src/Pure/System/options.ML

   (case getenv "ISABELLE_PROCESS_OPTIONS" of
     "" => ()
   | name =>
       let val path = Path.explode name in
         (case try File.read path of
-          SOME s => (set_default (decode (YXML.parse_body s)); ignore (try File.rm path))
+          SOME s =>
+            (set_default (decode (YXML.parse_body s));
+             if default_bool "ML_system_bootstrap" then () else ignore (try File.rm path))
         | NONE => ())
       end);
 
 val _ = load_default ();
 val _ = ML_Pretty.print_depth (default_int "ML_print_depth");