[codex] Fix mmseqs2 TrueMultimer custom template support

[DimaMolod]

Summary

This PR fixes create_individual_features.py so TrueMultimer custom template databases are forwarded into the mmseqs2 feature-generation path.

Closes #332.

Root cause

TrueMultimer already creates a local custom template database, but the mmseqs2 branch dropped that path and always called ColabFold with custom_template_path=None. As a result, multimeric templates were ignored whenever --use_mmseqs2 was enabled.

What changed

• add custom_template_path plumbing to create_and_save_monomer_objects()
• pass the generated TrueMultimer custom template database into make_mmseq_features()
• update MonomericObject.make_mmseq_features() to forward custom_template_path to ColabFold
• automatically enable template re-search when a custom template path is supplied
• add regression tests for the create_individual_features.py and objects.py code paths

Validation

• pytest -q test/integration/test_create_individual_features.py -k 'mmseqs or process_multimeric_features or create_and_save_monomer_objects'
• pytest -q test/unit/test_objects.py -k 'mmseq_features'
• pytest -q test/unit/test_mmseqs_species_identifiers.py
• pytest -q test/integration/test_create_individual_features.py