You can easily make your application run as a service on your hosts.
If you have few machines, you can use simple init.d service
To make your built application start as a service, all you need to do is :
sudo link -s /path/to/your/app/yourapp.jar /etc/init.d/yourappservice
And directly after that you can start the yourappservice as you have the service configured
On more complicated environments (many instances, or cloud env) you should probably use supervisor to control your services.
You can check it out here : http://supervisord.org/running.html#adding-a-program