitions/PrintAst.expected
+++ b/csharp/ql/test/library-tests/definitions/PrintAst.expected
@@ -272,8 +272,8 @@ definitions.cs:
 #  125|           0: [MethodCall] call to method M
 #  125|             -1: [BaseAccess] base access
 #  128|     6: [Method] M2`1
-#  128|       -1: [TypeMention] Void
 #  128|       -1: [TypeMention] I1
+#  128|       -1: [TypeMention] Void
 #-----|       1: (Type parameters)
 #  128|         0: [TypeParameter] T
 #  128|       4: [BlockStmt] {...}
@@ -356,8 +356,8 @@ definitions.cs:
 #  153|           0: [Parameter] value
 #  153|         4: [BlockStmt] {...}
 #  154|     6: [Method] M
-#  154|       -1: [TypeMention] A
 #  154|       -1: [TypeMention] I4
+#  154|       -1: [TypeMention] A
 #  154|       4: [ThrowExpr] throw ...
 #  154|         0: [ObjectCreation] object creation of type Exception
 #  154|           0: [TypeMention] Exception
--- a/csharp/ql/test/library-tests/overlay/base/A.cs
+++ b/csharp/ql/test/library-tests/overlay/base/A.cs
@@ -0,0 +1,66 @@
+using System;
+
+namespace ConsoleApp1
+{
+    public class A
+    {
+        private string name;
+        public A(string x)
+        {
+            name = x;
+        }
+
+        // Destructor
+        ~A()
+        {
+            Console.WriteLine("Destructor called!");
+        }
+
+        public string Prop { get; set; } = "Hello";
+
+        public object this[int i]
+        {
+            get { return new object(); }
+            set { }
+        }
+
+        /*
+         * An example event
+         */
+        public event EventHandler Clicked
+        {
+            add
+            {
+                Console.WriteLine("Handler added");
+            }
+            remove
+            {
+                Console.WriteLine("Handler removed");
+            }
+        }
+
+        public static A operator +(A a, A b)
+        {
+            return a;
+        }
+
+        [MyObsolete]
+        public void ObsoleteMethod() { }
+
+        public int OldMethod(int x)
+        {
+            var y = x + 1;
+            return y;
+        }
+
+        public override string ToString()
+        {
+            var x = $"A: {name}";
+            return x;
+        }
+    }
+
+    public class MyObsoleteAttribute : Attribute { }
+
+    public class B { }
+}
--- a/csharp/ql/test/library-tests/overlay/base/Program.cs
+++ b/csharp/ql/test/library-tests/overlay/base/Program.cs
@@ -0,0 +1,65 @@
+using System;
+
+namespace ConsoleApp1
+{
+    internal class Program
+    {
+        public static void Main(string[] args)
+        {
+            if (args.Length == 0)
+            {
+                Console.WriteLine("Print usage instructions here.");
+                return;
+            }
+            var x = args[0];
+            var a = new A(x);
+            Console.WriteLine(a.ToString());
+        }
+
+        private string programName;
+
+        public Program(string x)
+        {
+            programName = x;
+        }
+
+        // Program destructor
+        ~Program()
+        {
+            Console.WriteLine("Program destructor called!");
+        }
+
+        public string ProgramProp { get; set; } = "Hello World!";
+
+        public string this[int i]
+        {
+            get { return string.Empty; }
+            set { }
+        }
+
+        /*
+         * A program event.
+         */
+        public event EventHandler ProgramClicked
+        {
+            add
+            {
+                Console.WriteLine("Program handler added");
+            }
+            remove
+            {
+                Console.WriteLine("Program handler removed");
+            }
+        }
+
+        public static Program operator -(Program a, Program b)
+        {
+            return b;
+        }
+
+        [Program]
+        public void AnnotatedMethod() { }
+    }
+
+    public class ProgramAttribute : Attribute { }
+}
--- a/csharp/ql/test/library-tests/overlay/base/options
+++ b/csharp/ql/test/library-tests/overlay/base/options
@@ -0,0 +1 @@
+semmle-extractor-options: --standalone
--- a/csharp/ql/test/library-tests/overlay/base/test.expected
+++ b/csharp/ql/test/library-tests/overlay/base/test.expected
@@ -0,0 +1,276 @@
+expressions
+| A.cs:8:16:8:16 | call to constructor Object |
+| A.cs:10:13:10:16 | access to field name |
+| A.cs:10:13:10:16 | this access |
+| A.cs:10:13:10:20 | ... = ... |
+| A.cs:10:20:10:20 | access to parameter x |
+| A.cs:16:13:16:19 | access to type Console |
+| A.cs:16:13:16:51 | call to method WriteLine |
+| A.cs:16:31:16:50 | "Destructor called!" |
+| A.cs:19:23:19:26 | access to property Prop |
+| A.cs:19:23:19:26 | this access |
+| A.cs:19:42:19:50 | ... = ... |
+| A.cs:19:44:19:50 | "Hello" |
+| A.cs:23:26:23:37 | object creation of type Object |
+| A.cs:34:17:34:23 | access to type Console |
+| A.cs:34:17:34:50 | call to method WriteLine |
+| A.cs:34:35:34:49 | "Handler added" |
+| A.cs:38:17:38:23 | access to type Console |
+| A.cs:38:17:38:52 | call to method WriteLine |
+| A.cs:38:35:38:51 | "Handler removed" |
+| A.cs:44:20:44:20 | access to parameter a |
+| A.cs:52:17:52:17 | access to local variable y |
+| A.cs:52:17:52:25 | Int32 y = ... |
+| A.cs:52:21:52:21 | access to parameter x |
+| A.cs:52:21:52:25 | ... + ... |
+| A.cs:52:25:52:25 | 1 |
+| A.cs:53:20:53:20 | access to local variable y |
+| A.cs:58:17:58:17 | access to local variable x |
+| A.cs:58:17:58:32 | String x = ... |
+| A.cs:58:21:58:32 | $"..." |
+| A.cs:58:23:58:25 | "A: " |
+| A.cs:58:26:58:31 | {...} |
+| A.cs:58:27:58:30 | access to field name |
+| A.cs:58:27:58:30 | this access |
+| A.cs:59:20:59:20 | access to local variable x |
+| A.cs:63:18:63:36 | call to constructor Attribute |
+| A.cs:65:18:65:18 | call to constructor Object |
+| Program.cs:9:17:9:20 | access to parameter args |
+| Program.cs:9:17:9:27 | access to property Length |
+| Program.cs:9:17:9:32 | ... == ... |
+| Program.cs:9:32:9:32 | 0 |
+| Program.cs:11:17:11:23 | access to type Console |
+| Program.cs:11:17:11:67 | call to method WriteLine |
+| Program.cs:11:35:11:66 | "Print usage instructions here." |
+| Program.cs:14:17:14:17 | access to local variable x |
+| Program.cs:14:17:14:27 | String x = ... |
+| Program.cs:14:21:14:24 | access to parameter args |
+| Program.cs:14:21:14:27 | access to array element |
+| Program.cs:14:26:14:26 | 0 |
+| Program.cs:15:17:15:17 | access to local variable a |
+| Program.cs:15:17:15:28 | A a = ... |
+| Program.cs:15:21:15:28 | object creation of type A |
+| Program.cs:15:27:15:27 | access to local variable x |
+| Program.cs:16:13:16:19 | access to type Console |
+| Program.cs:16:13:16:43 | call to method WriteLine |
+| Program.cs:16:31:16:31 | access to local variable a |
+| Program.cs:16:31:16:42 | call to method ToString |
+| Program.cs:21:16:21:22 | call to constructor Object |
+| Program.cs:23:13:23:23 | access to field programName |
+| Program.cs:23:13:23:23 | this access |
+| Program.cs:23:13:23:27 | ... = ... |
+| Program.cs:23:27:23:27 | access to parameter x |
+| Program.cs:29:13:29:19 | access to type Console |
+| Program.cs:29:13:29:59 | call to method WriteLine |
+| Program.cs:29:31:29:58 | "Program destructor called!" |
+| Program.cs:32:23:32:33 | access to property ProgramProp |
+| Program.cs:32:23:32:33 | this access |
+| Program.cs:32:49:32:64 | ... = ... |
+| Program.cs:32:51:32:64 | "Hello World!" |
+| Program.cs:36:26:36:31 | access to type String |
+| Program.cs:36:26:36:37 | access to field Empty |
+| Program.cs:47:17:47:23 | access to type Console |
+| Program.cs:47:17:47:58 | call to method WriteLine |
+| Program.cs:47:35:47:57 | "Program handler added" |
+| Program.cs:51:17:51:23 | access to type Console |
+| Program.cs:51:17:51:60 | call to method WriteLine |
+| Program.cs:51:35:51:59 | "Program handler removed" |
+| Program.cs:57:20:57:20 | access to parameter b |
+| Program.cs:64:18:64:33 | call to constructor Attribute |
+statements
+| A.cs:9:9:11:9 | {...} |
+| A.cs:10:13:10:21 | ...; |
+| A.cs:15:9:17:9 | {...} |
+| A.cs:16:13:16:52 | ...; |
+| A.cs:23:17:23:40 | {...} |
+| A.cs:23:19:23:38 | return ...; |
+| A.cs:24:17:24:19 | {...} |
+| A.cs:33:13:35:13 | {...} |
+| A.cs:34:17:34:51 | ...; |
+| A.cs:37:13:39:13 | {...} |
+| A.cs:38:17:38:53 | ...; |
+| A.cs:43:9:45:9 | {...} |
+| A.cs:44:13:44:21 | return ...; |
+| A.cs:48:38:48:40 | {...} |
+| A.cs:51:9:54:9 | {...} |
+| A.cs:52:13:52:26 | ... ...; |
+| A.cs:53:13:53:21 | return ...; |
+| A.cs:57:9:60:9 | {...} |
+| A.cs:58:13:58:33 | ... ...; |
+| A.cs:59:13:59:21 | return ...; |
+| A.cs:63:18:63:36 | {...} |
+| A.cs:65:18:65:18 | {...} |
+| Program.cs:8:9:17:9 | {...} |
+| Program.cs:9:13:13:13 | if (...) ... |
+| Program.cs:10:13:13:13 | {...} |
+| Program.cs:11:17:11:68 | ...; |
+| Program.cs:12:17:12:23 | return ...; |
+| Program.cs:14:13:14:28 | ... ...; |
+| Program.cs:15:13:15:29 | ... ...; |
+| Program.cs:16:13:16:44 | ...; |
+| Program.cs:22:9:24:9 | {...} |
+| Program.cs:23:13:23:28 | ...; |
+| Program.cs:28:9:30:9 | {...} |
+| Program.cs:29:13:29:60 | ...; |
+| Program.cs:36:17:36:40 | {...} |
+| Program.cs:36:19:36:38 | return ...; |
+| Program.cs:37:17:37:19 | {...} |
+| Program.cs:46:13:48:13 | {...} |
+| Program.cs:47:17:47:59 | ...; |
+| Program.cs:50:13:52:13 | {...} |
+| Program.cs:51:17:51:61 | ...; |
+| Program.cs:56:9:58:9 | {...} |
+| Program.cs:57:13:57:21 | return ...; |
+| Program.cs:61:39:61:41 | {...} |
+| Program.cs:64:18:64:33 | {...} |
+methods
+| A.cs:48:21:48:34 | ObsoleteMethod |
+| A.cs:50:20:50:28 | OldMethod |
+| A.cs:56:32:56:39 | ToString |
+| Program.cs:7:28:7:31 | Main |
+| Program.cs:61:21:61:35 | AnnotatedMethod |
+types
+| A.cs:5:18:5:18 | A |
+| A.cs:63:18:63:36 | MyObsoleteAttribute |
+| A.cs:65:18:65:18 | B |
+| Program.cs:5:20:5:26 | Program |
+| Program.cs:64:18:64:33 | ProgramAttribute |
+parameters
+| A.cs:8:25:8:25 | x |
+| A.cs:19:35:19:37 | value |
+| A.cs:21:32:21:32 | i |
+| A.cs:21:32:21:32 | i |
+| A.cs:21:32:21:32 | i |
+| A.cs:24:13:24:15 | value |
+| A.cs:32:13:32:15 | value |
+| A.cs:36:13:36:18 | value |
+| A.cs:42:38:42:38 | a |
+| A.cs:42:43:42:43 | b |
+| A.cs:50:34:50:34 | x |
+| Program.cs:7:42:7:45 | args |
+| Program.cs:21:31:21:31 | x |
+| Program.cs:32:42:32:44 | value |
+| Program.cs:34:32:34:32 | i |
+| Program.cs:34:32:34:32 | i |
+| Program.cs:34:32:34:32 | i |
+| Program.cs:37:13:37:15 | value |
+| Program.cs:45:13:45:15 | value |
+| Program.cs:49:13:49:18 | value |
+| Program.cs:55:50:55:50 | a |
+| Program.cs:55:61:55:61 | b |
+operators
+| A.cs:42:34:42:34 | + |
+| Program.cs:55:40:55:40 | - |
+constructors
+| A.cs:8:16:8:16 | A |
+| Program.cs:21:16:21:22 | Program |
+destructors
+| A.cs:14:10:14:10 | ~A |
+| Program.cs:27:10:27:16 | ~Program |
+fields
+| A.cs:7:24:7:27 | name |
+| Program.cs:19:24:19:34 | programName |
+properties
+| A.cs:19:23:19:26 | Prop |
+| Program.cs:32:23:32:33 | ProgramProp |
+indexers
+| A.cs:21:23:21:26 | Item |
+| Program.cs:34:23:34:26 | Item |
+accessors
+| A.cs:19:30:19:32 | get_Prop |
+| A.cs:19:35:19:37 | set_Prop |
+| A.cs:23:13:23:15 | get_Item |
+| A.cs:24:13:24:15 | set_Item |
+| A.cs:32:13:32:15 | add_Clicked |
+| A.cs:36:13:36:18 | remove_Clicked |
+| Program.cs:32:37:32:39 | get_ProgramProp |
+| Program.cs:32:42:32:44 | set_ProgramProp |
+| Program.cs:36:13:36:15 | get_Item |
+| Program.cs:37:13:37:15 | set_Item |
+| Program.cs:45:13:45:15 | add_ProgramClicked |
+| Program.cs:49:13:49:18 | remove_ProgramClicked |
+attributes
+| A.cs:47:10:47:19 | [MyObsolete(...)] |
+| Program.cs:60:10:60:16 | [Program(...)] |
+events
+| A.cs:30:35:30:41 | Clicked |
+| Program.cs:43:35:43:48 | ProgramClicked |
+eventAccessors
+| A.cs:32:13:32:15 | add_Clicked |
+| A.cs:36:13:36:18 | remove_Clicked |
+| Program.cs:45:13:45:15 | add_ProgramClicked |
+| Program.cs:49:13:49:18 | remove_ProgramClicked |
+usingDirectives
+| A.cs:1:1:1:13 | using ...; |
+| Program.cs:1:1:1:13 | using ...; |
+commentLines
+| A.cs:13:9:13:21 | // ... |
+| A.cs:27:9:27:10 | /* ... */ |
+| A.cs:28:1:28:27 | /* ... */ |
+| A.cs:29:1:29:11 | /* ... */ |
+| Program.cs:26:9:26:29 | // ... |
+| Program.cs:40:9:40:10 | /* ... */ |
+| Program.cs:41:1:41:27 | /* ... */ |
+| Program.cs:42:1:42:11 | /* ... */ |
+commentBlocks
+| A.cs:13:9:13:21 | // ... |
+| A.cs:27:9:29:11 | /* ... */ |
+| Program.cs:26:9:26:29 | // ... |
+| Program.cs:40:9:42:11 | /* ... */ |
+typeMentions
+| A.cs:7:17:7:22 | String |
+| A.cs:8:18:8:23 | String |
+| A.cs:16:13:16:19 | Console |
+| A.cs:19:16:19:21 | String |
+| A.cs:21:16:21:21 | Object |
+| A.cs:21:28:21:30 | Int32 |
+| A.cs:23:30:23:35 | Object |
+| A.cs:34:17:34:23 | Console |
+| A.cs:38:17:38:23 | Console |
+| A.cs:42:23:42:23 | A |
+| A.cs:42:36:42:36 | A |
+| A.cs:42:41:42:41 | A |
+| A.cs:47:10:47:19 | MyObsoleteAttribute |
+| A.cs:48:16:48:19 | Void |
+| A.cs:50:16:50:18 | Int32 |
+| A.cs:50:30:50:32 | Int32 |
+| A.cs:52:13:52:15 | Int32 |
+| A.cs:56:25:56:30 | String |
+| A.cs:58:13:58:15 | String |
+| A.cs:63:40:63:48 | Attribute |
+| Program.cs:7:23:7:26 | Void |
+| Program.cs:7:33:7:38 | String |
+| Program.cs:7:33:7:40 | String[] |
+| Program.cs:11:17:11:23 | Console |
+| Program.cs:14:13:14:15 | String |
+| Program.cs:15:13:15:15 | A |
+| Program.cs:15:25:15:25 | A |
+| Program.cs:16:13:16:19 | Console |
+| Program.cs:19:17:19:22 | String |
+| Program.cs:21:24:21:29 | String |
+| Program.cs:29:13:29:19 | Console |
+| Program.cs:32:16:32:21 | String |
+| Program.cs:34:16:34:21 | String |
+| Program.cs:34:28:34:30 | Int32 |
+| Program.cs:36:26:36:31 | String |
+| Program.cs:47:17:47:23 | Console |
+| Program.cs:51:17:51:23 | Console |
+| Program.cs:55:23:55:29 | Program |
+| Program.cs:55:42:55:48 | Program |
+| Program.cs:55:53:55:59 | Program |
+| Program.cs:60:10:60:16 | ProgramAttribute |
+| Program.cs:61:16:61:19 | Void |
+| Program.cs:64:37:64:45 | Attribute |
+xmlLocatables
+| web.changed.config:2:1:12:17 | configuration |
+| web.changed.config:3:3:4:16 | system.web |
+| web.changed.config:5:3:11:22 | system.webServer |
+| web.changed.config:6:5:10:20 | httpProtocol |
+| web.changed.config:7:7:9:23 | customHeaders |
+| web.changed.config:8:9:8:42 | add |
+| web.changed.config:8:9:8:42 | name=MyOption |
+| web.changed.config:8:9:8:42 | value=1 |
+| web.unchanged.config:2:1:6:17 | configuration |
+| web.unchanged.config:3:3:5:16 | system.web |
+| web.unchanged.config:4:5:4:37 | httpCookies |
+| web.unchanged.config:4:5:4:37 | requireSSL=true |
--- a/csharp/ql/test/library-tests/overlay/base/test.qlref
+++ b/csharp/ql/test/library-tests/overlay/base/test.qlref
@@ -0,0 +1 @@
+query: ../test.ql
--- a/csharp/ql/test/library-tests/overlay/base/web.changed.config
+++ b/csharp/ql/test/library-tests/overlay/base/web.changed.config
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="utf-8" ?>
+<configuration>
+  <system.web>
+  </system.web>
+  <system.webServer>
+    <httpProtocol>
+      <customHeaders>
+        <add name="MyOption" value="1" />
+      </customHeaders>
+    </httpProtocol>
+  </system.webServer>
+</configuration>
--- a/csharp/ql/test/library-tests/overlay/base/web.unchanged.config
+++ b/csharp/ql/test/library-tests/overlay/base/web.unchanged.config
@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="utf-8" ?>
+<configuration>
+  <system.web>
+    <httpCookies requireSSL="true"/>
+  </system.web>
+</configuration>
--- a/csharp/ql/test/library-tests/overlay/codeql-test.yml
+++ b/csharp/ql/test/library-tests/overlay/codeql-test.yml
@@ -0,0 +1,3 @@
+overlay:
+  base: "base/"
+  overlay: "overlay/"
--- a/csharp/ql/test/library-tests/overlay/options
+++ b/csharp/ql/test/library-tests/overlay/options
@@ -0,0 +1 @@
+semmle-extractor-options: --standalone
--- a/csharp/ql/test/library-tests/overlay/overlay/A.cs
+++ b/csharp/ql/test/library-tests/overlay/overlay/A.cs
@@ -0,0 +1,70 @@
+using System;
+
+namespace ConsoleApp1
+{
+    public class C { }
+
+    public class A
+    {
+        private string name;
+        public A(string x)
+        {
+            name = x;
+        }
+
+        // Destructor
+        ~A()
+        {
+            Console.WriteLine("Destructor called!");
+        }
+
+        public string Prop { get; set; } = "Hello";
+
+        public object this[int i]
+        {
+            get { return new object(); }
+            set { }
+        }
+
+        /*
+         * An example event
+         */
+        public event EventHandler Clicked
+        {
+            add
+            {
+                Console.WriteLine("Handler added");
+            }
+            remove
+            {
+                Console.WriteLine("Handler removed");
+            }
+        }
+
