Make sure that TopLevel is no longer the actual root of the visual tree. This is needed for our future changes.

src/Avalonia.Base/Input/FocusManager.cs

@@ -13,7 +13,8 @@ namespace Avalonia.Input
     /// Manages focus for the application.
     /// </summary>
     [PrivateApi]
-    public class FocusManager : IFocusManager
+    public class 
+        FocusManager : IFocusManager
     {
         /// <summary>
         /// Private attached property for storing the currently focused element in a focus scope.
@@ -246,10 +247,10 @@ namespace Avalonia.Input
             if (scope is not Visual v)
                 return null;
 
-            var root = v.VisualRoot as Visual;
+            var root = v.PresentationSource?.InputRoot.FocusRoot as Visual;
 
             while (root is IHostedVisualTreeRoot hosted &&
-                hosted.Host?.VisualRoot is Visual parentRoot)
+                hosted.Host?.PresentationSource?.InputRoot.FocusRoot is {} parentRoot)
             {
                 root = parentRoot;
             }

src/Avalonia.Base/Input/IInputRoot.cs

@@ -26,5 +26,10 @@ namespace Avalonia.Input
         internal ITextInputMethodImpl? InputMethod { get; }
         
         internal InputElement RootElement { get; }
+        
+        // HACK: This is a temporary hack for "default focus" concept. 
+        // If nothing is focused we send keyboard events to Window. Since for now we always
+        // control PresentationSource, we simply pass the TopLevel as a separate parameter there.
+        internal InputElement FocusRoot { get; }
     }
 }

src/Avalonia.Base/Input/KeyboardDevice.cs

@@ -225,7 +225,7 @@ namespace Avalonia.Input
             if(e.Handled)
                 return;
 
-            var element = FocusedElement ?? e.Root.RootElement;
+            var element = FocusedElement ?? e.Root.FocusRoot;
 
             if (e is RawKeyEventArgs keyInput)
             {

src/Avalonia.Base/VisualTree/IHostedVisualTreeRoot.cs

@@ -3,7 +3,7 @@ namespace Avalonia.VisualTree
     /// <summary>
     /// Interface for controls that are at the root of a hosted visual tree, such as popups.
     /// </summary>
-    public interface IHostedVisualTreeRoot
+    internal interface IHostedVisualTreeRoot
     {
         /// <summary>
         /// Gets the visual tree host.

src/Avalonia.Controls/Automation/Peers/EmbeddableControlRootAutomationPeer.cs

@@ -59,7 +59,7 @@ namespace Avalonia.Controls.Automation.Peers
             var oldFocus = _focus;
             var c = focus as Control;
             
-            _focus = c?.VisualRoot == Owner ? c : null;
+            _focus = Owner.IsVisualAncestorOf(c) ? c : null;
 
             if (_focus != oldFocus)
             {

src/Avalonia.Controls/Automation/Peers/WindowBaseAutomationPeer.cs

@@ -70,7 +70,7 @@ namespace Avalonia.Automation.Peers
             var oldFocus = _focus;
             var c = focus as Control;
             
-            _focus = c?.VisualRoot == Owner ? c : null;
+            _focus = Owner.IsVisualAncestorOf(c) ? c : null;
             
             if (_focus != oldFocus)
             {

src/Avalonia.Controls/PresentationSource/PresentationSource.Input.cs

@@ -57,4 +57,6 @@ internal partial class PresentationSource
         }
         return candidate;
     }
+    
+    public InputElement FocusRoot { get; }
 }

src/Avalonia.Controls/PresentationSource/PresentationSource.cs

@@ -19,7 +19,8 @@ internal partial class PresentationSource : IPresentationSource, IInputRoot, IDi
 
     internal FocusManager FocusManager { get; } = new();
 
-    public PresentationSource(InputElement rootVisual, ITopLevelImpl platformImpl,
+    public PresentationSource(InputElement rootVisual, InputElement defaultFocusVisual,
+        ITopLevelImpl platformImpl,
         IAvaloniaDependencyResolver dependencyResolver, Func<Size> clientSizeProvider)
     {
         _clientSizeProvider = clientSizeProvider;
@@ -41,6 +42,7 @@ internal partial class PresentationSource : IPresentationSource, IInputRoot, IDi
         LayoutManager = CreateLayoutManager();
         
