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Upgrade question

We have been running Openfire since it was called Jive. I am currently running version 3.5.2 and would like to upgrade to the newest version. The problem is through all the years we have ended up with tables that aren’t used (from plugins that were removed) and just have general junk in our DB. it is to a point that our DB is so overfilled with archives and what not, that when I do a DB dump it takes me about 45 minutes and disconnects / delays messages.

Has anyone had any luck upgrading select tables such as roster/group/user only and kind of starting clean?