An important feature is the ability for users to modify data that has been imported and protect imported data from being modified.
Can you please provide more information as to what you mean by this? What data do you believe should be protected and what imported data should a user be able to modify?
In regards to the database itself, that needs to be locked down and any access to the folders JIRA acceses needs to be locked down locally.
If there are specific features you believe should be implemented I would also recommend going to JAC and creating a Suggestion. This will get the issue in front of the developers and they can consider implementing the feature in the future. If you do create a JAC ticket please provide the link so the Community can vote on it.
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