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Update repository structure

Christian Doh Dinga requested to merge 6-update-repo-structure into main

Closes #6 (closed)

@S.J.vanRijn, I have added most of the files to make it consistent with the DEMOSES-coupling repo.

However, I noticed that for now, the pre-commit hook is not working properly. It allowed me to push to origin even with failing tests and ruff non-compliant files.

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