Remove legacy LinearReferences class and update to use ElementReferences

[lbluque]

Summary

The LinearReferences and ElementReferences classes were essentially duplicated functionality. This removes the LinearReferences class and keeps ElementReferences - which is being used in UMA models.

• Remove the LinearReferences class from element_references.py, consolidating all element reference functionality into the single ElementReferences class already used by the training pipeline and YAML configs.
• Update fit_linear_references, create_element_references, and load_references_from_config to return ElementReferences instead of LinearReferences.
• Update normalizer.py to use the ElementReferences API (apply_refs) instead of the removed LinearReferences.dereference method.
• Add a getattr fallback in ElementReferences.compute_references so it works both after a model forward pass (where batch_full/atomic_numbers_full are set by the backbone) and in non-model contexts like reference fitting and normalizer estimation.
• Re-enable and fix the previously skipped tests in test_element_references.py to use the ElementReferences API.