src/Pure/Tools/build.scala

           session.init_protocol_handler(handler)
 
           val session_result = Future.promise[Process_Result]
 
           Isabelle_Process.start(session, options, logic = parent, cwd = info.dir.file, env = env,
-            sessions_structure = Some(deps.sessions_structure), store = store,
+            sessions_structure = Some(deps.sessions_structure), store = Some(store),
             phase_changed =
             {
               case Session.Ready => session.protocol_command("build_session", args_yxml)
               case Session.Terminated(result) => session_result.fulfill(result)
               case _ =>

             if (Sessions.is_pure(name)) {
               ML_Process(options, raw_ml_system = true, cwd = info.dir.file,
                 args =
                   (for ((root, _) <- Thy_Header.ml_roots) yield List("--use", root)).flatten :::
                   List("--eval", eval),
-                env = env, sessions_structure = Some(deps.sessions_structure), store = store,
+                env = env, sessions_structure = Some(deps.sessions_structure), store = Some(store),
                 cleanup = () => args_file.delete)
             }
             else {
               ML_Process(options, parent, List("--eval", eval), cwd = info.dir.file,
-                env = env, sessions_structure = Some(deps.sessions_structure), store = store,
+                env = env, sessions_structure = Some(deps.sessions_structure), store = Some(store),
                 cleanup = () => args_file.delete)
             }
 
           process.result(
             progress_stdout = (line: String) =>

     sessions: List[String] = Nil,
     selection: Sessions.Selection = Sessions.Selection.empty): Results =
   {
     val build_options = options.int.update("completion_limit", 0).bool.update("ML_statistics", true)
 
-    val store = Sessions.store(system_mode)
+    val store = Sessions.store(build_options, system_mode)
 
 
     /* session selection and dependencies */
 
     val full_sessions =