Build a polished README and Read the Docs site

[gonzalobenegas]

Outcome

Make the repository attractive to humans and give supported workflows one coherent documentation home.

Acceptance criteria

• Redesign the root README as a concise visual landing page with accurate install and quick-start paths.
• Build a Sphinx/MyST site for Read the Docs with installation, model support, scientific validation, tutorials, curated API reference, research guidance, development, and Hub-asset pages.
• Modernize only the three existing GPN, GPN-Star, and PhyloGPN quick-start notebooks without adding scientific scope.
• Render committed notebook code/plots statically through MyST-NB; do not execute notebooks in normal CI or on Read the Docs.
• Retain optional Colab launch links and strip secrets, absolute cluster paths, transient state, and unnecessary large outputs.
• Add minimal SECURITY.md, CONTRIBUTING.md, CITATION.cff, and release-facing project metadata. Do not add CODEOWNERS yet.
• Build docs and check links/references in CI, with a configuration suitable for Read the Docs PR previews.