WIP Decouple output directory from call to save

[andrewgryan]

De-couple hard coded directory locations to make it easier to separate concerns between script invocations.

[andrewgryan]

Now that I've gotten goofys to mount the S3 bucket the intention is to modify the code/cli to be flexible enough to accept a few high-level directory locations, so that --output-dir and --mount-dir or something suitably abstract can be supported

[andrewgryan]

This PR could pivot to be a migrate step to R package instead of only a decoupling from the file system

[andrewgryan]

@DPeterK this is a transitionary fossil, the main idea is to extract functions but is a perhaps better as a migration task now that we have a DIMEX package, it could be data_prep_* step(s)

[DPeterK]

Yes if the aim is to move all (?) IO into the API / server then the ideas here are probably better (eventually) migrated out of the DIMEX codebase