Files to replace on update

[Rekuen]

Hi, I'm making a script for Linux, that I will put on a cronjob, that will check if the server is online every 5 minutes, if not, it will download the latest build from http://builds.cuberite.org/ , update the server and start it again.

I would like to know what files should I replace on update, or what files I should not change.

I will publish a guide, with the update script, the stop script and the cronjob, so people could use it.

The result should be 2 cronjobs, one that checks if the server is online and if not update it, and one that stops the server in case is running to update it every X days.

And about the stop script , it is possible from a bash script to echo some message into the server, to warn the online users that the server is going down for update?
   
Thanks in advance.