+        public static A operator +(A a, A b)
+        {
+            return a;
+        }
+
+        [MyObsolete]
+        public void ObsoleteMethod() { }
+
+
+        public override string ToString()
+        {
+            string y;
+            y = $"Name: {name}";
+            return y;
+        }
+
+        public void NewMethod()
+        {
+            if (name.EndsWith("test"))
+            {
+                name = name.ToUpper();
+            }
+        }
+    }
+
+    public class MyObsoleteAttribute : Attribute { }
+}
--- a/csharp/ql/test/library-tests/overlay/overlay/Program.cs
+++ b/csharp/ql/test/library-tests/overlay/overlay/Program.cs
@@ -0,0 +1,65 @@
+using System;
+
+namespace ConsoleApp1
+{
+    internal class Program
+    {
+        public static void Main(string[] args)
+        {
+            if (args.Length == 0)
+            {
+                Console.WriteLine("Print usage instructions here.");
+                return;
+            }
+            var x = args[0];
+            var a = new A(x);
+            Console.WriteLine(a.ToString());
+        }
+
+        private string programName;
+
+        public Program(string x)
+        {
+            programName = x;
+        }
+
+        // Program destructor
+        ~Program()
+        {
+            Console.WriteLine("Program destructor called!");
+        }
+
+        public string ProgramProp { get; set; } = "Hello World!";
+
+        public string this[int i]
+        {
+            get { return string.Empty; }
+            set { }
+        }
+
+        /*
+         * A program event.
+         */
+        public event EventHandler ProgramClicked
+        {
+            add
+            {
+                Console.WriteLine("Program handler added");
+            }
+            remove
+            {
+                Console.WriteLine("Program handler removed");
+            }
+        }
+
+        public static Program operator -(Program a, Program b)
+        {
+            return b;
+        }
+
+        [Program]
+        public void AnnotatedMethod() { }
+    }
+
+    public class ProgramAttribute : Attribute { }
+}
--- a/csharp/ql/test/library-tests/overlay/overlay/options
+++ b/csharp/ql/test/library-tests/overlay/overlay/options
@@ -0,0 +1 @@
+semmle-extractor-options: --standalone
--- a/csharp/ql/test/library-tests/overlay/overlay/test.expected
+++ b/csharp/ql/test/library-tests/overlay/overlay/test.expected
@@ -0,0 +1,274 @@
+expressions
+| A.cs:5:18:5:18 | call to constructor Object |
+| A.cs:10:16:10:16 | call to constructor Object |
+| A.cs:12:13:12:16 | access to field name |
+| A.cs:12:13:12:16 | this access |
+| A.cs:12:13:12:20 | ... = ... |
+| A.cs:12:20:12:20 | access to parameter x |
+| A.cs:18:13:18:19 | access to type Console |
+| A.cs:18:13:18:51 | call to method WriteLine |
+| A.cs:18:31:18:50 | "Destructor called!" |
+| A.cs:21:23:21:26 | access to property Prop |
+| A.cs:21:23:21:26 | this access |
+| A.cs:21:42:21:50 | ... = ... |
+| A.cs:21:44:21:50 | "Hello" |
+| A.cs:25:26:25:37 | object creation of type Object |
+| A.cs:36:17:36:23 | access to type Console |
+| A.cs:36:17:36:50 | call to method WriteLine |
+| A.cs:36:35:36:49 | "Handler added" |
+| A.cs:40:17:40:23 | access to type Console |
+| A.cs:40:17:40:52 | call to method WriteLine |
+| A.cs:40:35:40:51 | "Handler removed" |
+| A.cs:46:20:46:20 | access to parameter a |
+| A.cs:55:20:55:20 | String y |
+| A.cs:56:13:56:13 | access to local variable y |
+| A.cs:56:13:56:31 | ... = ... |
+| A.cs:56:17:56:31 | $"..." |
+| A.cs:56:19:56:24 | "Name: " |
+| A.cs:56:25:56:30 | {...} |
+| A.cs:56:26:56:29 | access to field name |
+| A.cs:56:26:56:29 | this access |
+| A.cs:57:20:57:20 | access to local variable y |
+| A.cs:62:17:62:20 | access to field name |
+| A.cs:62:17:62:20 | this access |
+| A.cs:62:17:62:37 | call to method EndsWith |
+| A.cs:62:31:62:36 | "test" |
+| A.cs:64:17:64:20 | access to field name |
+| A.cs:64:17:64:20 | this access |
+| A.cs:64:17:64:37 | ... = ... |
+| A.cs:64:24:64:27 | access to field name |
+| A.cs:64:24:64:27 | this access |
+| A.cs:64:24:64:37 | call to method ToUpper |
+| A.cs:69:18:69:36 | call to constructor Attribute |
+| Program.cs:9:17:9:20 | access to parameter args |
+| Program.cs:9:17:9:27 | access to property Length |
+| Program.cs:9:17:9:32 | ... == ... |
+| Program.cs:9:32:9:32 | 0 |
+| Program.cs:11:17:11:23 | access to type Console |
+| Program.cs:11:17:11:67 | call to method WriteLine |
+| Program.cs:11:35:11:66 | "Print usage instructions here." |
+| Program.cs:14:17:14:17 | access to local variable x |
+| Program.cs:14:17:14:27 | String x = ... |
+| Program.cs:14:21:14:24 | access to parameter args |
+| Program.cs:14:21:14:27 | access to array element |
+| Program.cs:14:26:14:26 | 0 |
+| Program.cs:15:17:15:17 | access to local variable a |
+| Program.cs:15:17:15:28 | A a = ... |
+| Program.cs:15:21:15:28 | object creation of type A |
+| Program.cs:15:27:15:27 | access to local variable x |
+| Program.cs:16:13:16:19 | access to type Console |
+| Program.cs:16:13:16:43 | call to method WriteLine |
+| Program.cs:16:31:16:31 | access to local variable a |
+| Program.cs:16:31:16:42 | call to method ToString |
+| Program.cs:21:16:21:22 | call to constructor Object |
+| Program.cs:23:13:23:23 | access to field programName |
+| Program.cs:23:13:23:23 | this access |
+| Program.cs:23:13:23:27 | ... = ... |
+| Program.cs:23:27:23:27 | access to parameter x |
+| Program.cs:29:13:29:19 | access to type Console |
+| Program.cs:29:13:29:59 | call to method WriteLine |
+| Program.cs:29:31:29:58 | "Program destructor called!" |
+| Program.cs:32:23:32:33 | access to property ProgramProp |
+| Program.cs:32:23:32:33 | this access |
+| Program.cs:32:49:32:64 | ... = ... |
+| Program.cs:32:51:32:64 | "Hello World!" |
+| Program.cs:36:26:36:31 | access to type String |
+| Program.cs:36:26:36:37 | access to field Empty |
+| Program.cs:47:17:47:23 | access to type Console |
+| Program.cs:47:17:47:58 | call to method WriteLine |
+| Program.cs:47:35:47:57 | "Program handler added" |
+| Program.cs:51:17:51:23 | access to type Console |
+| Program.cs:51:17:51:60 | call to method WriteLine |
+| Program.cs:51:35:51:59 | "Program handler removed" |
+| Program.cs:57:20:57:20 | access to parameter b |
+| Program.cs:64:18:64:33 | call to constructor Attribute |
+statements
+| A.cs:5:18:5:18 | {...} |
+| A.cs:11:9:13:9 | {...} |
+| A.cs:12:13:12:21 | ...; |
+| A.cs:17:9:19:9 | {...} |
+| A.cs:18:13:18:52 | ...; |
+| A.cs:25:17:25:40 | {...} |
+| A.cs:25:19:25:38 | return ...; |
+| A.cs:26:17:26:19 | {...} |
+| A.cs:35:13:37:13 | {...} |
+| A.cs:36:17:36:51 | ...; |
+| A.cs:39:13:41:13 | {...} |
+| A.cs:40:17:40:53 | ...; |
+| A.cs:45:9:47:9 | {...} |
+| A.cs:46:13:46:21 | return ...; |
+| A.cs:50:38:50:40 | {...} |
+| A.cs:54:9:58:9 | {...} |
+| A.cs:55:13:55:21 | ... ...; |
+| A.cs:56:13:56:32 | ...; |
+| A.cs:57:13:57:21 | return ...; |
+| A.cs:61:9:66:9 | {...} |
+| A.cs:62:13:65:13 | if (...) ... |
+| A.cs:63:13:65:13 | {...} |
+| A.cs:64:17:64:38 | ...; |
+| A.cs:69:18:69:36 | {...} |
+| Program.cs:8:9:17:9 | {...} |
+| Program.cs:9:13:13:13 | if (...) ... |
+| Program.cs:10:13:13:13 | {...} |
+| Program.cs:11:17:11:68 | ...; |
+| Program.cs:12:17:12:23 | return ...; |
+| Program.cs:14:13:14:28 | ... ...; |
+| Program.cs:15:13:15:29 | ... ...; |
+| Program.cs:16:13:16:44 | ...; |
+| Program.cs:22:9:24:9 | {...} |
+| Program.cs:23:13:23:28 | ...; |
+| Program.cs:28:9:30:9 | {...} |
+| Program.cs:29:13:29:60 | ...; |
+| Program.cs:36:17:36:40 | {...} |
+| Program.cs:36:19:36:38 | return ...; |
+| Program.cs:37:17:37:19 | {...} |
+| Program.cs:46:13:48:13 | {...} |
+| Program.cs:47:17:47:59 | ...; |
+| Program.cs:50:13:52:13 | {...} |
+| Program.cs:51:17:51:61 | ...; |
+| Program.cs:56:9:58:9 | {...} |
+| Program.cs:57:13:57:21 | return ...; |
+| Program.cs:61:39:61:41 | {...} |
+| Program.cs:64:18:64:33 | {...} |
+methods
+| A.cs:50:21:50:34 | ObsoleteMethod |
+| A.cs:53:32:53:39 | ToString |
+| A.cs:60:21:60:29 | NewMethod |
+| Program.cs:7:28:7:31 | Main |
+| Program.cs:61:21:61:35 | AnnotatedMethod |
+types
+| A.cs:5:18:5:18 | C |
+| A.cs:7:18:7:18 | A |
+| A.cs:69:18:69:36 | MyObsoleteAttribute |
+| Program.cs:5:20:5:26 | Program |
+| Program.cs:64:18:64:33 | ProgramAttribute |
+parameters
+| A.cs:10:25:10:25 | x |
+| A.cs:21:35:21:37 | value |
+| A.cs:23:32:23:32 | i |
+| A.cs:23:32:23:32 | i |
+| A.cs:23:32:23:32 | i |
+| A.cs:26:13:26:15 | value |
+| A.cs:34:13:34:15 | value |
+| A.cs:38:13:38:18 | value |
+| A.cs:44:38:44:38 | a |
+| A.cs:44:43:44:43 | b |
+| Program.cs:7:42:7:45 | args |
+| Program.cs:21:31:21:31 | x |
+| Program.cs:32:42:32:44 | value |
+| Program.cs:34:32:34:32 | i |
+| Program.cs:34:32:34:32 | i |
+| Program.cs:34:32:34:32 | i |
+| Program.cs:37:13:37:15 | value |
+| Program.cs:45:13:45:15 | value |
+| Program.cs:49:13:49:18 | value |
+| Program.cs:55:50:55:50 | a |
+| Program.cs:55:61:55:61 | b |
+operators
+| A.cs:44:34:44:34 | + |
+| Program.cs:55:40:55:40 | - |
+constructors
+| A.cs:10:16:10:16 | A |
+| Program.cs:21:16:21:22 | Program |
+destructors
+| A.cs:16:10:16:10 | ~A |
+| Program.cs:27:10:27:16 | ~Program |
+fields
+| A.cs:9:24:9:27 | name |
+| Program.cs:19:24:19:34 | programName |
+properties
+| A.cs:21:23:21:26 | Prop |
+| Program.cs:32:23:32:33 | ProgramProp |
+indexers
+| A.cs:23:23:23:26 | Item |
+| Program.cs:34:23:34:26 | Item |
+accessors
+| A.cs:21:30:21:32 | get_Prop |
+| A.cs:21:35:21:37 | set_Prop |
+| A.cs:25:13:25:15 | get_Item |
+| A.cs:26:13:26:15 | set_Item |
+| A.cs:34:13:34:15 | add_Clicked |
+| A.cs:38:13:38:18 | remove_Clicked |
+| Program.cs:32:37:32:39 | get_ProgramProp |
+| Program.cs:32:42:32:44 | set_ProgramProp |
+| Program.cs:36:13:36:15 | get_Item |
+| Program.cs:37:13:37:15 | set_Item |
+| Program.cs:45:13:45:15 | add_ProgramClicked |
+| Program.cs:49:13:49:18 | remove_ProgramClicked |
+attributes
+| A.cs:49:10:49:19 | [MyObsolete(...)] |
+| Program.cs:60:10:60:16 | [Program(...)] |
+events
+| A.cs:32:35:32:41 | Clicked |
+| Program.cs:43:35:43:48 | ProgramClicked |
+eventAccessors
+| A.cs:34:13:34:15 | add_Clicked |
+| A.cs:38:13:38:18 | remove_Clicked |
+| Program.cs:45:13:45:15 | add_ProgramClicked |
+| Program.cs:49:13:49:18 | remove_ProgramClicked |
+usingDirectives
+| A.cs:1:1:1:13 | using ...; |
+| Program.cs:1:1:1:13 | using ...; |
+commentLines
+| A.cs:15:9:15:21 | // ... |
+| A.cs:29:9:29:10 | /* ... */ |
+| A.cs:30:1:30:27 | /* ... */ |
+| A.cs:31:1:31:11 | /* ... */ |
+| Program.cs:26:9:26:29 | // ... |
+| Program.cs:40:9:40:10 | /* ... */ |
+| Program.cs:41:1:41:27 | /* ... */ |
+| Program.cs:42:1:42:11 | /* ... */ |
+commentBlocks
+| A.cs:15:9:15:21 | // ... |
+| A.cs:29:9:31:11 | /* ... */ |
+| Program.cs:26:9:26:29 | // ... |
+| Program.cs:40:9:42:11 | /* ... */ |
+typeMentions
+| A.cs:9:17:9:22 | String |
+| A.cs:10:18:10:23 | String |
+| A.cs:18:13:18:19 | Console |
+| A.cs:21:16:21:21 | String |
+| A.cs:23:16:23:21 | Object |
+| A.cs:23:28:23:30 | Int32 |
+| A.cs:25:30:25:35 | Object |
+| A.cs:36:17:36:23 | Console |
+| A.cs:40:17:40:23 | Console |
+| A.cs:44:23:44:23 | A |
+| A.cs:44:36:44:36 | A |
+| A.cs:44:41:44:41 | A |
+| A.cs:49:10:49:19 | MyObsoleteAttribute |
+| A.cs:50:16:50:19 | Void |
+| A.cs:53:25:53:30 | String |
+| A.cs:55:13:55:18 | String |
+| A.cs:60:16:60:19 | Void |
+| A.cs:69:40:69:48 | Attribute |
+| Program.cs:7:23:7:26 | Void |
+| Program.cs:7:33:7:38 | String |
+| Program.cs:7:33:7:40 | String[] |
+| Program.cs:11:17:11:23 | Console |
+| Program.cs:14:13:14:15 | String |
+| Program.cs:15:13:15:15 | A |
+| Program.cs:15:25:15:25 | A |
+| Program.cs:16:13:16:19 | Console |
+| Program.cs:19:17:19:22 | String |
+| Program.cs:21:24:21:29 | String |
+| Program.cs:29:13:29:19 | Console |
+| Program.cs:32:16:32:21 | String |
+| Program.cs:34:16:34:21 | String |
+| Program.cs:34:28:34:30 | Int32 |
+| Program.cs:36:26:36:31 | String |
+| Program.cs:47:17:47:23 | Console |
+| Program.cs:51:17:51:23 | Console |
+| Program.cs:55:23:55:29 | Program |
+| Program.cs:55:42:55:48 | Program |
+| Program.cs:55:53:55:59 | Program |
+| Program.cs:60:10:60:16 | ProgramAttribute |
+| Program.cs:61:16:61:19 | Void |
+| Program.cs:64:37:64:45 | Attribute |
+xmlLocatables
+| web.changed.config:2:1:5:17 | configuration |
+| web.changed.config:3:3:4:16 | system.web |
+| web.unchanged.config:2:1:6:17 | configuration |
+| web.unchanged.config:3:3:5:16 | system.web |
+| web.unchanged.config:4:5:4:37 | httpCookies |
+| web.unchanged.config:4:5:4:37 | requireSSL=true |
--- a/csharp/ql/test/library-tests/overlay/overlay/test.qlref
+++ b/csharp/ql/test/library-tests/overlay/overlay/test.qlref
@@ -0,0 +1 @@
+query: ../test.ql
--- a/csharp/ql/test/library-tests/overlay/overlay/web.changed.config
+++ b/csharp/ql/test/library-tests/overlay/overlay/web.changed.config
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="utf-8" ?>
+<configuration>
+  <system.web>
+  </system.web>
+</configuration>
--- a/csharp/ql/test/library-tests/overlay/overlay/web.unchanged.config
+++ b/csharp/ql/test/library-tests/overlay/overlay/web.unchanged.config
@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="utf-8" ?>
+<configuration>
+  <system.web>
+    <httpCookies requireSSL="true"/>
+  </system.web>
+</configuration>
--- a/csharp/ql/test/library-tests/overlay/test.ql
+++ b/csharp/ql/test/library-tests/overlay/test.ql
@@ -0,0 +1,41 @@
+import csharp
+
+query predicate expressions(Expr e) { e.fromSource() }
+
+query predicate statements(Stmt s) { s.fromSource() }
+
+query predicate methods(Method m) { m.fromSource() }
+
+query predicate types(Type t) { t.fromSource() }
+
+query predicate parameters(Parameter p) { p.fromSource() }
+
+query predicate operators(Operator o) { o.fromSource() }
+
+query predicate constructors(Constructor c) { c.fromSource() }
+
+query predicate destructors(Destructor d) { d.fromSource() }
+
+query predicate fields(Field f) { f.fromSource() }
+
+query predicate properties(Property p) { p.fromSource() }
+
+query predicate indexers(Indexer i) { i.fromSource() }
+
+query predicate accessors(Accessor a) { a.fromSource() }
+
+query predicate attributes(Attribute a) { a.fromSource() }
+
+query predicate events(Event ev) { ev.fromSource() }
+
+query predicate eventAccessors(EventAccessor ea) { ea.fromSource() }
+
+query predicate usingDirectives(UsingDirective ud) { ud.fromSource() }
+
+query predicate commentLines(CommentLine cl) { any() }
+
+query predicate commentBlocks(CommentBlock cb) { any() }
+
+query predicate typeMentions(TypeMention tm) { any() }
+
+query predicate xmlLocatables(XmlLocatable xl) { any() }
--- a/csharp/ql/test/library-tests/overlay/testlocations.expected
+++ b/csharp/ql/test/library-tests/overlay/testlocations.expected
@@ -0,0 +1,5 @@
+elementsWithMultipleSourceLocations
+typeMentionsWithMultipleSourceLocations
+commentLinesWithMultipleSourceLocations
+commentBlocksWithMultipleSourceLocations
+removedEntities
--- a/csharp/ql/test/library-tests/overlay/testlocations.ql
+++ b/csharp/ql/test/library-tests/overlay/testlocations.ql
@@ -0,0 +1,29 @@
+import csharp
+
+// This is a consistency check that the overlay mechanism for cleaning up locations
+// works correctly.
+query predicate elementsWithMultipleSourceLocations(Element e, SourceLocation loc) {
+  e.fromSource() and
+  not e instanceof Namespace and
+  strictcount(SourceLocation l0 | l0 = e.getALocation()) > 1 and
+  loc = e.getALocation()
+}
+
+query predicate typeMentionsWithMultipleSourceLocations(TypeMention tm, SourceLocation loc) {
+  strictcount(SourceLocation l0 | l0 = tm.getLocation()) > 1 and
+  loc = tm.getLocation()
+}
+
+query predicate commentLinesWithMultipleSourceLocations(CommentLine cl, SourceLocation loc) {
+  strictcount(SourceLocation l0 | l0 = cl.getLocation()) > 1 and
+  loc = cl.getLocation()
+}
+
+query predicate commentBlocksWithMultipleSourceLocations(CommentBlock cb, SourceLocation loc) {
+  strictcount(SourceLocation l0 | l0 = cb.getLocation()) > 1 and
+  loc = cb.getLocation()
+}
+
+// This is a consistency check that the entities that are removed as a part of
+// the changes in the overlay are indeed removed from the database.
+query predicate removedEntities(Element e) { e.(Method).getName() = "OldMethod" }
--- a/go/codeql-extractor.yml
+++ b/go/codeql-extractor.yml
@@ -21,6 +21,7 @@ file_types:
    extensions:
      - .go
 legacy_qltest_extraction: true
+overlay_support_version: 20250626
 options:
  extract_tests:
    title: Whether to include Go test files in the CodeQL database.
--- a/go/downgrades/b1341734d6870b105e5c9d168ce7dec25d7f72d0/go.dbscheme
