Replace links with refs #406
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Some RST links to notebooks don't work, likely because nbsphinx links don't work that way and they should be refs instead. Not sure if they ever worked originally or if I messed up and misread the docs 😬
Edit: for more info, the reason the nb links didn't work in both the top-level analysis/README.rst and the lower-level examples/analysis/alignment-and-rms/README.rst was that the local links struggled to resolve to two different levels.
refs get around that.📚 Documentation preview 📚: https://mdanalysisuserguide--406.org.readthedocs.build/en/406/