Some fixups for app notifications:

chrome/browser/ui/webui/ntp/app_launcher_handler.cc

 // Copyright (c) 2011 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/webui/ntp/app_launcher_handler.h"
 
 #include <string>
 #include <vector>
 
 #include "base/auto_reset.h"
@@ skipping 259 matching lines @@
                  base::Unretained(this)));
   web_ui_->RegisterMessageCallback("saveAppPageName",
       base::Bind(&AppLauncherHandler::HandleSaveAppPageName,
                  base::Unretained(this)));
   web_ui_->RegisterMessageCallback("generateAppForLink",
       base::Bind(&AppLauncherHandler::HandleGenerateAppForLink,
                  base::Unretained(this)));
   web_ui_->RegisterMessageCallback("recordAppLaunchByURL",
       base::Bind(&AppLauncherHandler::HandleRecordAppLaunchByURL,
                  base::Unretained(this)));
+  web_ui_->RegisterMessageCallback("closeNotification",
+      base::Bind(&AppLauncherHandler::HandleNotificationClose,
+                 base::Unretained(this)));
 }
 
 void AppLauncherHandler::Observe(int type,
                                  const content::NotificationSource& source,
                                  const content::NotificationDetails& details) {
   if (type == chrome::NOTIFICATION_APP_INSTALLED_TO_NTP &&
           NewTabUI::NTP4Enabled()) {
     highlight_app_id_ = *content::Details<const std::string>(details).ptr();
     if (has_loaded_apps_)
       SetAppToBeHighlighted();
@@ skipping 540 matching lines @@
   double source;
   CHECK(args->GetDouble(1, &source));
 
   extension_misc::AppLaunchBucket bucket =
       static_cast<extension_misc::AppLaunchBucket>(static_cast<int>(source));
   CHECK(source < extension_misc::APP_LAUNCH_BUCKET_BOUNDARY);
 
   RecordAppLaunchByURL(Profile::FromWebUI(web_ui_), url, bucket);
 }
 
+void AppLauncherHandler::HandleNotificationClose(const ListValue* args) {
+  std::string extension_id;
+  CHECK(args->GetString(0, &extension_id));
+
+  const Extension* extension = extension_service_->GetExtensionById(
+      extension_id, true);
+  if (!extension)
+    return;
+
+  AppNotificationManager* notification_manager =
+      extension_service_->app_notification_manager();
+  notification_manager->ClearAll(extension_id);
+}
+
 void AppLauncherHandler::OnFaviconForApp(FaviconService::Handle handle,
                                          history::FaviconData data) {
   scoped_ptr<AppInstallInfo> install_info(
       favicon_consumer_.GetClientDataForCurrentRequest());
   scoped_ptr<WebApplicationInfo> web_app(new WebApplicationInfo());
   web_app->is_bookmark_app = install_info->is_bookmark_app;
   web_app->title = install_info->title;
   web_app->app_url = install_info->app_url;
   web_app->urls.push_back(install_info->app_url);
 
@@ skipping 186 matching lines @@
 
 void AppLauncherHandler::UninstallDefaultApps() {
   AppsPromo* apps_promo = extension_service_->apps_promo();
   const ExtensionIdSet& app_ids = apps_promo->old_default_apps();
   for (ExtensionIdSet::const_iterator iter = app_ids.begin();
        iter != app_ids.end(); ++iter) {
     if (extension_service_->GetExtensionById(*iter, true))
       extension_service_->UninstallExtension(*iter, false, NULL);
   }
 }