When you start a server that has already been running, it prompts for a new name. If you give it a new name, none of the settings you already had in the original server's server.json make it on the new server. So the first commit simply copies the server.json from orig server to the "server-#name#.json" file that would be created for the newly started server. This way, all the properties of the orig server are present on the second server.
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https://github.com/Ortus-Solutions/commandbox/pull/111