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I'm trying to get a good idea of the permission structure of my Atlassian applications. We have more than a few "admin" user groups and a bunch of permission schemes, but the application is pretty much open to all logged in users. I'm in the process of reducing this, but those 6 admin groups are confusing.
Which of these are built in? Is there a way to easily tell where these are being used?
ex. "jira-administrators" is explicitly listed in some projects, but not all, and I'm not sure why nor how many without going through all of my projects.
A good permission in Jira means it is simple enough yet robust to cater for your projects. administrators, jira-administrators and jira-admins basically would have the same level of permissions within Jira. Site-admins typically controls the site in general. However, depending on which admin UI that's currently present for you whether its the old or new version would determine the usefulness of those groups above. Back to your question, typically administrators, jira-administrators, site-admins, jira-admins-<site> are auto created but that depends on the admin UI you're currently using.
What I'll suggest is for you to perform a screening and refurbishing of site permissions (Global or project permissions) to ensure that access is only given to groups or project roles as intended. You can remove those groups or create the ones that makes more sense to you or your organization. However, make sure before running any changes that it doesn't affect the running operation for other users within those project. It will take time but creating a permission that is secure enough for your projects will serve you in the long term.