Make javascript dialogs into top-level windows.

chrome/browser/ui/app_modal_dialogs/javascript_app_modal_dialog.cc

 // Copyright (c) 2012 The Chromium Authors. All rights reserved.
 // Use of this source code is governed by a BSD-style license that can be
 // found in the LICENSE file.
 
 #include "chrome/browser/ui/app_modal_dialogs/javascript_app_modal_dialog.h"
 
 #include "chrome/browser/browser_shutdown.h"
 #include "chrome/browser/ui/app_modal_dialogs/native_app_modal_dialog.h"
 #include "content/public/browser/web_contents.h"
 #include "content/public/browser/web_contents_view.h"
@@ skipping 66 matching lines @@
   EnforceMaxTextSize(message_text, &message_text_);
   EnforceMaxPromptSize(default_prompt_text, &default_prompt_text_);
 }
 
 JavaScriptAppModalDialog::~JavaScriptAppModalDialog() {
 }
 
 NativeAppModalDialog* JavaScriptAppModalDialog::CreateNativeDialog() {
   gfx::NativeWindow parent_window =
       web_contents()->GetView()->GetTopLevelNativeWindow();
+
 #if defined(USE_AURA)
+#if defined(OS_WIN)
+  // JS dialogs should always be top-level windows in desktop Aura on Windows.
+  parent_window = NULL;
+#else
   if (!parent_window->GetRootWindow()) {
     // When we are part of a WebContents that isn't actually being displayed on
     // the screen, we can't actually attach to it.
     parent_window = NULL;
   }
-#endif
+#endif  // defined(OS_WIN)
+#endif  // defined(USE_AURA)
+
   return NativeAppModalDialog::CreateNativeJavaScriptPrompt(this,
                                                             parent_window);
 }
 
 bool JavaScriptAppModalDialog::IsJavaScriptModalDialog() {
   return true;
 }
 
 void JavaScriptAppModalDialog::Invalidate() {
   if (!valid_)
@@ skipping 51 matching lines @@
 
   callback_.Run(success, user_input);
 
   extra_data_->last_javascript_message_dismissal_ = base::TimeTicks::Now();
   extra_data_->suppress_javascript_messages_ = suppress_js_messages;
 
   // On Views, we can end up coming through this code path twice :(.
   // See crbug.com/63732.
   valid_ = false;
 }