Directory structuring

[Sparks29032]

Closes #1

[github-actions]

Warning! No news item is found for this PR. If this is a user-facing change/feature/fix,
please add a news item by copying the format from news/TEMPLATE.rst.

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[sbillinge]

@Sparks29032 (cc @tinatn29) Great, we are off! Please create a conda env for this locally, install pre-commit and then run pre-commit install to get all the linting running locally before you push.

Don't forget to put closes #2 in the top-most comment so the issue closes when the PR merges.

We are also now trying to get in the habit of using prefixes to PR names and commits to help keep track. This work is probably chore: directory structure.

But also in general, mention a few words about your intention for the reviewer.... Do you want me to merge this as it is, or is it an intermediate commit. Just a few words so we know what we are after doing....

[Sparks29032]

Closes #1

Once pre-commit passes, let us merge (without news since this is not a major feature change).

[Sparks29032]

@sbillinge Do we want a "tools" repository or another name for helper functions such as ones that convert from .cif to .cgr.

[sbillinge]

Thanks for the @Sparks29032 ! I move the closes #1 to the top level comment box where it has to be to work. Let's work on tagging issue/PR names and commit messages in future commits.