OK, here's john's patch plus my sync stuff.

chrome/browser/extensions/platform_app_browsertest.cc

 // 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.
 
 #include "base/bind.h"
 #include "base/file_util.h"
 #include "base/prefs/pref_service.h"
 #include "base/test/test_timeouts.h"
 #include "base/threading/platform_thread.h"
 #include "base/utf_string_conversions.h"
@@ skipping 768 matching lines @@
 #else
 #define MAYBE_Messaging Messaging
 #endif
 IN_PROC_BROWSER_TEST_F(PlatformAppBrowserTest, MAYBE_Messaging) {
   ExtensionApiTest::ResultCatcher result_catcher;
   LoadAndLaunchPlatformApp("messaging/app2");
   LoadAndLaunchPlatformApp("messaging/app1");
   EXPECT_TRUE(result_catcher.GetNextResult());
 }
 
-IN_PROC_BROWSER_TEST_F(PlatformAppBrowserTest, WebContentsHasFocus) {
+// TODO(linux_aura) http://crbug.com/163931
+#if defined(OS_LINUX) && !defined(OS_CHROMEOS) && defined(USE_AURA)
+#define MAYBE_WebContentsHasFocus DISABLED_WebContentsHasFocus
+#else
+#define MAYBE_WebContentsHasFocus WebContentsHasFocus
+#endif
+IN_PROC_BROWSER_TEST_F(PlatformAppBrowserTest, MAYBE_WebContentsHasFocus) {
   const Extension* extension = LoadAndLaunchPlatformApp("minimal");
   ShellWindow* window = CreateShellWindow(extension);
   EXPECT_TRUE(window->web_contents()->GetRenderWidgetHostView()->HasFocus());
   CloseShellWindow(window);
 }
 
 }  // namespace extensions