I inherited JIRA 3 years ago and never touched any of these permissions. Poking around and looking through the web I have not found anything which has indicated that it's possible to alter the permissions for the JIRA Administrator.
Is this in fact the case?
Correct. Admins get admin rights. That's it.
If you could alter the permissions, then it would be an admin who did it, so they could add/remove whatever they like. So it would be utterly pointless.
What Atlassian are looking at doing is more delegation, so an admin can enable non-admins or lesser admins to do more of the configuration (think of project admins being able to update components, versions and users in their projects)
Thanks for your response - I may not have been completely clear so let me try again... I have assigned a user to the JIRA-Administrators Group. I have also provided that user with what that means from here - https://confluence.atlassian.com/display/JIRA052/Managing+Global+Permissions#ManagingGlobalPermissions-sysadmin
The user is coming back saying that they should be able to do more.
As a Sys Admin, I do not see where the roles of that group can be defined/changed. It appears to me that they are out of the box and set as is.
So my overall question is: Can a Sys Admin change the the roles associated with the JIRA Administrators Group? If so, where is this done?
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As I already said, no, you can not change what permissions are available.
It sounds to me like you have given this user "JIRA Administrator" rights. But they are asking for system admin rights, so you need to put them in the system administrators group instead, if you want to grant them all those system rights. As it states in the documentation, a System Administrator can change what groups are granted those two levels of admin and who is in those groups.
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