[codex] Add flank-aware protein scanning

[iskandr]

Summary

Fixes #206.

This PR makes protein scanning preserve and forward N-/C-terminal peptide flanks for predictors that use flanking sequence context.

Changes:

• Add a shared peptide-context helper and explicit BasePredictor.predict_with_flanks(...) extension point.
• Keep non-flank-aware predictors on the existing deduplicated peptide path.
• Route flank-aware predictors through occurrence-level prediction so duplicate peptide strings with different source contexts remain distinct.
• Forward flanks from MHCflurry.predict_proteins(...) into Class1PresentationPredictor.predict(...), using the loaded MHCflurry processing model supported flank lengths when available.
• Preserve flank fields on emitted Prediction records.
• Reuse shared flank input validation and context generation in processing predictors.
• Bump version to 3.13.6.

Validation

• ./lint.sh
• ./test.sh -> 409 passed, 9 skipped, 2 xfailed

The MHCflurry regression test compares predict_proteins(...) output against a direct Class1PresentationPredictor.predict(..., n_flanks=..., c_flanks=...) call for the same peptide context.