Update `copyOrWarn` and `getFileSHA1Hash` to account for directories

[opotowsky]

What is the change?

copyOrWarn can now handle directories. This also includes an edit to getFileSHA1Hash so that it can handle directories too.

Why is the change being made?

Sometimes a directory needs to be copied too. Let's give the directories the attention they deserve!

This supports a case setting downstream that is a directory, not a file path.

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Checklist

• [x] This PR has only one purpose or idea.
• [x] Tests have been added/updated to verify any new/changed code.

• [x] The code style follows good practices.
• [x] The commit message(s) follow good practices.

• [x] The release notes have been updated if necessary.
• [x] The documentation is still up-to-date in the doc folder.
• [x] The dependencies are still up-to-date in pyproject.toml.

[john-science]

Hey Arrielle! Can you re-run the linters?

Thanks!

[opotowsky]

(working on some tests now + fixing some code, so this isn't quite ready yet)

Update @john-science : it's ready for review. I have a few comments and questions for you.