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50 documentation update to fill in introduction and usage #54

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I think I have the basic structure here, with updated documentation and some some notebooks that are "embedded" (i.e. just linked).

@arthur-lin1027 arthur-lin1027 linked an issue Dec 14, 2024 that may be closed by this pull request
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I think I will just add the AniSOAP JOSS paper to this PR too -- simple copy-paste.

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Documentation Update to Fill In Introduction and Usage
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