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Adding a SSH key for use with Dokku should be done with the sshcommand acl-add command. It formats the /home/dokku/.ssh/authorized_keys file in a very specific way.
- cat ~/.ssh/id_rsa.pub | \
- ssh root@dokku.ip.address "sudo sshcommand acl-add dokku <name>"
For more info on how Dokku handles user management, see here.