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docs: finish MSA CLI and preprocessing documentation for 3.0 - #117
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Updated replacement for #72, based on the current release branch. Matches baker-laboratory/atomworks-dev#484 without importing private history.
No runtime behavior changes. Full strict Sphinx builds passed on both dev and public versions; generated CLI usage inspected; Ruff lint/format and diff checks passed.
Merge this before production release #116. This incorporates the useful changes from #72; that PR does not need a separate merge.