[codex] Update AlphaFold3 submodule to v3.0.3

[DimaMolod]

Summary

• Update the alphafold3 submodule to the merged KosinskiLab/alphafold3 fork main at 86b9ea3, based on official AlphaFold 3 v3.0.3.
• Keep AlphaPulldown's fork-only gapped/discontinuous residue ID support on top of official AF3 v3.0.3.
• Update the alphafold submodule to 5bf5b9f for the NumPy 2 chain-feature merge fix exposed by the AP unit suite.
• Fix the AP smoke-test regression in mmseqs_species_identifiers by resolving the monkeypatchable species resolver dynamically instead of capturing it as a default argument.
• Set the AF3 container build version override so copied-tree builds report/install alphafold3==3.0.3 rather than the upstream 3.0.2 fallback.

Upstream Context

Official google-deepmind/alphafold3 released v3.0.3 on 2026-06-09 at 7b197fe859790fc3e04d03ea70dd0b9ba48881c9.

Release notes: https://github.com/google-deepmind/alphafold3/releases/tag/v3.0.3

The AF3 runtime dependency stack remains the Tokamax/JAX 0.9 stack from the RTX/Blackwell-compatible update:

• jax==0.9.1
• tokamax==0.0.11

The merged fork main contains the earlier RTX/Blackwell compatibility ancestry:

• 3890782: Tokamax attention/SwiGLU migration.
• 608edb6: Tokamax 0.0.11 and JAX 0.9.1 update.

Validation

• git -C alphafold3 merge-base --is-ancestor 7b197fe859790fc3e04d03ea70dd0b9ba48881c9 HEAD -> yes.
• git -C alphafold3 merge-base --is-ancestor 389078218c0604cf85caf4e2e9a830e456ff31d1 HEAD -> yes.
• git -C alphafold3 merge-base --is-ancestor 608edb684db9f6fd0e677fea01c4cefc60f8a8aa HEAD -> yes.
• OPENBLAS_NUM_THREADS=1 OMP_NUM_THREADS=1 MKL_NUM_THREADS=1 NUMEXPR_NUM_THREADS=1 pytest -n auto --dist loadfile test/unit -> 309 passed, 2 skipped.
• OPENBLAS_NUM_THREADS=1 OMP_NUM_THREADS=1 MKL_NUM_THREADS=1 NUMEXPR_NUM_THREADS=1 pytest test/integration -> 76 passed, 1 skipped.
• Focused final rerun on the merged submodule SHAs:
  pytest test/unit/test_mmseqs_species_identifiers.py::test_make_msa_features_resolves_mmseqs_species_identifiers test/unit/test_objects.py::test_multimeric_object_pairs_full_then_chopped_with_correct_features test/unit/test_alphafold3_backend_helpers.py -q -> 32 passed.
• GitHub CI for this PR: smoke-tests 3.10, smoke-tests 3.11, coverage, build-alphafold2-container, and build-alphafold3-container -> passed.
• Local SIF build and RTX PRO 6000 Slurm smoke are in progress; this draft will be marked ready after that GPU check passes.