We have our AD server set to read only w/ local groups. Our local directory is set up to support nested groups, and when we add users from the local directory to the sub-group, they're added to the parent groups as normal.
Unfortunately the users in our AD server don't get added to the same parent groups, they only get added to the group that you add them to.
For fun, even though our AD server isn't working our groups, we have it set to supprt nested groups as well, but that didn't change anything.
Do you have any user filter (User Object Filter) in place at your directory configuration in JIRA? In case you have, you may need to add the parameter 1.2.840.113522.214.171.1241 as in the example bellow:
The explanation to this parameter is in this page, basically it allows recursive search in your LDAP.
I hope it helps.
How could it be applied in our case, we are not filtering on group, we're filtering user accounts based on a property of them haing EmployeeID (that separates humans from non-human accounts), and the account not being disabled UserAccountControl:1.2.840.1135126.96.36.1993:=2.
Can this 1.2.840.1135188.8.131.521 parameter be applied in our case?
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