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Use copy of input files in output dir rather than extracting separately #76

@alexdewar

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@alexdewar

Since the MUSE2 PR EnergySystemsModellingLab/MUSE2#1282, we now have a copy of input files in the output dir. We should use this rather than running muse2 example extract beforehand.

Note that we can't do this yet, as the latest release (v2.1.0) doesn't contain this feature. Once v2.2.0 is released, we can make this change.

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