On populate, we allow CQL to be used as the language referenced by variables and populate-expression values, which is one mode of population.  However, there's another - similar to what we do with StructureMap, where you just invoke the CQL, it does all the relevant queries and generates the QuestionnaireResponse whole-cloth - just like StructureMap does (except no need for a batch-response of search-sets to pass into the process when using CQL).

The same sort of process makes even more sense on the extraction process.  "Launch this CQL, passing the questionnaire, and have it spit out the Bundle - or even create/update the resources directly".

Don't know that we want to take this on for the next release, but it's definitely viable technically and might be more attractive than StructureMap in some cases.