validate_expected_files_by_modality fails when called on valid files through .model_validate

[dbirman]

Describe the bug
The function validate_expected_files_by_modality fails because validated models generated from dictionaries don't recover Modality objects but instead recover a list of dictionaries.

To Reproduce
Steps to reproduce the behavior:

1. Load any valid metadata as a dict
2. Run Metadata.model_validate(dict)

    abbreviation = modality.abbreviation.replace("-", "_").upper()
                   ^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'dict' object has no attribute 'abbreviation'

Expected behavior
The function shouldn't crash on modality.abbreviation but should check if modality is a dict and use modality["abbreviation"] instead.