well, you can use Linux bash scripts run from the crontab to make it start on bootup. But the only way I can think of to shut down the system on server shutdown is running the server in a screen session. Then using another script to stop the server that enters the screen session, stops the Minecraft server, and then shuts down the system. Then you'd use that script whenever you want to stop the server.
There's probably better solutions out there but that's all I've got.