Use a hosted app's opener URL and not its origin to locate it.

chrome/browser/chrome_content_browser_client.h

 // 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.
 
 #ifndef CHROME_BROWSER_CHROME_CONTENT_BROWSER_CLIENT_H_
 #define CHROME_BROWSER_CHROME_CONTENT_BROWSER_CLIENT_H_
 #pragma once
 
 #include <set>
 #include <string>
@@ skipping 118 matching lines @@
   virtual void ShowDesktopNotification(
       const content::ShowDesktopNotificationHostMsgParams& params,
       int render_process_id,
       int render_view_id,
       bool worker) OVERRIDE;
   virtual void CancelDesktopNotification(
       int render_process_id,
       int render_view_id,
       int notification_id) OVERRIDE;
   virtual bool CanCreateWindow(
+      const GURL& opener_url,
       const GURL& source_origin,
       WindowContainerType container_type,
       content::ResourceContext* context,
       int render_process_id) OVERRIDE;
   virtual std::string GetWorkerProcessTitle(
       const GURL& url, content::ResourceContext* context) OVERRIDE;
   virtual void ResourceDispatcherHostCreated() OVERRIDE;
   virtual content::SpeechInputManagerDelegate*
       GetSpeechInputManagerDelegate() OVERRIDE;
   virtual ui::Clipboard* GetClipboard() OVERRIDE;
@@ skipping 30 matching lines @@
  private:
   // Set of origins that can use TCP/UDP private APIs from NaCl.
   std::set<std::string> allowed_socket_origins_;
 
   DISALLOW_COPY_AND_ASSIGN(ChromeContentBrowserClient);
 };
 
 }  // namespace chrome
 
 #endif  // CHROME_BROWSER_CHROME_CONTENT_BROWSER_CLIENT_H_