This should either be removed or morphed into a TODO. Theoretically, it is possible to pass environment to a filesystem, at least to an extent. Right now creating a file object is just giving a string, and it's completely defined by it. If any other parametrization which can change from file to file (from step to step) is to be used, a "file" in Drake would have to be a path plus one or more environment variables (i.e. configuration). They would have to be stringed along everywhere, and I think it would complicate the codebase significantly, so I'd rather avoid this approach. So I think you made the right decision to pass it through command-line.