Add explicit --model selection and robust ESMfold2 .cif + .json support

[Copilot]

ESMfold2 confidence JSON differs from AF3, which made .cif + .json inputs ambiguous and brittle under auto-detection. This PR adds explicit model-source selection and aligns parsing/detection so ESMfold2 keyed/raw PAE formats are handled predictably.

• Explicit model-source control

  • Added CLI flag: --model <af2|af3|boltz2|esmfold2>.
  • Propagated explicit model choice into score_interactions(..., model_type=...).
  • Added boltz2 -> boltz normalization.
  • When --model is provided, model-source auto-detection is bypassed (file-format detection remains extension-based).

• ESMfold2 confidence parsing + schema handling

  • Added ESMfold2 loader path for .cif + .json inputs.
  • Supports:
    • keyed dict payloads (predicted_aligned_error or pae)
    • raw top-level matrix payloads
    • .json.gz variants
  • Added NaN-tolerant pLDDT normalization and explicit fallback behavior when ESMfold2 pair ipTM is absent.

• Detection hardening for AF3 vs ESMfold2

  • Prioritizes AF3-specific markers when present.
  • Recognizes ESMfold2 signals for both keyed and raw formats.
  • Raises clear errors for unsupported top-level JSON types / unknown schemas instead of silently routing to the wrong parser.
  • Preserves missing-file error behavior for .cif + .json model detection paths.

• Parser and docs alignment

  • Tightened mmCIF _atom_site validation edge cases.
  • Updated CLI/README usage to document --model and .cif + .json ambiguity guidance.

# Explicit source selection (recommended for .cif + .json)
ipsae --model esmfold2 esmfold2_complex_pae.json esmfold2_complex.cif 10 10
ipsae --model af3      fold_x_full_data_0.json   fold_x_model_0.cif   10 10

# API
result = score_interactions(pae_file, structure_file, 10, 10, model_type="boltz2")