+++ b/go/downgrades/b1341734d6870b105e5c9d168ce7dec25d7f72d0/go.dbscheme
@@ -0,0 +1,552 @@
+/** Auto-generated dbscheme; do not edit. Run `make gen` in directory `go/` to regenerate. */
+
+
+/** Duplicate code **/
+
+duplicateCode(
+  unique int id : @duplication,
+  varchar(900) relativePath : string ref,
+  int equivClass : int ref);
+
+similarCode(
+  unique int id : @similarity,
+  varchar(900) relativePath : string ref,
+  int equivClass : int ref);
+
+@duplication_or_similarity = @duplication | @similarity;
+
+tokens(
+  int id : @duplication_or_similarity ref,
+  int offset : int ref,
+  int beginLine : int ref,
+  int beginColumn : int ref,
+  int endLine : int ref,
+  int endColumn : int ref);
+
+/** External data **/
+
+externalData(
+  int id : @externalDataElement,
+  varchar(900) path : string ref,
+  int column: int ref,
+  varchar(900) value : string ref
+);
+
+snapshotDate(unique date snapshotDate : date ref);
+
+sourceLocationPrefix(varchar(900) prefix : string ref);
+
+
+/*
+ * XML Files
+ */
+
+xmlEncoding(
+  unique int id: @file ref,
+  string encoding: string ref
+);
+
+xmlDTDs(
+  unique int id: @xmldtd,
+  string root: string ref,
+  string publicId: string ref,
+  string systemId: string ref,
+  int fileid: @file ref
+);
+
+xmlElements(
+  unique int id: @xmlelement,
+  string name: string ref,
+  int parentid: @xmlparent ref,
+  int idx: int ref,
+  int fileid: @file ref
+);
+
+xmlAttrs(
+  unique int id: @xmlattribute,
+  int elementid: @xmlelement ref,
+  string name: string ref,
+  string value: string ref,
+  int idx: int ref,
+  int fileid: @file ref
+);
+
+xmlNs(
+  int id: @xmlnamespace,
+  string prefixName: string ref,
+  string URI: string ref,
+  int fileid: @file ref
+);
+
+xmlHasNs(
+  int elementId: @xmlnamespaceable ref,
+  int nsId: @xmlnamespace ref,
+  int fileid: @file ref
+);
+
+xmlComments(
+  unique int id: @xmlcomment,
+  string text: string ref,
+  int parentid: @xmlparent ref,
+  int fileid: @file ref
+);
+
+xmlChars(
+  unique int id: @xmlcharacters,
+  string text: string ref,
+  int parentid: @xmlparent ref,
+  int idx: int ref,
+  int isCDATA: int ref,
+  int fileid: @file ref
+);
+
+@xmlparent = @file | @xmlelement;
+@xmlnamespaceable = @xmlelement | @xmlattribute;
+
+xmllocations(
+  int xmlElement: @xmllocatable ref,
+  int location: @location_default ref
+);
+
+@xmllocatable = @xmlcharacters | @xmlelement | @xmlcomment | @xmlattribute | @xmldtd | @file | @xmlnamespace;
+
+compilations(unique int id: @compilation, string cwd: string ref);
+
+#keyset[id, num]
+compilation_args(int id: @compilation ref, int num: int ref, string arg: string ref);
+
+#keyset[id, num, kind]
+compilation_time(int id: @compilation ref, int num: int ref, int kind: int ref, float secs: float ref);
+
+diagnostic_for(unique int diagnostic: @diagnostic ref, int compilation: @compilation ref, int file_number: int ref, int file_number_diagnostic_number: int ref);
+
+compilation_finished(unique int id: @compilation ref, float cpu_seconds: float ref, float elapsed_seconds: float ref);
+
+#keyset[id, num]
+compilation_compiling_files(int id: @compilation ref, int num: int ref, int file: @file ref);
+
+diagnostics(unique int id: @diagnostic, int severity: int ref, string error_tag: string ref, string error_message: string ref,
+            string full_error_message: string ref, int location: @location ref);
+
+locations_default(unique int id: @location_default, int file: @file ref, int beginLine: int ref, int beginColumn: int ref,
+                  int endLine: int ref, int endColumn: int ref);
+
+numlines(int element_id: @sourceline ref, int num_lines: int ref, int num_code: int ref, int num_comment: int ref);
+
+files(unique int id: @file, string name: string ref);
+
+folders(unique int id: @folder, string name: string ref);
+
+containerparent(int parent: @container ref, unique int child: @container ref);
+
+has_location(unique int locatable: @locatable ref, int location: @location ref);
+
+#keyset[parent, idx]
+comment_groups(unique int id: @comment_group, int parent: @file ref, int idx: int ref);
+
+comments(unique int id: @comment, int kind: int ref, int parent: @comment_group ref, int idx: int ref, string text: string ref);
+
+doc_comments(unique int node: @documentable ref, int comment: @comment_group ref);
+
+#keyset[parent, idx]
+exprs(unique int id: @expr, int kind: int ref, int parent: @exprparent ref, int idx: int ref);
+
+literals(unique int expr: @expr ref, string value: string ref, string raw: string ref);
+
+constvalues(unique int expr: @expr ref, string value: string ref, string exact: string ref);
+
+fields(unique int id: @field, int parent: @fieldparent ref, int idx: int ref);
+
+typeparamdecls(unique int id: @typeparamdecl, int parent: @typeparamdeclparent ref, int idx: int ref);
+
+#keyset[parent, idx]
+stmts(unique int id: @stmt, int kind: int ref, int parent: @stmtparent ref, int idx: int ref);
+
+#keyset[parent, idx]
+decls(unique int id: @decl, int kind: int ref, int parent: @declparent ref, int idx: int ref);
+
+#keyset[parent, idx]
+specs(unique int id: @spec, int kind: int ref, int parent: @gendecl ref, int idx: int ref);
+
+scopes(unique int id: @scope, int kind: int ref);
+
+scopenesting(unique int inner: @scope ref, int outer: @scope ref);
+
+scopenodes(unique int node: @scopenode ref, int scope: @localscope ref);
+
+objects(unique int id: @object, int kind: int ref, string name: string ref);
+
+objectscopes(unique int object: @object ref, int scope: @scope ref);
+
+objecttypes(unique int object: @object ref, int tp: @type ref);
+
+methodreceivers(unique int method: @object ref, int receiver: @object ref);
+
+fieldstructs(unique int field: @object ref, int struct: @structtype ref);
+
+methodhosts(int method: @object ref, int host: @definedtype ref);
+
+defs(int ident: @ident ref, int object: @object ref);
+
+uses(int ident: @ident ref, int object: @object ref);
+
+types(unique int id: @type, int kind: int ref);
+
+type_of(unique int expr: @expr ref, int tp: @type ref);
+
+typename(unique int tp: @type ref, string name: string ref);
+
+key_type(unique int map: @maptype ref, int tp: @type ref);
+
+element_type(unique int container: @containertype ref, int tp: @type ref);
+
+base_type(unique int ptr: @pointertype ref, int tp: @type ref);
+
+underlying_type(unique int defined: @definedtype ref, int tp: @type ref);
+
+#keyset[parent, index]
+component_types(int parent: @compositetype ref, int index: int ref, string name: string ref, int tp: @type ref);
+
+#keyset[parent, index]
+struct_tags(int parent: @structtype ref, int index: int ref, string tag: string ref);
+
+#keyset[interface, index]
+interface_private_method_ids(int interface: @interfacetype ref, int index: int ref, string id: string ref);
+
+array_length(unique int tp: @arraytype ref, string len: string ref);
+
+type_objects(unique int tp: @type ref, int object: @object ref);
+
+packages(unique int id: @package, string name: string ref, string path: string ref, int scope: @packagescope ref);
+
+#keyset[parent, idx]
+modexprs(unique int id: @modexpr, int kind: int ref, int parent: @modexprparent ref, int idx: int ref);
+
+#keyset[parent, idx]
+modtokens(string token: string ref, int parent: @modexpr ref, int idx: int ref);
+
+#keyset[package, idx]
+errors(unique int id: @error, int kind: int ref, string msg: string ref, string rawpos: string ref,
+       string file: string ref, int line: int ref, int col: int ref, int package: @package ref, int idx: int ref);
+
+has_ellipsis(int id: @callorconversionexpr ref);
+
+variadic(int id: @signaturetype ref);
+
+#keyset[parent, idx]
+typeparam(unique int tp: @typeparamtype ref, string name: string ref, int bound: @compositetype ref,
+          int parent: @typeparamparentobject ref, int idx: int ref);
+
+@container = @file | @folder;
+
+@locatable = @xmllocatable | @node | @localscope;
+
+@node = @documentable | @exprparent | @modexprparent | @fieldparent | @stmtparent | @declparent | @typeparamdeclparent
+      | @scopenode | @comment_group | @comment;
+
+@documentable = @file | @field | @typeparamdecl | @spec | @gendecl | @funcdecl | @modexpr;
+
+@exprparent = @funcdef | @file | @expr | @field | @stmt | @decl | @typeparamdecl | @spec;
+
+@modexprparent = @file | @modexpr;
+
+@fieldparent = @decl | @structtypeexpr | @functypeexpr | @interfacetypeexpr;
+
+@stmtparent = @funcdef | @stmt | @decl;
+
+@declparent = @file | @declstmt;
+
+@typeparamdeclparent = @funcdecl | @typespec;
+
+@funcdef = @funclit | @funcdecl;
+
+@scopenode = @file | @functypeexpr | @blockstmt | @ifstmt | @caseclause | @switchstmt | @commclause | @loopstmt;
+
+@location = @location_default;
+
+@sourceline = @locatable;
+
+case @comment.kind of
+  0 = @slashslashcomment
+| 1 = @slashstarcomment;
+
+case @expr.kind of
+  0 = @badexpr
+| 1 = @ident
+| 2 = @ellipsis
+| 3 = @intlit
+| 4 = @floatlit
+| 5 = @imaglit
+| 6 = @charlit
+| 7 = @stringlit
+| 8 = @funclit
+| 9 = @compositelit
+| 10 = @parenexpr
+| 11 = @selectorexpr
+| 12 = @indexexpr
+| 13 = @genericfunctioninstantiationexpr
+| 14 = @generictypeinstantiationexpr
+| 15 = @sliceexpr
+| 16 = @typeassertexpr
+| 17 = @callorconversionexpr
+| 18 = @starexpr
+| 19 = @keyvalueexpr
+| 20 = @arraytypeexpr
+| 21 = @structtypeexpr
+| 22 = @functypeexpr
+| 23 = @interfacetypeexpr
+| 24 = @maptypeexpr
+| 25 = @typesetliteralexpr
+| 26 = @plusexpr
+| 27 = @minusexpr
+| 28 = @notexpr
+| 29 = @complementexpr
+| 30 = @derefexpr
+| 31 = @addressexpr
+| 32 = @arrowexpr
+| 33 = @lorexpr
+| 34 = @landexpr
+| 35 = @eqlexpr
+| 36 = @neqexpr
+| 37 = @lssexpr
+| 38 = @leqexpr
+| 39 = @gtrexpr
+| 40 = @geqexpr
+| 41 = @addexpr
+| 42 = @subexpr
+| 43 = @orexpr
+| 44 = @xorexpr
+| 45 = @mulexpr
+| 46 = @quoexpr
+| 47 = @remexpr
+| 48 = @shlexpr
+| 49 = @shrexpr
+| 50 = @andexpr
+| 51 = @andnotexpr
+| 52 = @sendchantypeexpr
+| 53 = @recvchantypeexpr
+| 54 = @sendrcvchantypeexpr;
+
+@basiclit = @intlit | @floatlit | @imaglit | @charlit | @stringlit;
+
+@operatorexpr = @logicalexpr | @arithmeticexpr | @bitwiseexpr | @unaryexpr | @binaryexpr;
+
+@logicalexpr = @logicalunaryexpr | @logicalbinaryexpr;
+
+@arithmeticexpr = @arithmeticunaryexpr | @arithmeticbinaryexpr;
+
+@bitwiseexpr = @bitwiseunaryexpr | @bitwisebinaryexpr;
+
+@unaryexpr = @logicalunaryexpr | @bitwiseunaryexpr | @arithmeticunaryexpr | @derefexpr | @addressexpr | @arrowexpr;
+
+@logicalunaryexpr = @notexpr;
+
+@bitwiseunaryexpr = @complementexpr;
+
+@arithmeticunaryexpr = @plusexpr | @minusexpr;
+
+@binaryexpr = @logicalbinaryexpr | @bitwisebinaryexpr | @arithmeticbinaryexpr | @comparison;
+
+@logicalbinaryexpr = @lorexpr | @landexpr;
+
+@bitwisebinaryexpr = @shiftexpr | @orexpr | @xorexpr | @andexpr | @andnotexpr;
+
+@arithmeticbinaryexpr = @addexpr | @subexpr | @mulexpr | @quoexpr | @remexpr;
+
+@shiftexpr = @shlexpr | @shrexpr;
+
+@comparison = @equalitytest | @relationalcomparison;
+
+@equalitytest = @eqlexpr | @neqexpr;
+
+@relationalcomparison = @lssexpr | @leqexpr | @gtrexpr | @geqexpr;
+
+@chantypeexpr = @sendchantypeexpr | @recvchantypeexpr | @sendrcvchantypeexpr;
+
+case @stmt.kind of
+  0 = @badstmt
+| 1 = @declstmt
+| 2 = @emptystmt
+| 3 = @labeledstmt
+| 4 = @exprstmt
+| 5 = @sendstmt
+| 6 = @incstmt
+| 7 = @decstmt
+| 8 = @gostmt
+| 9 = @deferstmt
+| 10 = @returnstmt
+| 11 = @breakstmt
+| 12 = @continuestmt
+| 13 = @gotostmt
+| 14 = @fallthroughstmt
+| 15 = @blockstmt
+| 16 = @ifstmt
+| 17 = @caseclause
+| 18 = @exprswitchstmt
+| 19 = @typeswitchstmt
+| 20 = @commclause
+| 21 = @selectstmt
+| 22 = @forstmt
+| 23 = @rangestmt
+| 24 = @assignstmt
+| 25 = @definestmt
+| 26 = @addassignstmt
+| 27 = @subassignstmt
+| 28 = @mulassignstmt
+| 29 = @quoassignstmt
+| 30 = @remassignstmt
+| 31 = @andassignstmt
+| 32 = @orassignstmt
+| 33 = @xorassignstmt
+| 34 = @shlassignstmt
+| 35 = @shrassignstmt
+| 36 = @andnotassignstmt;
+
+@incdecstmt = @incstmt | @decstmt;
+
+@assignment = @simpleassignstmt | @compoundassignstmt;
+
+@simpleassignstmt = @assignstmt | @definestmt;
+
+@compoundassignstmt = @addassignstmt | @subassignstmt | @mulassignstmt | @quoassignstmt | @remassignstmt
+                    | @andassignstmt | @orassignstmt | @xorassignstmt | @shlassignstmt | @shrassignstmt | @andnotassignstmt;
+
+@branchstmt = @breakstmt | @continuestmt | @gotostmt | @fallthroughstmt;
+
+@switchstmt = @exprswitchstmt | @typeswitchstmt;
+
+@loopstmt = @forstmt | @rangestmt;
+
+case @decl.kind of
+  0 = @baddecl
+| 1 = @importdecl
+| 2 = @constdecl
+| 3 = @typedecl
+| 4 = @vardecl
+| 5 = @funcdecl;
+
+@gendecl = @importdecl | @constdecl | @typedecl | @vardecl;
+
+case @spec.kind of
+  0 = @importspec
+| 1 = @valuespec
+| 2 = @typedefspec
+| 3 = @aliasspec;
+
+@typespec = @typedefspec | @aliasspec;
+
+case @object.kind of
+  0 = @pkgobject
+| 1 = @decltypeobject
+| 2 = @builtintypeobject
+| 3 = @declconstobject
+| 4 = @builtinconstobject
+| 5 = @declvarobject
+| 6 = @declfunctionobject
+| 7 = @builtinfunctionobject
+| 8 = @labelobject;
+
+@typeparamparentobject = @decltypeobject | @declfunctionobject;
+
+@declobject = @decltypeobject | @declconstobject | @declvarobject | @declfunctionobject;
+
+@builtinobject = @builtintypeobject | @builtinconstobject | @builtinfunctionobject;
+
+@typeobject = @decltypeobject | @builtintypeobject;
+
+@valueobject = @constobject | @varobject | @functionobject;
+
+@constobject = @declconstobject | @builtinconstobject;
+
+@varobject = @declvarobject;
+
+@functionobject = @declfunctionobject | @builtinfunctionobject;
+
+case @scope.kind of
+  0 = @universescope
+| 1 = @packagescope
+| 2 = @localscope;
+
+case @type.kind of
+  0 = @invalidtype
+| 1 = @boolexprtype
+| 2 = @inttype
+| 3 = @int8type
+| 4 = @int16type
+| 5 = @int32type
+| 6 = @int64type
+| 7 = @uinttype
+| 8 = @uint8type
+| 9 = @uint16type
+| 10 = @uint32type
+| 11 = @uint64type
+| 12 = @uintptrtype
+| 13 = @float32type
+| 14 = @float64type
+| 15 = @complex64type
+| 16 = @complex128type
+| 17 = @stringexprtype
+| 18 = @unsafepointertype
+| 19 = @boolliteraltype
+| 20 = @intliteraltype
+| 21 = @runeliteraltype
+| 22 = @floatliteraltype
+| 23 = @complexliteraltype
+| 24 = @stringliteraltype
+| 25 = @nilliteraltype
+| 26 = @typeparamtype
+| 27 = @arraytype
+| 28 = @slicetype
+| 29 = @structtype
+| 30 = @pointertype
+| 31 = @interfacetype
+| 32 = @tupletype
+| 33 = @signaturetype
+| 34 = @maptype
+| 35 = @sendchantype
+| 36 = @recvchantype
+| 37 = @sendrcvchantype
+| 38 = @definedtype
+| 39 = @typesetliteraltype;
+
+@basictype = @booltype | @numerictype | @stringtype | @literaltype | @invalidtype | @unsafepointertype;
+
+@booltype = @boolexprtype | @boolliteraltype;
+
+@numerictype = @integertype | @floattype | @complextype;
+
+@integertype = @signedintegertype | @unsignedintegertype;
+
+@signedintegertype = @inttype | @int8type | @int16type | @int32type | @int64type | @intliteraltype | @runeliteraltype;
+
+@unsignedintegertype = @uinttype | @uint8type | @uint16type | @uint32type | @uint64type | @uintptrtype;
+
+@floattype = @float32type | @float64type | @floatliteraltype;
+
+@complextype = @complex64type | @complex128type | @complexliteraltype;
+
+@stringtype = @stringexprtype | @stringliteraltype;
+
+@literaltype = @boolliteraltype | @intliteraltype | @runeliteraltype | @floatliteraltype | @complexliteraltype
+             | @stringliteraltype | @nilliteraltype;
+
+@compositetype = @typeparamtype | @containertype | @structtype | @pointertype | @interfacetype | @tupletype
+               | @signaturetype | @definedtype | @typesetliteraltype;
+
+@containertype = @arraytype | @slicetype | @maptype | @chantype;
+
+@chantype = @sendchantype | @recvchantype | @sendrcvchantype;
+
+case @modexpr.kind of
+  0 = @modcommentblock
+| 1 = @modline
+| 2 = @modlineblock
+| 3 = @modlparen
+| 4 = @modrparen;
+
+case @error.kind of
+  0 = @unknownerror
+| 1 = @listerror
+| 2 = @parseerror
+| 3 = @typeerror;
+
--- a/go/downgrades/b1341734d6870b105e5c9d168ce7dec25d7f72d0/old.dbscheme
+++ b/go/downgrades/b1341734d6870b105e5c9d168ce7dec25d7f72d0/old.dbscheme
@@ -0,0 +1,563 @@
+/** Auto-generated dbscheme; do not edit. Run `make gen` in directory `go/` to regenerate. */
+
+
+/** Duplicate code **/
+
+duplicateCode(
+  unique int id : @duplication,
+  varchar(900) relativePath : string ref,
+  int equivClass : int ref);
+
+similarCode(
+  unique int id : @similarity,
+  varchar(900) relativePath : string ref,
+  int equivClass : int ref);
+
+@duplication_or_similarity = @duplication | @similarity;
+
+tokens(
+  int id : @duplication_or_similarity ref,
+  int offset : int ref,
+  int beginLine : int ref,
+  int beginColumn : int ref,
+  int endLine : int ref,
