Hello Martin,
Hauptwerk's component installer can't currently (v3.30) install (non-compiled) CODM organ definitions, since they're considered to be user data files. We might add functionality to import/export them in the future.
Hence at present if creating a sample set you would need to supply the compiled 'full-format' ODF and/or the user would need to download and copy the CODM ODF manually. (Please contact us if you need any installation package IDs, organ IDs or temperament IDs allocated, since they must be globally unique.)
Maybe the other subdirectories ImpulsResponses and Temperaments may also work.
Files can be included with the Temperaments folder as well (but not currently ImpulseResponses).
Best regards, Martin.
Hauptwerk software designer/developer, Milan Digital Audio.