demote 'system_thread' to just 'system_context'

demote 'system_thread' to just 'system_context'

I don't need the extra 'class Thread' metadata for the ModelChecker 'system
thread,' and the dual use of class Thread for both system and user threads was
causing problems. So I separate them: class Thread is used only for user
threads. This changes a few interfaces throughout the code.