fix: Move back to cookiecutter

[xmnlab]

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[xmnlab]

@Saransh-cpp @EverVino @Anavelyz @YurelyCamacho ,
currently scicookie is not working on pipx ... so the plan is to move back to cookiecutter
and as a follow up, move from the sh to cookiecutter api

I am merging this PR now ... but feel free to point any issue here and I will work on that as a follow up

[github-actions]

🎉 This PR is included in version 0.8.2 🎉

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