Add complete MixMHCpred 3.0 support

[iskandr]

Summary

• support the official MixMHCpred 3.0 release, including pan-allele prediction, MHC-I sequence alignment/prediction, and motif/HTML artifact generation
• expose every native score/rank column and best-allele field, plus closest-training/database allele distances and pan-allele provenance, through structured Python results
• enforce cysteine exclusion in mhctools instead of passing v3's removed and silently ignored -c option
• add exact v3 regression output, optional official-checkout end-to-end tests, stale/empty-output guards, docs, install guidance, and the mixmhcpred dependency extra
• retain MixMHCpred 2.x behavior and the legacy parser API
• pin the dev lint toolchain to Ruff 0.15.21 after fresh installs began failing on Ruff 0.16's changed defaults (tracked in Pin Ruff below 0.16 until new default rules are addressed #268)

MixMHCpred's academic license prohibits redistribution without written permission, so this PR intentionally does not vendor its roughly 200 MB checkout/models. MIXMHCPRED_PATH accepts either the official checkout directory or executable, and the README gives an exact tagged-clone setup.

Verification

• ./lint.sh
• ./test.sh — 682 passed, 53 skipped, 2 xfailed
• MIXMHCPRED_V3_PATH=/path/to/official/v3 pytest -q tests/test_mixmhcpred.py — 13 passed (includes known + pan allele anchors and MAFFT sequence mode)
• local MixMHCpred 2.0.2 compatibility smoke test
• uv build

Closes #266.
Refs #268.