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

chrome/browser/ui/gtk/create_application_shortcuts_dialog_gtk.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 "chrome/browser/ui/gtk/create_application_shortcuts_dialog_gtk.h"
 
 #include <string>
 
 #include "base/bind.h"
 #include "base/environment.h"
@@ skipping 197 matching lines @@
 void CreateApplicationShortcutsDialogGtk::OnCreateDialogResponse(
     GtkWidget* widget, int response) {
   DCHECK(BrowserThread::CurrentlyOn(BrowserThread::UI));
 
   if (response == GTK_RESPONSE_ACCEPT) {
     ShellIntegration::ShortcutLocations creation_locations;
     creation_locations.on_desktop =
         gtk_toggle_button_get_active(GTK_TOGGLE_BUTTON(desktop_checkbox_));
     creation_locations.in_applications_menu =
         gtk_toggle_button_get_active(GTK_TOGGLE_BUTTON(menu_checkbox_));
+    creation_locations.applications_menu_subdir = shortcut_menu_subdir_;
     BrowserThread::PostTask(BrowserThread::FILE, FROM_HERE,
         base::Bind(&CreateApplicationShortcutsDialogGtk::CreateDesktopShortcut,
                    this, shortcut_info_, creation_locations));
 
     OnCreatedShortcut();
   } else {
     Release();
   }
 }
 
@@ skipping 65 matching lines @@
 CreateWebApplicationShortcutsDialogGtk::CreateWebApplicationShortcutsDialogGtk(
     GtkWindow* parent,
     content::WebContents* web_contents)
   : CreateApplicationShortcutsDialogGtk(parent),
     web_contents_(web_contents) {
 
   // Get shortcut information now, it's needed for our UI.
   web_app::GetShortcutInfoForTab(web_contents, &shortcut_info_);
   CreateIconPixBuf(shortcut_info_.favicon);
 
+  // NOTE: Leave shortcut_menu_subdir_ blank to create URL app shortcuts in the
+  // top-level menu.
+
   CreateDialogBox(parent);
 }
 
 void CreateWebApplicationShortcutsDialogGtk::OnCreatedShortcut() {
   Browser* browser = chrome::FindBrowserWithWebContents(web_contents_);
   if (browser)
     chrome::ConvertTabToAppWindow(browser, web_contents_);
 }
 
 CreateChromeApplicationShortcutsDialogGtk::
     CreateChromeApplicationShortcutsDialogGtk(
         GtkWindow* parent,
         Profile* profile,
         const Extension* app)
       : CreateApplicationShortcutsDialogGtk(parent),
         app_(app),
         profile_path_(profile->GetPath())  {
 
+  // Place Chrome app shortcuts in the "Chrome Apps" submenu.
+  shortcut_menu_subdir_ =
+      l10n_util::GetStringUTF16(IDS_APP_SHORTCUTS_SUBDIR_NAME);
+
   // Get shortcut information and icon now; they are needed for our UI.
   web_app::UpdateShortcutInfoAndIconForApp(
       *app, profile,
       base::Bind(
           &CreateChromeApplicationShortcutsDialogGtk::OnShortcutInfoLoaded,
           this));
 }
 
 // Called when the app's ShortcutInfo (with icon) is loaded.
 void CreateChromeApplicationShortcutsDialogGtk::OnShortcutInfoLoaded(
@@ skipping 10 matching lines @@
   DCHECK(BrowserThread::CurrentlyOn(BrowserThread::FILE));
 
   if (web_app::CreateShortcutsOnFileThread(shortcut_info, creation_locations)) {
     Release();
   } else {
     BrowserThread::PostTask(BrowserThread::UI, FROM_HERE,
         base::Bind(&CreateChromeApplicationShortcutsDialogGtk::ShowErrorDialog,
                    this));
   }
 }