src/Pure/System/options.scala

 
     val prefs =
       changed.sortBy(_._1)
         .map({ case (x, y, z) => x + " = " + Outer_Syntax.quote_string(y) + z + "\n" }).mkString
 
-    Isabelle_System.mkdirs(file.dir)
+    Isabelle_System.make_directory(file.dir)
     File.write_backup(file, "(* generated by Isabelle " + Date.now() + " *)\n\n" + prefs)
   }
 }