If my Confluence and Crucible are using Crowd, and Crowd is running within JIRA, and users are migrated from Crowd to AD so that the user can log into JIRA now using the AD password (same username), does this require any additional setup in Confluence? Can I still use Remote JIRA Directory / Atlassian Crowd as the directory?
In general that is fine, there may be caveats in your specific implementation. I would recommend you test this in a staging environment.
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