Start menu shortcuts for apps on Windows are now inside a "Chrome Apps" submenu.

chrome/browser/web_applications/web_app_win.cc

Index: chrome/browser/web_applications/web_app_win.cc
diff --git a/chrome/browser/web_applications/web_app_win.cc b/chrome/browser/web_applications/web_app_win.cc
index 98d9e2c5bc9ffbfbe77b4e4fb721508e1844ccc5..9b326a14a85c1fad144be89daf714d52f76d2c6b 100644
--- a/chrome/browser/web_applications/web_app_win.cc
+++ b/chrome/browser/web_applications/web_app_win.cc
@@ -19,6 +19,8 @@
 #include "chrome/installer/launcher_support/chrome_launcher_support.h"
 #include "chrome/installer/util/util_constants.h"
 #include "content/public/browser/browser_thread.h"
+#include "grit/chromium_strings.h"
+#include "ui/base/l10n/l10n_util.h"
 #include "ui/gfx/icon_util.h"
 #include "ui/gfx/image/image.h"
 #include "ui/gfx/image/image_family.h"
@@ -240,6 +242,11 @@ bool CreatePlatformShortcuts(
     shortcut_properties.set_icon(icon_file, 0);
     shortcut_properties.set_app_id(app_id);
     shortcut_properties.set_dual_mode(false);
+    if (!file_util::PathExists(shortcut_file.DirName()) &&
+        !file_util::CreateDirectory(shortcut_file.DirName())) {
+      NOTREACHED();
+      return false;
+    }
     success = base::win::CreateOrUpdateShortcutLink(
         shortcut_file, shortcut_properties,
         base::win::SHORTCUT_CREATE_ALWAYS) && success;
@@ -283,6 +290,10 @@ void DeletePlatformShortcuts(
   all_shortcut_locations.in_applications_menu = true;
   all_shortcut_locations.in_quick_launch_bar = true;
   all_shortcut_locations.on_desktop = true;
+  // Delete shortcuts from the Chrome Apps subdirectory.
+  // This matches the subdir name set by CreateApplicationShortcutView::Accept.
+  all_shortcut_locations.applications_menu_subdir =
+      l10n_util::GetStringUTF16(IDS_APP_SHORTCUTS_SUBDIR_NAME);
   std::vector<base::FilePath> shortcut_paths = GetShortcutPaths(
       all_shortcut_locations);
   if (base::win::GetVersion() >= base::win::VERSION_WIN7)