src/Pure/System/isabelle_process.scala

       command_input = input_actor(command_stream)
       val message = message_actor(message_stream)
 
       val rc = process_result.join
       system_output("process terminated")
+      close_input()
       for ((thread, _) <- List(standard_input, stdout, stderr, command_input, message))
         thread.join
       system_output("process_manager terminated")
       exit_message(rc)
     }

 
   def join() { process_manager.join() }
 
   def terminate()
   {
-    close()
+    close_input()
     system_output("Terminating Isabelle process")
     terminate_process()
   }
 
 

   {
     receiver(new Input(name, args.toList))
     input_bytes(name, args.map(Standard_System.string_bytes): _*)
   }
 
-  def close(): Unit = { close(command_input); close(standard_input) }
+  def close_input(): Unit = { close(command_input); close(standard_input) }
 }