I am trying to delete a jira group but it gives me this error message "You do not have permission to remove this group from all the directories in which it occurs". I am a system administrator on jira
The problem is exactly what it says it is. You have a user directory which you do not have access to write to. JIRA admin grants you JIRA admin, it doesn't grant you rights to edit the content of external directories unless you explicitly set it to.
Go to admin -> user directories, I suspect you'll find at least one is read-only. Even if it's not that, then the account used to connect JIRA to it does not have permissions in the directory.
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