Some fixups for app notifications:

chrome/browser/resources/ntp4/apps_page.js

 // 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.
 
 cr.define('ntp4', function() {
   'use strict';
 
   var localStrings = new LocalStrings;
 
   var APP_LAUNCH = {
@@ skipping 283 matching lines @@
         this.appImgSrc_ = null;
       }
       this.classList.remove('icon-loading');
     },
 
     // Shows a notification text below the app icon and stuffs the attributes
     // necessary to show the bubble when the user clicks on the notification
     // text.
     setupNotification_: function(notification) {
       // Remove the old notification from this node (if any).
-      if (this.appNotification_)
+      if (this.appNotification_ && this.appNotification_.parentNode)
         this.appNotification_.parentNode.removeChild(this.appNotification_);
 
       if (notification) {
         // Add a new notification to this node.
         var appNotification = this.ownerDocument.createElement('span');
         appNotification.className = 'app-notification';
         appNotification.textContent = notification['title'];
         appNotification.addEventListener('click',
                                          this.onNotificationClick_.bind(this));
         appNotification.notificationTitle = notification['title'];
@@ skipping 133 matching lines @@
       messageDiv.textContent = message;
       container.appendChild(messageDiv);
       if (link && linkMessage) {
         var anchor = this.ownerDocument.createElement('a');
         anchor.href = link;
         anchor.textContent = linkMessage;
         container.appendChild(anchor);
       }
 
       var infoBubble = new cr.ui.Bubble;
+      infoBubble.appId = this.appData_.id;
       infoBubble.anchorNode = e.target;
       infoBubble.content = container;
+      infoBubble.handleCloseEvent = function() {
+        chrome.send('closeNotification', [this.appId]);
+        this.hide();
+      };
       infoBubble.show();
     },
 
     /**
      * Adds a node to the list of targets that will launch the app. This list
      * is also used in onMousedown to determine whether the app contents should
      * be shown as active (if we don't do this, then clicking anywhere in
      * appContents, even a part that is outside the ideally clickable region,
      * will cause the app icon to look active).
      * @param {HTMLElement} node The node that should be clickable.
@@ skipping 321 matching lines @@
     appNotificationChanged: appNotificationChanged,
     AppsPage: AppsPage,
     launchAppAfterEnable: launchAppAfterEnable,
   };
 });
 
 // TODO(estade): update the content handlers to use ntp namespace instead of
 // making these global.
 var appNotificationChanged = ntp4.appNotificationChanged;
 var launchAppAfterEnable = ntp4.launchAppAfterEnable;