feat(dgeni): remove atoms and molecules from design doc IDs

[griest024]

PR Checklist

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• The commit message follows our guidelines: https://github.com/graycoreio/daffodil/blob/develop/CONTRIBUTING.md#commit
• Tests for the changes have been added (for bug fixes / features)
• Docs have been added / updated (for bug fixes / features)

PR Type

What kind of change does this PR introduce?

[ ] Bugfix
[x] Feature
[ ] Code style update (formatting, local variables)
[ ] Refactoring (no functional changes, no api changes)
[ ] Build related changes
[ ] CI related changes
[ ] Documentation content changes
[ ] Other... Please describe:

Does this PR introduce a breaking change?

[ ] Yes
[x] No

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