feature: properly map file/directory paths for task evaluation

[peterhuene]

With the initial implementation of task evaluations in #265, only File/Directory values that are transitively referenced by the command get mapped into container environments.

This means that auxiliary inputs to a task, such as specifying a bai input that isn't referenced by the command directly, will not be mapped into the container environment; note that in wdl-analysis we have a heuristic to suppress unused inputs with specific suffixes (bai being one of them) for this reason as well.

While referencing a struct value that contains multiple files should map all of the structs paths, we should probably map, at the very least, all inputs along with any private declarations explicitly referenced by the command; alternatively, just map all inputs and all private declarations regardless of being referenced by the command.