+  int endColumn : int ref);
+
+/** External data **/
+
+externalData(
+  int id : @externalDataElement,
+  varchar(900) path : string ref,
+  int column: int ref,
+  varchar(900) value : string ref
+);
+
+snapshotDate(unique date snapshotDate : date ref);
+
+sourceLocationPrefix(varchar(900) prefix : string ref);
+
+/** Overlay support **/
+
+databaseMetadata(
+  string metadataKey: string ref,
+  string value: string ref
+);
+
+overlayChangedFiles(
+  string path: string ref
+);
+
+
+/*
+ * XML Files
+ */
+
+xmlEncoding(
+  unique int id: @file ref,
+  string encoding: string ref
+);
+
+xmlDTDs(
+  unique int id: @xmldtd,
+  string root: string ref,
+  string publicId: string ref,
+  string systemId: string ref,
+  int fileid: @file ref
+);
+
+xmlElements(
+  unique int id: @xmlelement,
+  string name: string ref,
+  int parentid: @xmlparent ref,
+  int idx: int ref,
+  int fileid: @file ref
+);
+
+xmlAttrs(
+  unique int id: @xmlattribute,
+  int elementid: @xmlelement ref,
+  string name: string ref,
+  string value: string ref,
+  int idx: int ref,
+  int fileid: @file ref
+);
+
+xmlNs(
+  int id: @xmlnamespace,
+  string prefixName: string ref,
+  string URI: string ref,
+  int fileid: @file ref
+);
+
+xmlHasNs(
+  int elementId: @xmlnamespaceable ref,
+  int nsId: @xmlnamespace ref,
+  int fileid: @file ref
+);
+
+xmlComments(
+  unique int id: @xmlcomment,
+  string text: string ref,
+  int parentid: @xmlparent ref,
+  int fileid: @file ref
+);
+
+xmlChars(
+  unique int id: @xmlcharacters,
+  string text: string ref,
+  int parentid: @xmlparent ref,
+  int idx: int ref,
+  int isCDATA: int ref,
+  int fileid: @file ref
+);
+
+@xmlparent = @file | @xmlelement;
+@xmlnamespaceable = @xmlelement | @xmlattribute;
+
+xmllocations(
+  int xmlElement: @xmllocatable ref,
+  int location: @location_default ref
+);
+
+@xmllocatable = @xmlcharacters | @xmlelement | @xmlcomment | @xmlattribute | @xmldtd | @file | @xmlnamespace;
+
+compilations(unique int id: @compilation, string cwd: string ref);
+
+#keyset[id, num]
+compilation_args(int id: @compilation ref, int num: int ref, string arg: string ref);
+
+#keyset[id, num, kind]
+compilation_time(int id: @compilation ref, int num: int ref, int kind: int ref, float secs: float ref);
+
+diagnostic_for(unique int diagnostic: @diagnostic ref, int compilation: @compilation ref, int file_number: int ref, int file_number_diagnostic_number: int ref);
+
+compilation_finished(unique int id: @compilation ref, float cpu_seconds: float ref, float elapsed_seconds: float ref);
+
+#keyset[id, num]
+compilation_compiling_files(int id: @compilation ref, int num: int ref, int file: @file ref);
+
+diagnostics(unique int id: @diagnostic, int severity: int ref, string error_tag: string ref, string error_message: string ref,
+            string full_error_message: string ref, int location: @location ref);
+
+locations_default(unique int id: @location_default, int file: @file ref, int beginLine: int ref, int beginColumn: int ref,
+                  int endLine: int ref, int endColumn: int ref);
+
+numlines(int element_id: @sourceline ref, int num_lines: int ref, int num_code: int ref, int num_comment: int ref);
+
+files(unique int id: @file, string name: string ref);
+
+folders(unique int id: @folder, string name: string ref);
+
+containerparent(int parent: @container ref, unique int child: @container ref);
+
+has_location(unique int locatable: @locatable ref, int location: @location ref);
+
+#keyset[parent, idx]
+comment_groups(unique int id: @comment_group, int parent: @file ref, int idx: int ref);
+
+comments(unique int id: @comment, int kind: int ref, int parent: @comment_group ref, int idx: int ref, string text: string ref);
+
+doc_comments(unique int node: @documentable ref, int comment: @comment_group ref);
+
+#keyset[parent, idx]
+exprs(unique int id: @expr, int kind: int ref, int parent: @exprparent ref, int idx: int ref);
+
+literals(unique int expr: @expr ref, string value: string ref, string raw: string ref);
+
+constvalues(unique int expr: @expr ref, string value: string ref, string exact: string ref);
+
+fields(unique int id: @field, int parent: @fieldparent ref, int idx: int ref);
+
+typeparamdecls(unique int id: @typeparamdecl, int parent: @typeparamdeclparent ref, int idx: int ref);
+
+#keyset[parent, idx]
+stmts(unique int id: @stmt, int kind: int ref, int parent: @stmtparent ref, int idx: int ref);
+
+#keyset[parent, idx]
+decls(unique int id: @decl, int kind: int ref, int parent: @declparent ref, int idx: int ref);
+
+#keyset[parent, idx]
+specs(unique int id: @spec, int kind: int ref, int parent: @gendecl ref, int idx: int ref);
+
+scopes(unique int id: @scope, int kind: int ref);
+
+scopenesting(unique int inner: @scope ref, int outer: @scope ref);
+
+scopenodes(unique int node: @scopenode ref, int scope: @localscope ref);
+
+objects(unique int id: @object, int kind: int ref, string name: string ref);
+
+objectscopes(unique int object: @object ref, int scope: @scope ref);
+
+objecttypes(unique int object: @object ref, int tp: @type ref);
+
+methodreceivers(unique int method: @object ref, int receiver: @object ref);
+
+fieldstructs(unique int field: @object ref, int struct: @structtype ref);
+
+methodhosts(int method: @object ref, int host: @definedtype ref);
+
+defs(int ident: @ident ref, int object: @object ref);
+
+uses(int ident: @ident ref, int object: @object ref);
+
+types(unique int id: @type, int kind: int ref);
+
+type_of(unique int expr: @expr ref, int tp: @type ref);
+
+typename(unique int tp: @type ref, string name: string ref);
+
+key_type(unique int map: @maptype ref, int tp: @type ref);
+
+element_type(unique int container: @containertype ref, int tp: @type ref);
+
+base_type(unique int ptr: @pointertype ref, int tp: @type ref);
+
+underlying_type(unique int defined: @definedtype ref, int tp: @type ref);
+
+#keyset[parent, index]
+component_types(int parent: @compositetype ref, int index: int ref, string name: string ref, int tp: @type ref);
+
+#keyset[parent, index]
+struct_tags(int parent: @structtype ref, int index: int ref, string tag: string ref);
+
+#keyset[interface, index]
+interface_private_method_ids(int interface: @interfacetype ref, int index: int ref, string id: string ref);
+
+array_length(unique int tp: @arraytype ref, string len: string ref);
+
+type_objects(unique int tp: @type ref, int object: @object ref);
+
+packages(unique int id: @package, string name: string ref, string path: string ref, int scope: @packagescope ref);
+
+#keyset[parent, idx]
+modexprs(unique int id: @modexpr, int kind: int ref, int parent: @modexprparent ref, int idx: int ref);
+
+#keyset[parent, idx]
+modtokens(string token: string ref, int parent: @modexpr ref, int idx: int ref);
+
+#keyset[package, idx]
+errors(unique int id: @error, int kind: int ref, string msg: string ref, string rawpos: string ref,
+       string file: string ref, int line: int ref, int col: int ref, int package: @package ref, int idx: int ref);
+
+has_ellipsis(int id: @callorconversionexpr ref);
+
+variadic(int id: @signaturetype ref);
+
+#keyset[parent, idx]
+typeparam(unique int tp: @typeparamtype ref, string name: string ref, int bound: @compositetype ref,
+          int parent: @typeparamparentobject ref, int idx: int ref);
+
+@container = @file | @folder;
+
+@locatable = @xmllocatable | @node | @localscope;
+
+@node = @documentable | @exprparent | @modexprparent | @fieldparent | @stmtparent | @declparent | @typeparamdeclparent
+      | @scopenode | @comment_group | @comment;
+
+@documentable = @file | @field | @typeparamdecl | @spec | @gendecl | @funcdecl | @modexpr;
+
+@exprparent = @funcdef | @file | @expr | @field | @stmt | @decl | @typeparamdecl | @spec;
+
+@modexprparent = @file | @modexpr;
+
+@fieldparent = @decl | @structtypeexpr | @functypeexpr | @interfacetypeexpr;
+
+@stmtparent = @funcdef | @stmt | @decl;
+
+@declparent = @file | @declstmt;
+
+@typeparamdeclparent = @funcdecl | @typespec;
+
+@funcdef = @funclit | @funcdecl;
+
+@scopenode = @file | @functypeexpr | @blockstmt | @ifstmt | @caseclause | @switchstmt | @commclause | @loopstmt;
+
+@location = @location_default;
+
+@sourceline = @locatable;
+
+case @comment.kind of
+  0 = @slashslashcomment
+| 1 = @slashstarcomment;
+
+case @expr.kind of
+  0 = @badexpr
+| 1 = @ident
+| 2 = @ellipsis
+| 3 = @intlit
+| 4 = @floatlit
+| 5 = @imaglit
+| 6 = @charlit
+| 7 = @stringlit
+| 8 = @funclit
+| 9 = @compositelit
+| 10 = @parenexpr
+| 11 = @selectorexpr
+| 12 = @indexexpr
+| 13 = @genericfunctioninstantiationexpr
+| 14 = @generictypeinstantiationexpr
+| 15 = @sliceexpr
+| 16 = @typeassertexpr
+| 17 = @callorconversionexpr
+| 18 = @starexpr
+| 19 = @keyvalueexpr
+| 20 = @arraytypeexpr
+| 21 = @structtypeexpr
+| 22 = @functypeexpr
+| 23 = @interfacetypeexpr
+| 24 = @maptypeexpr
+| 25 = @typesetliteralexpr
+| 26 = @plusexpr
+| 27 = @minusexpr
+| 28 = @notexpr
+| 29 = @complementexpr
+| 30 = @derefexpr
+| 31 = @addressexpr
+| 32 = @arrowexpr
+| 33 = @lorexpr
+| 34 = @landexpr
+| 35 = @eqlexpr
+| 36 = @neqexpr
+| 37 = @lssexpr
+| 38 = @leqexpr
+| 39 = @gtrexpr
+| 40 = @geqexpr
+| 41 = @addexpr
+| 42 = @subexpr
+| 43 = @orexpr
+| 44 = @xorexpr
+| 45 = @mulexpr
+| 46 = @quoexpr
+| 47 = @remexpr
+| 48 = @shlexpr
+| 49 = @shrexpr
+| 50 = @andexpr
+| 51 = @andnotexpr
+| 52 = @sendchantypeexpr
+| 53 = @recvchantypeexpr
+| 54 = @sendrcvchantypeexpr;
+
+@basiclit = @intlit | @floatlit | @imaglit | @charlit | @stringlit;
+
+@operatorexpr = @logicalexpr | @arithmeticexpr | @bitwiseexpr | @unaryexpr | @binaryexpr;
+
+@logicalexpr = @logicalunaryexpr | @logicalbinaryexpr;
+
+@arithmeticexpr = @arithmeticunaryexpr | @arithmeticbinaryexpr;
+
+@bitwiseexpr = @bitwiseunaryexpr | @bitwisebinaryexpr;
+
+@unaryexpr = @logicalunaryexpr | @bitwiseunaryexpr | @arithmeticunaryexpr | @derefexpr | @addressexpr | @arrowexpr;
+
+@logicalunaryexpr = @notexpr;
+
+@bitwiseunaryexpr = @complementexpr;
+
+@arithmeticunaryexpr = @plusexpr | @minusexpr;
+
+@binaryexpr = @logicalbinaryexpr | @bitwisebinaryexpr | @arithmeticbinaryexpr | @comparison;
+
+@logicalbinaryexpr = @lorexpr | @landexpr;
+
+@bitwisebinaryexpr = @shiftexpr | @orexpr | @xorexpr | @andexpr | @andnotexpr;
+
+@arithmeticbinaryexpr = @addexpr | @subexpr | @mulexpr | @quoexpr | @remexpr;
+
+@shiftexpr = @shlexpr | @shrexpr;
+
+@comparison = @equalitytest | @relationalcomparison;
+
+@equalitytest = @eqlexpr | @neqexpr;
+
+@relationalcomparison = @lssexpr | @leqexpr | @gtrexpr | @geqexpr;
+
+@chantypeexpr = @sendchantypeexpr | @recvchantypeexpr | @sendrcvchantypeexpr;
+
+case @stmt.kind of
+  0 = @badstmt
+| 1 = @declstmt
+| 2 = @emptystmt
+| 3 = @labeledstmt
+| 4 = @exprstmt
+| 5 = @sendstmt
+| 6 = @incstmt
+| 7 = @decstmt
+| 8 = @gostmt
+| 9 = @deferstmt
+| 10 = @returnstmt
+| 11 = @breakstmt
+| 12 = @continuestmt
+| 13 = @gotostmt
+| 14 = @fallthroughstmt
+| 15 = @blockstmt
+| 16 = @ifstmt
+| 17 = @caseclause
+| 18 = @exprswitchstmt
+| 19 = @typeswitchstmt
+| 20 = @commclause
+| 21 = @selectstmt
+| 22 = @forstmt
+| 23 = @rangestmt
+| 24 = @assignstmt
+| 25 = @definestmt
+| 26 = @addassignstmt
+| 27 = @subassignstmt
+| 28 = @mulassignstmt
+| 29 = @quoassignstmt
+| 30 = @remassignstmt
+| 31 = @andassignstmt
+| 32 = @orassignstmt
+| 33 = @xorassignstmt
+| 34 = @shlassignstmt
+| 35 = @shrassignstmt
+| 36 = @andnotassignstmt;
+
+@incdecstmt = @incstmt | @decstmt;
+
+@assignment = @simpleassignstmt | @compoundassignstmt;
+
+@simpleassignstmt = @assignstmt | @definestmt;
+
+@compoundassignstmt = @addassignstmt | @subassignstmt | @mulassignstmt | @quoassignstmt | @remassignstmt
+                    | @andassignstmt | @orassignstmt | @xorassignstmt | @shlassignstmt | @shrassignstmt | @andnotassignstmt;
+
+@branchstmt = @breakstmt | @continuestmt | @gotostmt | @fallthroughstmt;
+
+@switchstmt = @exprswitchstmt | @typeswitchstmt;
+
+@loopstmt = @forstmt | @rangestmt;
+
+case @decl.kind of
+  0 = @baddecl
+| 1 = @importdecl
+| 2 = @constdecl
+| 3 = @typedecl
+| 4 = @vardecl
+| 5 = @funcdecl;
+
+@gendecl = @importdecl | @constdecl | @typedecl | @vardecl;
+
+case @spec.kind of
+  0 = @importspec
+| 1 = @valuespec
+| 2 = @typedefspec
+| 3 = @aliasspec;
+
+@typespec = @typedefspec | @aliasspec;
+
+case @object.kind of
+  0 = @pkgobject
+| 1 = @decltypeobject
+| 2 = @builtintypeobject
+| 3 = @declconstobject
+| 4 = @builtinconstobject
+| 5 = @declvarobject
+| 6 = @declfunctionobject
+| 7 = @builtinfunctionobject
+| 8 = @labelobject;
+
+@typeparamparentobject = @decltypeobject | @declfunctionobject;
+
+@declobject = @decltypeobject | @declconstobject | @declvarobject | @declfunctionobject;
+
+@builtinobject = @builtintypeobject | @builtinconstobject | @builtinfunctionobject;
+
+@typeobject = @decltypeobject | @builtintypeobject;
+
+@valueobject = @constobject | @varobject | @functionobject;
+
+@constobject = @declconstobject | @builtinconstobject;
+
+@varobject = @declvarobject;
+
+@functionobject = @declfunctionobject | @builtinfunctionobject;
+
+case @scope.kind of
+  0 = @universescope
+| 1 = @packagescope
+| 2 = @localscope;
+
+case @type.kind of
+  0 = @invalidtype
+| 1 = @boolexprtype
+| 2 = @inttype
+| 3 = @int8type
+| 4 = @int16type
+| 5 = @int32type
+| 6 = @int64type
+| 7 = @uinttype
+| 8 = @uint8type
+| 9 = @uint16type
+| 10 = @uint32type
+| 11 = @uint64type
+| 12 = @uintptrtype
+| 13 = @float32type
+| 14 = @float64type
+| 15 = @complex64type
+| 16 = @complex128type
+| 17 = @stringexprtype
+| 18 = @unsafepointertype
+| 19 = @boolliteraltype
+| 20 = @intliteraltype
+| 21 = @runeliteraltype
+| 22 = @floatliteraltype
+| 23 = @complexliteraltype
+| 24 = @stringliteraltype
+| 25 = @nilliteraltype
+| 26 = @typeparamtype
+| 27 = @arraytype
+| 28 = @slicetype
+| 29 = @structtype
+| 30 = @pointertype
+| 31 = @interfacetype
+| 32 = @tupletype
+| 33 = @signaturetype
+| 34 = @maptype
+| 35 = @sendchantype
+| 36 = @recvchantype
+| 37 = @sendrcvchantype
+| 38 = @definedtype
+| 39 = @typesetliteraltype;
+
+@basictype = @booltype | @numerictype | @stringtype | @literaltype | @invalidtype | @unsafepointertype;
+
+@booltype = @boolexprtype | @boolliteraltype;
+
+@numerictype = @integertype | @floattype | @complextype;
+
+@integertype = @signedintegertype | @unsignedintegertype;
+
+@signedintegertype = @inttype | @int8type | @int16type | @int32type | @int64type | @intliteraltype | @runeliteraltype;
+
+@unsignedintegertype = @uinttype | @uint8type | @uint16type | @uint32type | @uint64type | @uintptrtype;
+
+@floattype = @float32type | @float64type | @floatliteraltype;
+
+@complextype = @complex64type | @complex128type | @complexliteraltype;
+
+@stringtype = @stringexprtype | @stringliteraltype;
+
+@literaltype = @boolliteraltype | @intliteraltype | @runeliteraltype | @floatliteraltype | @complexliteraltype
+             | @stringliteraltype | @nilliteraltype;
+
+@compositetype = @typeparamtype | @containertype | @structtype | @pointertype | @interfacetype | @tupletype
+               | @signaturetype | @definedtype | @typesetliteraltype;
+
+@containertype = @arraytype | @slicetype | @maptype | @chantype;
+
+@chantype = @sendchantype | @recvchantype | @sendrcvchantype;
+
+case @modexpr.kind of
+  0 = @modcommentblock
+| 1 = @modline
+| 2 = @modlineblock
+| 3 = @modlparen
+| 4 = @modrparen;
+
+case @error.kind of
+  0 = @unknownerror
+| 1 = @listerror
+| 2 = @parseerror
+| 3 = @typeerror;
+
--- a/go/downgrades/b1341734d6870b105e5c9d168ce7dec25d7f72d0/upgrade.properties
+++ b/go/downgrades/b1341734d6870b105e5c9d168ce7dec25d7f72d0/upgrade.properties
@@ -0,0 +1,4 @@
+description: Add databaseMetadata and overlayChangedFiles relations
+compatibility: full
+databaseMetadata.rel: delete
+overlayChangedFiles.rel: delete
--- a/go/extractor/cli/go-autobuilder/BUILD.bazel
+++ b/go/extractor/cli/go-autobuilder/BUILD.bazel
@@ -12,6 +12,7 @@ go_library(
        "//go/extractor/autobuilder",
        "//go/extractor/diagnostics",
        "//go/extractor/project",
+        "//go/extractor/srcarchive",
        "//go/extractor/toolchain",
        "//go/extractor/util",
    ],
--- a/go/extractor/cli/go-autobuilder/go-autobuilder.go
+++ b/go/extractor/cli/go-autobuilder/go-autobuilder.go
@@ -13,6 +13,7 @@ import (
 	"github.com/github/codeql-go/extractor/autobuilder"
 	"github.com/github/codeql-go/extractor/diagnostics"
 	"github.com/github/codeql-go/extractor/project"
+	"github.com/github/codeql-go/extractor/srcarchive"
 	"github.com/github/codeql-go/extractor/toolchain"
 	"github.com/github/codeql-go/extractor/util"
 )
@@ -273,7 +274,7 @@ func createPathTransformerFile(newdir string) *os.File {
 		log.Fatalf("Failed to chdir into %s: %s\n", newdir, err.Error())
 	}

