Don't include hidden windows in IsAppWindowRegisteredInAnyProfile.

chrome/browser/ui/cocoa/apps/quit_with_apps_controller_mac.cc

 // Copyright 2014 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/cocoa/apps/quit_with_apps_controller_mac.h"
 
 #include "base/command_line.h"
 #include "base/i18n/number_formatting.h"
 #include "base/prefs/pref_registry_simple.h"
 #include "base/prefs/pref_service.h"
@@ skipping 133 matching lines @@
           web_app::GetExtensionIdFromApplicationName(browser->app_name()),
           ExtensionRegistry::ENABLED);
       if (extension->is_hosted_app()) {
         hosted_apps_open = true;
         break;
       }
     }
 
     // Quit immediately if there are no packaged app windows or hosted apps open
     // or the confirmation has been suppressed. Ignore panels.
-    if (!AppWindowRegistryUtil::IsAppWindowRegisteredInAnyProfile(
+    if (!AppWindowRegistryUtil::IsAppWindowVisibleInAnyProfile(
             extensions::AppWindow::WINDOW_TYPE_DEFAULT) &&
         !hosted_apps_open) {
       return true;
     }
   } else {
     // Quit immediately if there are no windows or the confirmation has been
     // suppressed.
-    if (!AppWindowRegistryUtil::IsAppWindowRegisteredInAnyProfile(
+    if (!AppWindowRegistryUtil::IsAppWindowVisibleInAnyProfile(
             extensions::AppWindow::WINDOW_TYPE_DEFAULT))
       return true;
   }
 
   // If there are browser windows, and this notification has been suppressed for
   // this session or permanently, then just return false to prevent Chrome from
   // quitting. If there are no browser windows, or Chrome is restarting, always
   // show the notification.
   bool is_restart = g_browser_process->local_state()->GetBoolean(
       prefs::kRestartLastSessionOnShutdown);
@@ skipping 24 matching lines @@
 
   // Always return false, the notification UI can be used to quit all apps which
   // will cause Chrome to quit.
   return false;
 }
 
 // static
 void QuitWithAppsController::RegisterPrefs(PrefRegistrySimple* registry) {
   registry->RegisterBooleanPref(prefs::kNotifyWhenAppsKeepChromeAlive, true);
 }