Hello
We are adding the $extract operation to our facade too at the moment.
It seems clinical reasoning is quite strongly linked to getting data from a repository, so you probably need to write your own IRepository instance to use the ExtractProcessor from said library to resolve Questionnaire / QuestionnaireResponse and other resources.
To register the operation, simply use the HAPI annotations for a new operation. After running the extraction, you get a transaction bundle which you could either process inside your extraction operation, or handle it seperately on your bundle-endpoint, depending on how you would like to proceed from there.
Hope this helps.
Best regards,
Robert