Fix the mapping between CWL inputs, which are in JSON format, and Python types, for CWL steps that contain inline Python script.

The solution is to convert the CWL `$(inputs)` once to a Python `dict`, by using the `json.loads()` function, passing the `$(inputs)` as a raw Python string. Next, any input argument can be accessed as an entry in a Python `dict`.

Also, to avoid potential "Argument list too long" errors, all inline Python scripts that expand the `$(inputs)` argument are now automatically turned into a script *file*, instead of being passed as a (potentially huge) string on the command line.


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