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Determine how to handle relative filepaths #44

@gpauloski

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@gpauloski

Describe the Request

Should they be relative to the run_dir or where the PWD.

run_dir would make the code easier, but would be confusing for things like datasets.

Maybe filepaths can support a {run_dir} term that gets replaces? Not sure how to best handle this when there are configs all over the place.

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