-	// set up SEMMLE_PATH_TRANSFORMER to ensure paths in the source archive and the snapshot
+	// set up CODEQL_PATH_TRANSFORMER to ensure paths in the source archive and the snapshot
 	// match the original source location, not the location we moved it to
 	pt, err := os.CreateTemp("", "path-transformer")
 	if err != nil {
@@ -283,7 +284,7 @@ func createPathTransformerFile(newdir string) *os.File {
 }

 // Writes the path transformer file
-func writePathTransformerFile(pt *os.File, realSrc, root, newdir string) {
+func writePathTransformerFile(pt *os.File, realSrc, newdir string) {
 	_, err := pt.WriteString("#" + realSrc + "\n" + newdir + "//\n")
 	if err != nil {
 		log.Fatalf("Unable to write path transformer file: %s.", err.Error())
@@ -292,9 +293,9 @@ func writePathTransformerFile(pt *os.File, realSrc, root, newdir string) {
 	if err != nil {
 		log.Fatalf("Unable to close path transformer file: %s.", err.Error())
 	}
-	err = os.Setenv("SEMMLE_PATH_TRANSFORMER", pt.Name())
+	err = os.Setenv("CODEQL_PATH_TRANSFORMER", pt.Name())
 	if err != nil {
-		log.Fatalf("Unable to set SEMMLE_PATH_TRANSFORMER environment variable: %s.\n", err.Error())
+		log.Fatalf("Unable to set CODEQL_PATH_TRANSFORMER environment variable: %s.\n", err.Error())
 	}
 }

