docs: add ARCHITECTURE.md and sharpen README positioning for review

[Gavin-Borges]

Summary

Documentation pass to present the current v2.0 architecture accurately for an expert/grant review.

ARCHITECTURE.md (new, root)

Authoritative current-state reference (supersedes the stale course-era note in docs/architecture/):

• Two-track model architecture, honestly gated: the validated RF/XGBoost production scorer (mode_31) vs the GINEConv + ESM-2 GNN research track, with the 5-gate promotion table and current v4 status (4 of 5 pass; AUC-PR >= 0.85 gate open).
• Six-stage Snakemake pipeline, feature representation (21/30/31/33/50/166), data governance (quarantine, freeze mode, SHA-256 manifests), reproducibility, security/OpenSSF posture, and a repository map.
• Notes that 3D structural GNN edges are in-development, not active in v2.3.

README.md

• Positioning block: dry-lab pipeline, two-track design, HPV/EBV focus, links to ARCHITECTURE.md.
• OpenSSF Passing/Silver/Gold tier table with the remaining second-maintainer gap.
• Aligned stale GNN references (v2.1/t6 -> v2.3 GINEConv + ESM-2 t12, 480-dim).

Notes

• Performance numbers kept at the committed v4 figures, consistent with the paper and claims register (v5 reconciliation is a separate gated milestone).
• All authored text is ASCII (0 em-dashes); encoding rule respected.
• Full local test suite green (1097 passed / 2 skipped); ruff/mypy/bandit clean on tracked code; pip-audit clean except the known/mitigated torch CVE.