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who are not logged into jira/jira service desk/confluence past 90 days export user list and send notification to user automatically.
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There is "no out of the box" available to my knowledge but with some scripting you should get what you want.The article ("Find the last login date for a user in Jira server") is possible a good starting point. Using those database queries you can show the last login timestamps:
After that a script you would have you write and adapt to you own needs can check if the dates are within the past 90 days-timerange. A notification could be done in the same script - or you outsource it to a second script.
In case you want to disable users after 90 days not logged in please consider that this might or might not be possible right away - in case of external user management (Active Directory / LDAP / ...) it will not be possible to deactivate them locally.