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Separate input and output path specification for flexibility #495

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@leewujung

A common use/test scenario is that many people pull input data from the same location but generate outputs (e.g., consolidate NASC files and reports) in a different location. So we should change the way input and output paths are set up now so that the input can use the same approach (right now a single DATA_ROOT) and the output paths can be specified in a more granular way.

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