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Refactored directory structure for Python wrapper

Goran Jelic-Cizmek requested to merge feature/dir_refactor into feature/conda

Note that there is a breaking change: the binary previously produced by make has now been renamed to coffe-cli since the name resulted in a conflict with the newly-made coffe directory (it was either this, or renaming the Python wrapper to pycoffe or similar).

Edited by Goran Jelic-Cizmek

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