Fix window shape on Linux/windows by re-adding call to SetShape().

chrome/browser/ui/views/apps/chrome_native_app_window_views.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/views/apps/chrome_native_app_window_views.h"
 
 #include "apps/ui/views/app_window_frame_view.h"
 #include "base/command_line.h"
 #include "chrome/app/chrome_command_ids.h"
 #include "chrome/browser/app_mode/app_mode_utils.h"
@@ skipping 661 matching lines @@
   }
   chrome::DrawTaskbarDecoration(GetNativeWindow(), icon);
 }
 
 void ChromeNativeAppWindowViews::UpdateShape(scoped_ptr<SkRegion> region) {
   bool had_shape = shape_;
   shape_ = region.Pass();
 
   aura::Window* native_window = widget()->GetNativeWindow();
   if (shape_) {
+    widget()->SetShape(new SkRegion(*shape_));
     native_window->layer()->SetAlphaShape(
         make_scoped_ptr(new SkRegion(*shape_)));
     if (!had_shape) {
       native_window->SetEventTargeter(scoped_ptr<ui::EventTargeter>(
           new ShapedAppWindowTargeter(native_window, this)));
     }
   } else {
     widget()->SetShape(NULL);
     if (had_shape)
       native_window->SetEventTargeter(scoped_ptr<ui::EventTargeter>());
@@ skipping 26 matching lines @@
     InitializePanelWindow(create_params);
   } else {
     InitializeDefaultWindow(create_params);
   }
   extension_keybinding_registry_.reset(new ExtensionKeybindingRegistryViews(
       Profile::FromBrowserContext(app_window->browser_context()),
       widget()->GetFocusManager(),
       extensions::ExtensionKeybindingRegistry::PLATFORM_APPS_ONLY,
       NULL));
 }