The Autodesk v1 API is deprecated as of July 17 2017. The v2 API does not appear support setting references between part files as currently provided by the https://developer.api.autodesk.com/references/v1/setreference
endpoint.
How can one set references between part files so an assembly can be translated using the v2 Model Derivative api? The answer must explicitly not make use of the ability to upload a zip containing all files to the api. A zip of all files is not an option in my case.