Support WDL 1.2 "extended" syntax for `File` and `Directory` values

[adamnovak]

These are discussed in the WDL 1.2 spec and involve using objects, or strings holding JSON-serialized objects, as File and Directory input values. The idea is that this can help key a call cache entry better according to what was actually in an input or intermediate Directory.

Toil wants to support these in DataBiosphere/toil#5409, and ideally wants to move to these as the internal format overall (because it provides a convenient place to stash extra fields like Toil file store location and means a Directory can self-describe the whole tree it represents). But it looks like it's going to require some work at the MiniWDL layer to even start to read these.