This question is in reference to Atlassian Documentation: Federating JIRA - Managing Multiple Instances
When federating multiple instances, is there a difference between SaaS vs on-prem JIRA?
Yes - there are differences in the add-ons, user directory options, configuration flexibility and code stability ("Stablity" isn't what it sounds like - both platforms are stable, but Cloud is updated with the latest version frequently, and updates can easily change your interfaces. Cloud is not stable in terms of what is deployed on it - you can see several mass code changes within a few weeks)
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