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On my on-premise Jira server used to test migration to cloud, I've got 5 user-installed apps that have to be renewed.
How is this handled by Migration Assistant?
Jira Cloud Migration Assistant tool does not migrate any 3rd party apps. you will have to check with individual vendors if they have a migration pathway. As of today, many major plugin vendors in the marketplace have a migration pathway. Raising support reuest with vendors can also be helpful so they can provide you the documentation and assistance required to migrate app data to cloud. Let me know if you need any help on this.
The migration assistant does not care about the local version of Apps. It will gladly migrate, send off the data to the vendor, and let the vendor's process fail, resulting in you having to repeat the migration from scratch.
I recommend checking the vendor's Migration pathway documentation (link on Marketplace listing), as some require the latest Server/DC version, while others do not. It all depends on their migration needs and process (Atlassian passes this off to them).