Add scientific fixtures and a supported-model matrix

[gonzalobenegas]

Outcome

Establish the scientific compatibility contract before deleting or reorganizing historical sources.

Acceptance criteria

• Add a machine-readable support matrix for GPN, GPN-Star, deprecated GPN-MSA inference, Sorghum gene-expression inference, and PhyloGPN inference.
• Pin immutable Hugging Face revisions for the representative published checkpoints.
• Add small, non-pickle fixtures with biological coordinates, species/allele order, model revision, dtype/device, expected logits/probabilities/LLRs or expression outputs, and explicit tolerances.
• Derive MSA fixtures from existing shared SCF alignments without downloading or committing a whole-genome MSA.
• Reproduce and independently review the notebook-derived expected values.
• Run fixture regressions offline on every PR; keep network/model downloads outside normal CI.
• Document score sign, masking, coordinate, soft-mask, and calibration conventions.

This issue does not include architecture refactors; behavior is captured first.