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This page lists a few things to be aware of when upgrading from JIRA 3.0.x to JIRA 3.1. To perform the actual upgrade, see the upgrade documentation. For upgrading from JIRA 2.x to JIRA 3.x see JIRA 3.0 Upgrade Notes

MySQL Users dB upgrade (JRA-5635)

The size of the descriptor field in the jiraworkflow table has been increased. MySQL users will see warnings when they start their app server. This can be fixed by running the SQL below. This will also allow for Workflows of up to 4GB as opposed to just 64k