This question is in reference to Atlassian Documentation: Permissions overview
I created a workflow that provides the ability to reject stories that are then closed. I also had my service group create a new product owner permission scheme and provided the permission to the product owner to reject. Although it appears everything is set up correctly the functionality is still not being realized by the product owner user.
No, they're not. LDAP is about users and groups only. Permission schemes are purely JIRA artefacts and live and work within JIRA only.
Unless you've got some heavily customised code that has moved them out of JIRA and they are overlaid by AD data somehow, in which case, you need to get the AD people to apply them to the projects (but I can't help you with that because I've never seen that done before)
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