Build comprehensive documentation site

[aalexmmaldonado]

Description
Use Sphinx or MkDocs to generate a documentation site covering installation, core concepts, API reference, tutorials, and example galleries. Include automatic docstring extraction, cross‑references, and a search index. Integrate docs build into CI to catch errors early.

Key tasks:

• Write a quickstart guide demonstrating end‑to‑end usage.
• Author tutorial sections for schemas, storage, digestion, workflows, and export.
• Configure intersphinx to link to external libraries (e.g., Pydantic, MDAnalysis).
• Set up Read the Docs or GitHub Pages deployment.

Acceptance Criteria

• Documentation site builds without warnings or errors.
• Searchable API reference covering all public modules and classes.
• Tutorial notebooks rendered and linked, with Binder badges for live execution.
• CI pipeline fails if any broken links or missing docs are detected.