In a live deployment you would not usually want to stop and start Elixir Repertoire Server manually but will want it to run in the background as a service or daemon when the machine is booted up. The details of how to do this will vary between platforms and will require some system administration knowledge and root privileges.
On Linux or other Unix like systems, you have to modify the startServer.sh file to specific to the Unix platform. On a Windows system, you can use a utility such as the Java Service Wrapper to deploy the server as a Window server service. The bin directory contains an example script. To run Repertoire Server as a Windows service, be sure to copy your server licence file into the RepertoireServer\ext directory. For latest information, please read windows-service-readme.txt in the RepertoireServer\bin directory. You may refer to http://wrapper.tanukisoftware.org/ for in-depth discussion of this product.
Specific details for running the server as a system service are described on the web at http://www.elixirtech.com/. Choose the Support menu option and check for your specific platform in the online documentation.