Some fixups for app notifications:

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

Index: chrome/browser/ui/webui/ntp/app_launcher_handler.cc
===================================================================
--- chrome/browser/ui/webui/ntp/app_launcher_handler.cc	(revision 106989)
+++ chrome/browser/ui/webui/ntp/app_launcher_handler.cc	(working copy)
@@ -277,6 +277,9 @@
   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,
@@ -837,6 +840,20 @@
   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(