This depends on the plugin, not all plugins are compatible with even a minor JIRA upgrade, so it has happened to us that plugins that were licensed in JIRA 4 worked in JIRA 5.x but could not be upgraded due to having to repurchase (paid updates) for a new license and once we moved to 6.2.1 the were no longer working. If it's a critical plugin i would suggest paying for it or start thinking of how to work without it.
I have multiple projects that use variations of the same base workflow. The variations depend on the requirements of the project or issue type. The variations mostly come in the form of new statuses ...
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