         RootVisual = rootVisual;
+        FocusRoot = defaultFocusVisual;
     }
 
     // In WPF it's a Visual and it's nullable. For now we have it as non-nullable InputElement since 

src/Avalonia.Controls/ToolTipService.cs

@@ -38,7 +38,7 @@ namespace Avalonia.Controls
             if (e is RawPointerEventArgs pointerEvent)
             {
                 bool isTooltipEvent = false;
-                if (_tipControl?.GetValue(ToolTip.ToolTipProperty) is { } currentTip && e.Root.RootElement == currentTip.PopupHost)
+                if (_tipControl?.GetValue(ToolTip.ToolTipProperty) is { } currentTip && e.Root == (currentTip.PopupHost as Visual)?.GetInputRoot())
                 {
                     isTooltipEvent = true;
                     _lastTipEventTime = pointerEvent.Timestamp;

src/Avalonia.Controls/TopLevel.cs

@@ -189,8 +189,12 @@ namespace Avalonia.Controls
             PlatformImpl = impl ?? throw new InvalidOperationException(
                 "Could not create window implementation: maybe no windowing subsystem was initialized?");
             dependencyResolver ??= AvaloniaLocator.Current;
-            _source = new PresentationSource(this, impl, dependencyResolver, () => ClientSize);
-            _source.RootVisual = this;
+
+            var hostVisual = new TopLevelHost(this);
+            ((ISetLogicalParent)hostVisual).SetParent(this);
+
+            _source = new PresentationSource(hostVisual, this,
+                impl, dependencyResolver, () => ClientSize);
             _source.Renderer.SceneInvalidated += SceneInvalidated;
 
             _scaling = ValidateScaling(impl.RenderScaling);

src/Avalonia.Controls/TopLevelHost.cs

@@ -0,0 +1,21 @@
+using Avalonia.Input;
+
+namespace Avalonia.Controls;
+
+/// <summary>
+/// For now this is a stub class that is needed to prevent people from assuming that TopLevel sits at the root of the
+/// visual tree.
+/// In future 12.x releases it will serve more roles like hosting popups and CSD.
+/// </summary>
+internal class TopLevelHost : Control
+{
+    static TopLevelHost()
+    {
+        KeyboardNavigation.TabNavigationProperty.OverrideDefaultValue<TopLevelHost>(KeyboardNavigationMode.Cycle);
+    }
+
+    public TopLevelHost(TopLevel tl)
+    {
+        VisualChildren.Add(tl);
+    }
+}

src/Avalonia.X11/X11Window.cs

@@ -268,8 +268,8 @@ namespace Avalonia.X11
                     : Task.FromResult<IStorageProvider?>(null),
                 () => GtkSystemDialog.TryCreate(this),
                 // TODO: This will be incompatible with "root element is not a TopLevel" scenarios,
-                // we should probably have a separate API for this
-                () => Task.FromResult(InputRoot.RootElement is TopLevel tl
+                // HACK: this relies on focus root being TopLevel which currently is true
+                () => Task.FromResult(InputRoot.FocusRoot is TopLevel tl
                     ? (IStorageProvider?)new ManagedStorageProvider(tl)
                     : null)
             });

tests/Avalonia.Base.UnitTests/Rendering/CompositorInvalidationClippingTests.cs

@@ -15,6 +15,8 @@ public class CompositorInvalidationClippingTests : CompositorTestsBase
         return count;
     }
 
+    private const int TopLevelOverhead = 2; // TopLevel + TopLevelHost
+    
     [Theory,
         // If canvas itself has no background, the second render won't draw any visuals at all, since
         // root visual's subtree bounds will exactly match the second visual 
@@ -22,9 +24,9 @@ public class CompositorInvalidationClippingTests : CompositorTestsBase
         InlineData(true, false, false, 1, 0),
         InlineData(false, true, false, 1, 0),
         // If canvas has background, the second render will draw only the canvas visual itself
-        InlineData(false, false, true, 5, 4),
-        InlineData(true, false,   true,5, 4),
-        InlineData(false, true,  true, 5, 4),
+        InlineData(false, false, true, 4 + TopLevelOverhead, 3 + TopLevelOverhead),
+        InlineData(true, false,   true,4 + TopLevelOverhead, 3 + TopLevelOverhead),
+        InlineData(false, true,  true, 4 + TopLevelOverhead, 3 + TopLevelOverhead),
     ]
     public void Do_Not_Re_Render_Unaffected_Visual_Trees(bool clipToBounds, bool clipGeometry,
         bool canvasHasContent,

tests/Avalonia.Controls.UnitTests/FlyoutTests.cs

@@ -256,7 +256,7 @@ namespace Avalonia.Controls.UnitTests
                 var hitTester = new Mock<IHitTester>();
                 window.HitTesterOverride = hitTester.Object;
                 hitTester.Setup(x =>
-                    x.HitTestFirst(new Point(90, 90), window, It.IsAny<Func<Visual, bool>>()))
+                    x.HitTestFirst(new Point(90, 90), (Visual)window.VisualRoot!, It.IsAny<Func<Visual, bool>>()))
                     .Returns(button);
 
                 var e = CreatePointerPressedEventArgs(window, new Point(90, 90));
@@ -299,7 +299,7 @@ namespace Avalonia.Controls.UnitTests
                 var hitTester = new Mock<IHitTester>();
                 window.HitTesterOverride = hitTester.Object;
                 hitTester.Setup(x =>
-                    x.HitTestFirst(new Point(90, 90), window, It.IsAny<Func<Visual, bool>>()))
+                    x.HitTestFirst(new Point(90, 90), (Visual)window.VisualRoot!, It.IsAny<Func<Visual, bool>>()))
                     .Returns(button);
 
