The harvester uses the namespace URI to detect the provided metadata format (http://www.clarin.eu/cmd/1 for CMDI 1.2, http://www.clarin.eu/cmd/ for older versions), so all prefixes get included automatically. See the OAI-PMH for CMDI documentation for examples of configurations for providing CMDI over OAI-PMH.
If you nevertheless encounter unexpected behaviour, please contact harvester@clarin.eu.