Add paired command-line predictor API

[iskandr]

Fixes #259.

Summary:

• Add BaseCommandlinePredictor.predict_pairs(...) and predict_pairs_dataframe(...).
• Accept either parallel peptide/allele lists or iterable (peptide, allele) pairs.
• Validate pair alleles against the tool-supported allele list without mutating self.alleles.
• Group work by allele, run existing peptide command paths once per allele, and reassemble PeptideResult objects in input order.
• Bump version to 3.31.5.

Validation:

• pytest tests/test_commandline_predict_pairs.py -q
• pytest tests/test_allele_batching.py tests/test_commandline_predict_pairs.py -q
• ./lint.sh
• ./test.sh (664 passed, 51 skipped, 2 xfailed)