I've spent some time Ansiblizing JIRA and realize docker might make more sense for what we need. Will we end up getting rejected for support if for some reason we had an issue with this particular form of deploying JIRA?
I want to upvote this question again and again, but merely have a single vote, but it's yours. I am pretty sure you know the answer to this question. Anything as futuristic like Dockers, SSL or apache rewrite proxies will unfortunately push past the modest boundaries once outlined, then written in stone by our humble masters.
So, the question is, how would Atlassian Support know that you deployed JIRA using Docker? I've deployed the standard JIRA package in many ways before now and I usually explain how it was deployed, and then prove that any changes in the deployed package are still within the realms of something that is reasonable to support. Use the same Java version that is supported etc
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