src/Pure/System/isabelle_system.scala

 
       val cygwin_root1 =
         if (Platform.is_windows)
           bootstrap_directory(cygwin_root, "CYGWIN_ROOT", "cygwin.root", "Cygwin root")
         else ""
+
+      if (Platform.is_windows) Cygwin.init(isabelle_root1, cygwin_root1)
 
       def set_cygwin_root()
       {
         if (Platform.is_windows)
           _settings = Some(_settings.getOrElse(Map.empty) + ("CYGWIN_ROOT" -> cygwin_root1))