Better integration with SUSHI

[brynrhodes]

The CQF Toooling currently does not integrate well with the SUSHI aspect of FHIR IG publishing. A complete description of the issue is found here:

https://github.com/PATH-Global-Health/MERindicators/issues/12

The gist is that we need to be able to specify the path to the resources being processed, rather than assuming they are in the conventional location.

We should also support a parameter that determines whether or not to create the artifact bundles