@@ -447,7 +448,7 @@ func installDependencies(workspace project.GoWorkspace) {
 }

 // Run the extractor.
-func extract(workspace project.GoWorkspace) bool {
+func extract(workspace project.GoWorkspace, sourceRoot string) bool {
 	extractor, err := util.GetExtractorPath()
 	if err != nil {
 		log.Fatalf("Could not determine path of extractor: %v.\n", err)
@@ -458,6 +459,12 @@ func extract(workspace project.GoWorkspace) bool {
 		extractorArgs = append(extractorArgs, workspace.ModMode.ArgsForGoVersion(toolchain.GetEnvGoSemVer())...)
 	}

+	if util.IsOverlayExtraction() {
+		// When we are extracting an overlay, pass the source root to the extractor so that it knows
+		// how to resolve the relative paths in the list of changed files.
+		extractorArgs = append(extractorArgs, "--source-root", sourceRoot)
+	}
+
 	if len(workspace.Modules) == 0 {
 		// There may be no modules if we are using e.g. Dep or Glide
 		extractorArgs = append(extractorArgs, "./...")
@@ -501,9 +508,6 @@ func installDependenciesAndBuild() {

 	srcdir := getSourceDir()

-	// we set `SEMMLE_PATH_TRANSFORMER` ourselves in some cases, so blank it out first for consistency
-	os.Setenv("SEMMLE_PATH_TRANSFORMER", "")
-
 	// determine how to install dependencies and whether a GOPATH needs to be set up before
 	// extraction
 	workspaces := project.GetWorkspaceInfo(true)
@@ -534,7 +538,21 @@ func installDependenciesAndBuild() {
 			pt := createPathTransformerFile(paths.newdir)
 			defer os.Remove(pt.Name())

