Ugh, why? A properly configured system should just run and keep running. For years if there's no failure... oh... hang on, you're running Windows... Sorry.
Anyway, your best bet is to install Jira as a service and make sure it behaves the stop-start commands issued by the service manager. Set it to automatic start, and it will restart as the machine comes back up after reboot. The only issue I've run into with this is that you have to be certain that the database is available before the Jira service starts, or it will error and then sit there until you make it available and restart it.
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