Based off of your question, you've already setup apache to work as a reverse proxy for Jira I assume. Your best bet would to put this inside your virtual host section in your apache config. I don't beleive .htaccess will be an option in this configuration.
Don't forget to enable mod_rewrite with:
If you are not using apache as a reverse proxy, and only using Jira with the built in Tomcat, this will not work.
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