-			writePathTransformerFile(pt, paths.realSrc, paths.root, paths.newdir)
+			// We're about to create out own path transformer, so that paths containing the
+			// temporary GOPATH point to the right location. However, if there was already an
+			// incoming path transformer, the right location will be what _it_ wanted to transform
+			// paths to.
+			existingPathTransformer, err := srcarchive.LoadProjectLayoutFromEnv()
+			if err != nil {
+				log.Fatalf("Unable to load path transformer: %s.\n", err.Error())
+			}
+			var realSrc string
+			if existingPathTransformer == nil {
+				realSrc = paths.realSrc
+			} else {
+				realSrc = existingPathTransformer.To
+			}
+			writePathTransformerFile(pt, realSrc, paths.newdir)
 			setGopath(paths.root)
 		}
 	}
@@ -575,6 +593,12 @@ func installDependenciesAndBuild() {
 		buildWithCustomCommands(inst)
 	}

+	// The autobuilder is invoked with its working directory set to the source directory.
+	sourceRoot, err := os.Getwd()
+	if err != nil {
+		log.Fatalf("Failed to get current working directory: %s\n", err.Error())
+	}
+
 	// Attempt to extract all workspaces; we will tolerate individual extraction failures here
 	for i, workspace := range workspaces {
 		if workspace.ModMode == project.ModVendor {
@@ -595,7 +619,7 @@ func installDependenciesAndBuild() {
 			}
 		}

-		workspaces[i].Extracted = extract(workspace)
+		workspaces[i].Extracted = extract(workspace, sourceRoot)

 		if !workspaces[i].Extracted {
 			unsuccessfulProjects = append(unsuccessfulProjects, workspace.BaseDir)
@@ -620,6 +644,8 @@ func installDependenciesAndBuild() {
 	} else {
 		log.Printf("Success: extraction succeeded for all %d discovered project(s).\n", len(workspaces))
 	}
+
+	util.WriteOverlayBaseMetadata()
 }

 func main() {
--- a/go/extractor/cli/go-extractor/go-extractor.go
+++ b/go/extractor/cli/go-extractor/go-extractor.go
@@ -24,9 +24,10 @@ func usage() {

 // extractTests is set (a) if we were manually commanded to extract tests via the relevant
 // environment variable / extractor option, or (b) we're mimicking a `go test` command.
-func parseFlags(args []string, mimic bool, extractTests bool) ([]string, []string, bool) {
+func parseFlags(args []string, mimic bool, extractTests bool) ([]string, []string, bool, string) {
 	i := 0
 	buildFlags := []string{}
+	var sourceRoot string
 	for ; i < len(args) && strings.HasPrefix(args[i], "-"); i++ {
 		if args[i] == "--" {
 			i++
@@ -61,6 +62,18 @@ func parseFlags(args []string, mimic bool, extractTests bool) ([]string, []strin
 				} else {
 					log.Fatalf("--mimic requires an argument, e.g. --mimic go")
 				}
+			case "--source-root":
+				// The extractor can be called by the autobuilder with the working directory set to
+				// the directory containing the workspace we're extracting, and this may be a
+				// subdirectory of the actual source root. This argument lets us resolve paths that
+				// are relative to that source root, e.g. for the list of overlay changed files.
+				if i+1 < len(args) {
+					i++
+					sourceRoot = args[i]
+					log.Printf("Source root is %s", sourceRoot)
+				} else {
+					log.Fatalf("--source-root requires an argument, e.g. --source-root /path/to/root")
+				}
 			}
 		}

@@ -93,14 +106,14 @@ func parseFlags(args []string, mimic bool, extractTests bool) ([]string, []strin
 	cpuprofile = os.Getenv("CODEQL_EXTRACTOR_GO_CPU_PROFILE")
 	memprofile = os.Getenv("CODEQL_EXTRACTOR_GO_MEM_PROFILE")

-	return buildFlags, args[i:], extractTests
+	return buildFlags, args[i:], extractTests, sourceRoot
 }

 func main() {
 	util.SetLogLevel()

 	extractTestsDefault := os.Getenv("CODEQL_EXTRACTOR_GO_OPTION_EXTRACT_TESTS") == "true"
-	buildFlags, patterns, extractTests := parseFlags(os.Args[1:], false, extractTestsDefault)
+	buildFlags, patterns, extractTests, sourceRoot := parseFlags(os.Args[1:], false, extractTestsDefault)

 	if cpuprofile != "" {
 		f, err := os.Create(cpuprofile)
@@ -120,7 +133,7 @@ func main() {
 	}

 	log.Printf("Build flags: '%s'; patterns: '%s'\n", strings.Join(buildFlags, " "), strings.Join(patterns, " "))
-	err := extractor.ExtractWithFlags(buildFlags, patterns, extractTests)
+	err := extractor.ExtractWithFlags(buildFlags, patterns, extractTests, sourceRoot)
 	if err != nil {
 		errString := err.Error()
 		if strings.Contains(errString, "unexpected directory layout:") {
--- a/go/extractor/dbscheme/tables.go
+++ b/go/extractor/dbscheme/tables.go
@@ -43,6 +43,17 @@ externalData(
 snapshotDate(unique date snapshotDate : date ref);

 sourceLocationPrefix(varchar(900) prefix : string ref);
+
+/** Overlay support **/
+
+databaseMetadata(
+  string metadataKey: string ref,
+  string value: string ref
+);
+
+overlayChangedFiles(
+  string path: string ref
+);
 `)

 // Copied directly from the XML dbscheme
--- a/go/extractor/extractor.go
+++ b/go/extractor/extractor.go
@@ -11,6 +11,7 @@ import (
 	"go/types"
 	"io"
 	"log"
+	"log/slog"
 	"os"
 	"path/filepath"
 	"reflect"
@@ -58,16 +59,11 @@ func init() {
 	}
 }

-// Extract extracts the packages specified by the given patterns
-func Extract(patterns []string) error {
-	return ExtractWithFlags(nil, patterns, false)
-}
-
 // ExtractWithFlags extracts the packages specified by the given patterns and build flags
-func ExtractWithFlags(buildFlags []string, patterns []string, extractTests bool) error {
+func ExtractWithFlags(buildFlags []string, patterns []string, extractTests bool, sourceRoot string) error {
 	startTime := time.Now()

-	extraction := NewExtraction(buildFlags, patterns)
+	extraction := NewExtraction(buildFlags, patterns, sourceRoot)
 	defer extraction.StatWriter.Close()

 	modEnabled := os.Getenv("GO111MODULE") != "off"
@@ -323,16 +319,17 @@ func ExtractWithFlags(buildFlags []string, patterns []string, extractTests bool)
 type Extraction struct {
 	// A lock for preventing concurrent writes to maps and the stat trap writer, as they are not
 	// thread-safe
-	Lock         sync.Mutex
-	LabelKey     string
-	Label        trap.Label
-	StatWriter   *trap.Writer
-	WaitGroup    sync.WaitGroup
-	GoroutineSem *semaphore
-	FdSem        *semaphore
-	NextFileId   int
-	FileInfo     map[string]*FileInfo
-	SeenGoMods   map[string]bool
+	Lock           sync.Mutex
+	LabelKey       string
+	Label          trap.Label
+	StatWriter     *trap.Writer
+	WaitGroup      sync.WaitGroup
+	GoroutineSem   *semaphore
+	FdSem          *semaphore
+	NextFileId     int
+	FileInfo       map[string]*FileInfo
+	SeenGoMods     map[string]bool
+	OverlayChanges map[string]bool
 }

 type FileInfo struct {
@@ -367,7 +364,7 @@ func (extraction *Extraction) GetNextErr(path string) int {
 	return res
 }

-func NewExtraction(buildFlags []string, patterns []string) *Extraction {
+func NewExtraction(buildFlags []string, patterns []string, sourceRoot string) *Extraction {
 	hash := md5.New()
 	io.WriteString(hash, "go")
 	for _, buildFlag := range buildFlags {
@@ -379,6 +376,22 @@ func NewExtraction(buildFlags []string, patterns []string) *Extraction {
 	}
 	sum := hash.Sum(nil)

+	overlayChangeList := util.GetOverlayChanges(sourceRoot)
+	var overlayChanges map[string]bool
+	if overlayChangeList == nil {
+		overlayChanges = nil
+	} else {
+		overlayChanges = make(map[string]bool)
+		for _, changedFilePath := range overlayChangeList {
+			absPath, err := filepath.Abs(changedFilePath)
+			if err != nil {
+				log.Fatalf("Error resolving absolute path of overlay change %s: %s", changedFilePath, err.Error())
+			}
+			overlayChanges[absPath] = true
+			slog.Info("Overlay changed file", "path", absPath)
+		}
+	}
+
 	i := 0
 	var path string
 	// split compilation files into directories to avoid filling a single directory with too many files
@@ -438,10 +451,11 @@ func NewExtraction(buildFlags []string, patterns []string) *Extraction {
 		FdSem: newSemaphore(100),
 		// this semaphore is used to limit the number of goroutines spawned, so we
 		// don't run into memory issues
-		GoroutineSem: newSemaphore(MaxGoRoutines),
-		NextFileId:   0,
-		FileInfo:     make(map[string]*FileInfo),
-		SeenGoMods:   make(map[string]bool),
+		GoroutineSem:   newSemaphore(MaxGoRoutines),
+		NextFileId:     0,
+		FileInfo:       make(map[string]*FileInfo),
+		SeenGoMods:     make(map[string]bool),
+		OverlayChanges: overlayChanges,
 	}
 }

@@ -720,6 +734,16 @@ func (extraction *Extraction) extractFile(ast *ast.File, pkg *packages.Package)
 		return nil
 	}
 	path := normalizedPath(ast, fset)
+	// If we're extracting an overlay, we want to skip extraction of files that haven't changed.
+	// Since some files may be outside the source directory (e.g. files preprocessed by cgo) we
+	// can't easily know if they have changed (or came from source files that changed), so we always
+	// extract a file if it's not in the package directory.
+	if extraction.OverlayChanges != nil &&
+		!extraction.OverlayChanges[path] &&
+		strings.HasPrefix(path+string(filepath.Separator), pkg.Dir) {
+		slog.Info("Skipping unchanged file in overlay extraction", "path", path)
+		return nil
+	}

 	extraction.FdSem.acquire(3)

@@ -791,12 +815,12 @@ func (extraction *Extraction) extractFileInfo(tw *trap.Writer, file string, isDu
 			displayPath = rawPath
 		}
 		if i == len(components)-1 {
-			lbl := tw.Labeler.FileLabelFor(file)
+			lbl := tw.Labeler.FileLabelFor(path)
 			dbscheme.FilesTable.Emit(tw, lbl, displayPath)
 			dbscheme.ContainerParentTable.Emit(tw, parentLbl, lbl)
 			dbscheme.HasLocationTable.Emit(tw, lbl, emitLocation(tw, lbl, 0, 0, 0, 0))
 			extraction.Lock.Lock()
-			slbl := extraction.StatWriter.Labeler.FileLabelFor(file)
+			slbl := extraction.StatWriter.Labeler.FileLabelFor(path)
 			if !isDummy {
 				dbscheme.CompilationCompilingFilesTable.Emit(extraction.StatWriter, extraction.Label, extraction.GetFileIdx(file), slbl)
 			}
--- a/go/extractor/go.mod
+++ b/go/extractor/go.mod
@@ -9,8 +9,8 @@ toolchain go1.25.0
 // when adding or removing dependencies, run
 //    bazel mod tidy
 require (
-	golang.org/x/mod v0.29.0
-	golang.org/x/tools v0.38.0
+	golang.org/x/mod v0.30.0
+	golang.org/x/tools v0.39.0
 )

-require golang.org/x/sync v0.17.0 // indirect
+require golang.org/x/sync v0.18.0 // indirect
--- a/go/extractor/go.sum
+++ b/go/extractor/go.sum
@@ -1,8 +1,8 @@
 github.com/google/go-cmp v0.6.0 h1:ofyhxvXcZhMsU5ulbFiLKl/XBFqE1GSq7atu8tAmTRI=
 github.com/google/go-cmp v0.6.0/go.mod h1:17dUlkBOakJ0+DkrSSNjCkIjxS6bF9zb3elmeNGIjoY=
-golang.org/x/mod v0.29.0 h1:HV8lRxZC4l2cr3Zq1LvtOsi/ThTgWnUk/y64QSs8GwA=
-golang.org/x/mod v0.29.0/go.mod h1:NyhrlYXJ2H4eJiRy/WDBO6HMqZQ6q9nk4JzS3NuCK+w=
-golang.org/x/sync v0.17.0 h1:l60nONMj9l5drqw6jlhIELNv9I0A4OFgRsG9k2oT9Ug=
-golang.org/x/sync v0.17.0/go.mod h1:9KTHXmSnoGruLpwFjVSX0lNNA75CykiMECbovNTZqGI=
-golang.org/x/tools v0.38.0 h1:Hx2Xv8hISq8Lm16jvBZ2VQf+RLmbd7wVUsALibYI/IQ=
-golang.org/x/tools v0.38.0/go.mod h1:yEsQ/d/YK8cjh0L6rZlY8tgtlKiBNTL14pGDJPJpYQs=
+golang.org/x/mod v0.30.0 h1:fDEXFVZ/fmCKProc/yAXXUijritrDzahmwwefnjoPFk=
+golang.org/x/mod v0.30.0/go.mod h1:lAsf5O2EvJeSFMiBxXDki7sCgAxEUcZHXoXMKT4GJKc=
+golang.org/x/sync v0.18.0 h1:kr88TuHDroi+UVf+0hZnirlk8o8T+4MrK6mr60WkH/I=
+golang.org/x/sync v0.18.0/go.mod h1:9KTHXmSnoGruLpwFjVSX0lNNA75CykiMECbovNTZqGI=
+golang.org/x/tools v0.39.0 h1:ik4ho21kwuQln40uelmciQPp9SipgNDdrafrYA4TmQQ=
+golang.org/x/tools v0.39.0/go.mod h1:JnefbkDPyD8UU2kI5fuf8ZX4/yUeh9W877ZeBONxUqQ=
--- a/go/extractor/gomodextractor.go
+++ b/go/extractor/gomodextractor.go
@@ -20,6 +20,11 @@ func (extraction *Extraction) extractGoMod(path string) error {
 		path = normPath
 	}

+	if extraction.OverlayChanges != nil && !extraction.OverlayChanges[path] {
+		// This go.mod did not change since the base was extracted
+		return nil
+	}
+
 	extraction.Lock.Lock()
 	if extraction.SeenGoMods[path] {
 		extraction.Lock.Unlock()
--- a/go/extractor/srcarchive/BUILD.bazel
+++ b/go/extractor/srcarchive/BUILD.bazel
@@ -10,6 +10,7 @@ go_library(
    ],
    importpath = "github.com/github/codeql-go/extractor/srcarchive",
    visibility = ["//visibility:public"],
+    deps = ["//go/extractor/util"],
 )

 go_test(
--- a/go/extractor/srcarchive/projectlayout.go
+++ b/go/extractor/srcarchive/projectlayout.go
@@ -6,6 +6,8 @@ import (
 	"fmt"
 	"os"
 	"strings"
+
+	"github.com/github/codeql-go/extractor/util"
 )

