I will need to connect my JIRA to internal AD. On JIRA I already have all my users created by me and all groups/permissions.
If I connect JIRA to AD, will affect all groups that I already created on JIRA?
It depends on what the groups are doing etc. In theory the groups that are the same should be migrated automatically - ditto with users.
your permissions should not be effected. However, if one of the groups that you created exists in your ldap directory, you'll get the group updated to be reflected to what's in the ldap directory.
i would suggest/recommend doing this migration on a staging setup before doing it on the real instance.
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