Modernize package layout, dependencies, quality tooling, and CI

[gonzalobenegas]

Outcome

Create a small, explicit package surface with reproducible quality gates.

Acceptance criteria

• Move maintained code to src/gpn in a mechanical layer.
• Finish dependency boundaries for base, data, inference, training, docs, and development; no analysis/dataset-building dependencies in the root project.
• Remove deprecated GPN-MSA training dependencies and obsolete/import-side-effect paths.
• Add stable gpn CLI entry points while retaining inexpensive old python -m shims for one release.
• Add Ruff formatting/lint, pre-commit, built-wheel tests, and incremental mypy.
• Adopt jaxtyping incrementally on public/high-risk array APIs with runtime checks in tests/development.
• Keep Python 3.11 and 3.13 CI fast and offline.
• Add root AGENTS.md, contribution guidance, changelog/release guidance, and dependency-placement rules.
• Ensure importing gpn never downloads a model or accesses the network.