 // ProjectLayout describes a very simple project layout rewriting paths starting
@@ -16,7 +18,7 @@ import (
 //	# to
 //	from//
 type ProjectLayout struct {
-	from, to string
+	From, To string
 }

 // normaliseSlashes adds an initial slash to `path` if there isn't one, and trims
@@ -28,6 +30,25 @@ func normaliseSlashes(path string) string {
 	return strings.TrimSuffix(path, "/")
 }

+// LoadProjectLayoutFromEnv loads a project layout from the file referenced by the
+// {CODEQL,SEMMLE}_PATH_TRANSFORMER environment variable. If neither env var is set, returns nil. If
+// the file cannot be read or does not have the right format, it returns an error.
+func LoadProjectLayoutFromEnv() (*ProjectLayout, error) {
+	pt := util.Getenv("CODEQL_PATH_TRANSFORMER", "SEMMLE_PATH_TRANSFORMER")
+	if pt == "" {
+		return nil, nil
+	}
+	ptf, err := os.Open(pt)
+	if err != nil {
+		return nil, err
+	}
+	projLayout, err := LoadProjectLayout(ptf)
+	if err != nil {
+		return nil, err
+	}
+	return projLayout, nil
+}
+
 // LoadProjectLayout loads a project layout from the given file, returning an error
 // if the file does not have the right format
 func LoadProjectLayout(file *os.File) (*ProjectLayout, error) {
@@ -41,7 +62,7 @@ func LoadProjectLayout(file *os.File) (*ProjectLayout, error) {
 	if !strings.HasPrefix(line, "#") {
 		return nil, fmt.Errorf("first line of project layout should start with #, but got %s", line)
 	}
-	res.to = normaliseSlashes(strings.TrimSpace(strings.TrimPrefix(line, "#")))
+	res.To = normaliseSlashes(strings.TrimSpace(strings.TrimPrefix(line, "#")))

 	if !scanner.Scan() {
 		return nil, errors.New("empty section in project-layout file")
@@ -57,7 +78,7 @@ func LoadProjectLayout(file *os.File) (*ProjectLayout, error) {
 	if strings.HasPrefix(line, "-") || strings.Contains(line, "*") || strings.Contains(line, "//") {
 		return nil, errors.New("unsupported project-layout feature")
 	}
-	res.from = normaliseSlashes(line)
+	res.From = normaliseSlashes(line)

 	for scanner.Scan() {
 		if strings.TrimSpace(scanner.Text()) != "" {
@@ -71,11 +92,11 @@ func LoadProjectLayout(file *os.File) (*ProjectLayout, error) {
 // transformString transforms `str` as specified by the project layout: if it starts with the `from`
 // prefix, that prefix is relaced by `to`; otherwise the string is returned unchanged
 func (p *ProjectLayout) transformString(str string) string {
-	if str == p.from {
-		return p.to
+	if str == p.From {
+		return p.To
 	}
-	if strings.HasPrefix(str, p.from+"/") {
-		return p.to + "/" + str[len(p.from)+1:]
+	if strings.HasPrefix(str, p.From+"/") {
+		return p.To + "/" + str[len(p.From)+1:]
 	}
 	return str
 }
--- a/go/extractor/srcarchive/projectlayout_test.go
+++ b/go/extractor/srcarchive/projectlayout_test.go
@@ -28,6 +28,32 @@ func mkProjectLayout(projectLayoutSource string, t *testing.T) (*ProjectLayout,
 	return LoadProjectLayout(pt)
 }

+func mkProjectLayoutFromEnv(projectLayoutSource string, t *testing.T) (*ProjectLayout, error) {
+	pt, err := os.CreateTemp("", "path-transformer-from-env")
+	if err != nil {
+		t.Fatalf("Unable to create temporary file for project layout: %s", err.Error())
+	}
+	defer os.Remove(pt.Name())
+	_, err = pt.WriteString(projectLayoutSource)
+	if err != nil {
+		t.Fatalf("Unable to write to temporary file for project layout: %s", err.Error())
+	}
+	err = pt.Close()
+	if err != nil {
+		t.Fatalf("Unable to close path transformer file: %s.", err.Error())
+	}
+
+	pt, err = os.Open(pt.Name())
+	if err != nil {
+		t.Fatalf("Unable to open path transformer file: %s.", err.Error())
+	}
+
+	os.Setenv("CODEQL_PATH_TRANSFORMER", pt.Name())
+	defer os.Unsetenv("CODEQL_PATH_TRANSFORMER")
+
+	return LoadProjectLayoutFromEnv()
+}
+
 func testTransformation(projectLayout *ProjectLayout, t *testing.T, path string, expected string) {
 	actual := projectLayout.Transform(path)
 	if actual != expected {
@@ -35,16 +61,12 @@ func testTransformation(projectLayout *ProjectLayout, t *testing.T, path string,
 	}
 }

-func TestValidProjectLayout(t *testing.T) {
-	p, err := mkProjectLayout(`
+const validProjectLayoutSource = `
 # /opt/src
 /opt/src/root/src/org/repo//
-`, t)
-
-	if err != nil {
-		t.Fatalf("Error loading project layout: %s", err.Error())
-	}
+`

+func testTransformationsForValidProjectLayout(p *ProjectLayout, t *testing.T) {
 	testTransformation(p, t, "/opt/src/root/src/org/repo", "/opt/src")
 	testTransformation(p, t, "/opt/src/root/src/org/repo/", "/opt/src/")
 	testTransformation(p, t, "/opt/src/root/src/org/repo/main.go", "/opt/src/main.go")
@@ -53,6 +75,26 @@ func TestValidProjectLayout(t *testing.T) {
 	testTransformation(p, t, "opt/src/root/src/org/repo", "opt/src/root/src/org/repo")
 }

+func TestValidProjectLayout(t *testing.T) {
+	p, err := mkProjectLayout(validProjectLayoutSource, t)
+
+	if err != nil {
+		t.Fatalf("Error loading project layout: %s", err.Error())
+	}
+
+	testTransformationsForValidProjectLayout(p, t)
+}
+
+func TestValidProjectLayoutFromEnv(t *testing.T) {
+	p, err := mkProjectLayoutFromEnv(validProjectLayoutSource, t)
+
+	if err != nil {
+		t.Fatalf("Error loading project layout: %s", err.Error())
+	}
+
+	testTransformationsForValidProjectLayout(p, t)
+}
+
 func TestWindowsPaths(t *testing.T) {
 	p, err := mkProjectLayout(`
 # /c:/virtual
--- a/go/extractor/srcarchive/srcarchive.go
+++ b/go/extractor/srcarchive/srcarchive.go
@@ -4,6 +4,7 @@ import (
 	"errors"
 	"io"
 	"log"
+	"log/slog"
 	"os"
 	"path/filepath"
 	"strings"
@@ -12,16 +13,14 @@ import (
 var pathTransformer *ProjectLayout

 func init() {
-	pt := os.Getenv("SEMMLE_PATH_TRANSFORMER")
-	if pt != "" {
-		ptf, err := os.Open(pt)
-		if err != nil {
-			log.Fatalf("Unable to open path transformer %s: %s.\n", pt, err.Error())
-		}
-		pathTransformer, err = LoadProjectLayout(ptf)
-		if err != nil {
-			log.Fatalf("Unable to initialize path transformer: %s.\n", err.Error())
+	pt, err := LoadProjectLayoutFromEnv()
+	if err == nil {
+		pathTransformer = pt
+		if pathTransformer != nil {
+			slog.Info("Loaded path transformer", "from", pathTransformer.From, "to", pathTransformer.To)
 		}
+	} else {
+		log.Fatalf("Unable to load path transformer: %s.\n", err.Error())
 	}
 }

@@ -69,7 +68,7 @@ func srcArchive() (string, error) {
 	return srcArchive, nil
 }

-// TransformPath applies the transformations specified by `SEMMLE_PATH_TRANSFORMER` (if any) to the
+// TransformPath applies the transformations specified by `CODEQL_PATH_TRANSFORMER` (if any) to the
 // given path
 func TransformPath(path string) string {
 	if pathTransformer != nil {
--- a/go/extractor/trap/labels.go
+++ b/go/extractor/trap/labels.go
@@ -3,7 +3,9 @@ package trap
 import (
 	"fmt"
 	"go/types"
+	"path/filepath"

+	"github.com/github/codeql-go/extractor/srcarchive"
 	"github.com/github/codeql-go/extractor/util"
 )

@@ -67,14 +69,14 @@ func (l *Labeler) GlobalID(key string) Label {
 // FileLabel returns the label for a file with path `path`.
 func (l *Labeler) FileLabel() Label {
 	if l.fileLabel == InvalidLabel {
-		l.fileLabel = l.FileLabelFor(l.tw.path)
+		l.fileLabel = l.FileLabelFor(srcarchive.TransformPath(l.tw.path))
 	}
 	return l.fileLabel
 }

 // FileLabelFor returns the label for the file for which the trap writer `tw` is associated
 func (l *Labeler) FileLabelFor(path string) Label {
-	return l.GlobalID(util.EscapeTrapSpecialChars(path) + ";sourcefile")
+	return l.GlobalID(util.EscapeTrapSpecialChars(filepath.ToSlash(path)) + ";sourcefile")
 }

 // LocalID associates a label with the given AST node `nd` and returns it
--- a/go/extractor/util/BUILD.bazel
+++ b/go/extractor/util/BUILD.bazel
@@ -7,6 +7,7 @@ go_library(
    srcs = [
        "extractvendordirs.go",
        "logging.go",
+        "overlays.go",
        "registryproxy.go",
        "semver.go",
        "util.go",
--- a/go/extractor/util/overlays.go
+++ b/go/extractor/util/overlays.go
@@ -0,0 +1,70 @@
+package util
+
+import (
+	"encoding/json"
+	"log"
+	"os"
+	"path/filepath"
+)
+
+func IsOverlayExtraction() bool {
+	_, present := os.LookupEnv("CODEQL_EXTRACTOR_GO_OVERLAY_METADATA_IN")
+	return present
+}
+
+// If the relevant environment variable is set, indicating that we are extracting an overlay
+// database, GetOverlayChanges returns the list of relative paths of files that have changed (or
+// been deleted). Otherwise, it returns `nil`.
+func GetOverlayChanges(sourceRoot string) []string {
+	if overlayChangesJsonPath, present := os.LookupEnv("CODEQL_EXTRACTOR_GO_OVERLAY_CHANGES"); present {
+		log.Printf("Reading overlay changes from: %s", overlayChangesJsonPath)
+
+		file, err := os.Open(overlayChangesJsonPath)
+		if err != nil {
+			log.Fatalf("Failed to open overlay changes JSON file: %s", err)
+		}
+		defer file.Close()
+
+		var overlayData struct {
+			Changes []string `json:"changes"`
+		}
+
+		decoder := json.NewDecoder(file)
+		if err := decoder.Decode(&overlayData); err != nil {
+			log.Fatalf("Failed to decode overlay changes JSON file: %s", err)
+		}
+
+		absPaths := make([]string, 0, len(overlayData.Changes))
+		if sourceRoot == "" {
+			// This shouldn't happen, because it implies the extractor was invoked in some way other
+			// than from the autobuilder. However, we'll only attempt to build an overlay if there
+			// exists an overlay _base_, and only the autobuilder writes the metadata file that
+			// ensures a database is created as an overlay-base.
+			log.Fatalf("Extractor is running in overlay mode, but --source-root was not provided")
+		}
+		for _, relPath := range overlayData.Changes {
+			absPaths = append(absPaths, filepath.Clean(sourceRoot+"/"+relPath))
+		}
+
+		return absPaths
+	} else {
+		return nil
+	}
+}
+
+// WriteOverlayBaseMetadata creates an empty metadata file if we are extracting an overlay base;
+// otherwise, it does nothing.
+func WriteOverlayBaseMetadata() {
+	if metadataPath, present := os.LookupEnv("CODEQL_EXTRACTOR_GO_OVERLAY_BASE_METADATA_OUT"); present {
+		log.Printf("Writing overlay base metadata to: %s", metadataPath)
+
+		// In principle, we could store some metadata here and read it back when extracting the
+		// overlay. For now, we don't need to store anything, but the CLI still requires us to write
+		// something, so just create an empty file.
+		file, err := os.Create(metadataPath)
+		if err != nil {
+			log.Fatalf("Failed to create overlay base metadata file: %s", err)
+		}
+		file.Close()
+	}
+}
--- a/go/ql/lib/change-notes/2025-11-11-path-transformer.md
+++ b/go/ql/lib/change-notes/2025-11-11-path-transformer.md
@@ -0,0 +1,7 @@
+---
+category: fix
+---
+* Some fixes relating to use of path transformers when extracting a database:
+  * Fixed a problem where the path transformer would be ignored when extracting older codebases that predate the use of Go modules.
+  * The environment variable `CODEQL_PATH_TRANSFORMER` is now recognized, in addition to `SEMMLE_PATH_TRANSFORMER`.
+  * Fixed some cases where the extractor emitted paths without applying the path transformer.
--- a/go/ql/lib/go.dbscheme
+++ b/go/ql/lib/go.dbscheme
@@ -36,6 +36,17 @@ snapshotDate(unique date snapshotDate : date ref);

 sourceLocationPrefix(varchar(900) prefix : string ref);

+/** Overlay support **/
+
+databaseMetadata(
+  string metadataKey: string ref,
+  string value: string ref
+);
+
+overlayChangedFiles(
+  string path: string ref
+);
+

 /*
 * XML Files
--- a/go/ql/lib/qlpack.yml
+++ b/go/ql/lib/qlpack.yml
@@ -14,3 +14,4 @@ dependencies:
 dataExtensions:
  - ext/*.model.yml
 warnOnImplicitThis: true
+compileForOverlayEval: true
--- a/go/ql/lib/semmle/go/Locations.qll
+++ b/go/ql/lib/semmle/go/Locations.qll
@@ -1,6 +1,7 @@
 /** Provides classes for working with locations and program elements that have locations. */

 import go
+private import semmle.go.Overlay

 /**
 * A location as given by a file, a start line, a start column,
--- a/Show More
+++ b/Show More