I don't see a "deactivate" link for users in JIRA 6.3.15 nor in 6.4.12.
The shown operations in the UserBrowser are: Groups Project Roles Edit Delete
The operation is missing for all users and it doesn't matter if the user is in groups or not.
The directories are all Read-Write.
Do I have to enable the "Deactivate" feature somehow?
I see from the docs that this feature is not available for certain external user directory connectors such as LDAP. Check this KB https://confluence.atlassian.com/jirakb/unable-to-deactivate-users-using-deactivate-feature-in-jira-295309946.html and see if this is your case.
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