In game, you can use the #worldshutdown command. You set a timer and the frequency that warnings will be displayed to everyone on the server as the countdown goes down. I normally use "#worldshutdown 300 30" and that gives a warning every 30 seconds and shuts down the server after 5 minutes.
Then, once the server is down, you can just close out of the windows. That is how I did it on windows. On linux, I use the #worldshutdown and then run the ./stop command to run the script that does the stop on the server to end the processes and clean up the log files.
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