Application shortcuts in Linux are now installed into a "Chrome Apps" folder.

chrome/browser/ui/gtk/create_application_shortcuts_dialog_gtk.h

 // 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.
 
 #ifndef CHROME_BROWSER_UI_GTK_CREATE_APPLICATION_SHORTCUTS_DIALOG_GTK_H_
 #define CHROME_BROWSER_UI_GTK_CREATE_APPLICATION_SHORTCUTS_DIALOG_GTK_H_
 
 #include "base/basictypes.h"
 #include "base/compiler_specific.h"
 #include "base/memory/ref_counted.h"
@@ skipping 52 matching lines @@
   virtual void ShowErrorDialog();
 
   GtkWindow* parent_;
 
   // UI elements.
   GtkWidget* desktop_checkbox_;
   GtkWidget* menu_checkbox_;
 
   // ShortcutInfo for the new shortcut.
   ShellIntegration::ShortcutInfo shortcut_info_;
+  string16 shortcut_menu_subdir_;
 
   // Image associated with the site or app, scaled to the appropriate size to
   // display in the dialog box.
   GdkPixbuf* favicon_pixbuf_;
 
   // Dialog box that allows the user to create an application shortcut.
   GtkWidget* create_dialog_;
 
   // Dialog box that shows the error message.
   GtkWidget* error_dialog_;
@@ skipping 48 matching lines @@
   void OnShortcutInfoLoaded(
       const ShellIntegration::ShortcutInfo& shortcut_info);
 
  private:
   const extensions::Extension* app_;
   base::FilePath profile_path_;
   DISALLOW_COPY_AND_ASSIGN(CreateChromeApplicationShortcutsDialogGtk);
 };
 
 #endif  // CHROME_BROWSER_UI_GTK_CREATE_APPLICATION_SHORTCUTS_DIALOG_GTK_H_