You won't be able to do this really - your JIRA lives on the atlassian.net on the url given, and it only uses that url, so the best you can do is proxy bugs.mywebsite.com to the Cloud server, and accept that as soon as anyone clicks on a link, they'll land on myjirainstance.atlassian.com. I'd not bother, just put a simple redirect on a dummy page at bugs.mywebsite.com
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