                 var e = CreatePointerPressedEventArgs(window, new Point(90, 90));

tests/Avalonia.Controls.UnitTests/Primitives/PopupRootTests.cs

@@ -100,7 +100,7 @@ namespace Avalonia.Controls.UnitTests.Primitives
         }
         
         [Fact]
-        public void PopupRoot_Should_Have_Null_VisualParent()
+        public void PopupRoot_Should_Have_TopLevelHost_VisualParent()
         {
             using (UnitTestApplication.Start(TestServices.StyledWindow))
             {
@@ -108,7 +108,7 @@ namespace Avalonia.Controls.UnitTests.Primitives
 
                 target.Open();
 
-                Assert.Null(((Visual)target.Host!).GetVisualParent());
+                Assert.IsType<TopLevelHost>(((Visual)target.Host!).GetVisualParent());
             }
         }
         

tests/Avalonia.Controls.UnitTests/Primitives/PopupTests.cs

@@ -607,7 +607,7 @@ namespace Avalonia.Controls.UnitTests.Primitives
                 window.Content = border;
 
                 hitTester.Setup(x =>
-                    x.HitTestFirst(new Point(10, 15), window, It.IsAny<Func<Visual, bool>>()))
+                    x.HitTestFirst(new Point(10, 15), (Visual)window.VisualRoot!, It.IsAny<Func<Visual, bool>>()))
                     .Returns(border);
 
                 border.PointerPressed += (s, e) =>

tests/Avalonia.Controls.UnitTests/ToolTipTests.cs

@@ -26,7 +26,7 @@ namespace Avalonia.Controls.UnitTests
             var toolTip = control.GetValue(ToolTip.ToolTipProperty);
             Assert.NotNull(toolTip);
             Assert.IsType<PopupRoot>(toolTip.PopupHost);
-            Assert.Same(toolTip.VisualRoot, toolTip.PopupHost);
+            Assert.Same(TopLevel.GetTopLevel(toolTip), toolTip.PopupHost);
         }
     }
 
@@ -574,7 +574,7 @@ namespace Avalonia.Controls.UnitTests
                     point = new Point(id, int.MaxValue);
                 }
 
-                hitTesterMock.Setup(m => m.HitTestFirst(point, window, It.IsAny<Func<Visual, bool>>()))
+                hitTesterMock.Setup(m => m.HitTestFirst(point, It.IsAny<Visual>(), It.IsAny<Func<Visual, bool>>()))
                     .Returns(control);
 
                 var root = control?.GetInputRoot() ?? window.InputRoot;
@@ -585,7 +585,7 @@ namespace Avalonia.Controls.UnitTests
 
                 if (lastRoot != null && lastRoot != root)
                 {
-                    ((TopLevel)lastRoot.RootElement)?.PlatformImpl?.Input?.Invoke(new RawPointerEventArgs(s_mouseDevice, timestamp,
+                    ((PresentationSource)lastRoot)?.PlatformImpl?.Input?.Invoke(new RawPointerEventArgs(s_mouseDevice, timestamp,
                         lastRoot, RawPointerEventType.LeaveWindow, new Point(-1,-1), RawInputModifiers.None));
                 }
 

tests/Avalonia.Controls.UnitTests/TopLevelTests.cs

@@ -222,7 +222,7 @@ namespace Avalonia.Controls.UnitTests
         }
 
         [Fact]
-        public void Adding_Top_Level_As_Child_Should_Not_Exception()
+        public void Adding_Top_Level_As_Child_Should_Throw_Exception()
         {
             using (UnitTestApplication.Start(TestServices.StyledWindow))
             {
@@ -233,8 +233,7 @@ namespace Avalonia.Controls.UnitTests
                 target.Template = CreateTemplate();
                 target.Content = child;
                 target.ApplyTemplate();
-
-                target.Presenter!.ApplyTemplate();
+                Assert.Throws<InvalidOperationException>(() => target.Presenter!.ApplyTemplate());
             }
         }
 

tests/Avalonia.RenderTests/TestRenderRoot.cs

@@ -75,6 +75,6 @@ namespace Avalonia.Skia.RenderTests
         public IInputElement? PointerOverElement { get; set; }
         public ITextInputMethodImpl? InputMethod { get; }
         public InputElement RootElement => this;
-
+        public InputElement FocusRoot => this;
     }
 }

tests/Avalonia.UnitTests/TestRoot.cs

@@ -80,6 +80,7 @@ namespace Avalonia.UnitTests
         public IInputElement? PointerOverElement { get; set; }
         public ITextInputMethodImpl? InputMethod { get; }
         public InputElement RootElement => this;
+        public InputElement FocusRoot => this;
 
         public bool ShowAccessKeys { get; set; }