[Aura] Support always-on-top top level window.

ui/aura_shell/shell.cc

Index: ui/aura_shell/shell.cc
diff --git a/ui/aura_shell/shell.cc b/ui/aura_shell/shell.cc
index c16b63cd4313cb1206a4b0ff5d710de427a78229..dc40423beb690ee3840f3c19588454a8548f6f58 100644
--- a/ui/aura_shell/shell.cc
+++ b/ui/aura_shell/shell.cc
@@ -92,6 +92,9 @@ Shell::Shell(ShellDelegate* delegate)
 }
 
 Shell::~Shell() {
+  DCHECK(instance_ == this);
+  instance_ = NULL;
+
   // Make sure we delete WorkspaceController before launcher is
   // deleted as it has a reference to launcher model.
   workspace_controller_.reset();
@@ -130,6 +133,11 @@ void Shell::Init() {
     (*i)->Show();
   }
 
+  internal::StackingController* stacking_controller =
+      static_cast<internal::StackingController*>(
+          desktop_window->stacking_client());
+  stacking_controller->Init();
+
   internal::DesktopLayoutManager* desktop_layout =
       new internal::DesktopLayoutManager(desktop_window);
   desktop_window->SetLayoutManager(desktop_layout);