fix: Rename model_run_ids as trajectory_ids

[mchantry]

Description

Renames model_run_ids to trajectory_ids to remove confusion with run_ids.

Type of Change

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• Documentation update

Issue Number

Code Compatibility

• I have performed a self-review of my code

Code Performance and Testing

• I have added tests that prove my fix is effective or that my feature works
• I ran the complete Pytest test suite locally, and they pass
• I have tested the changes on a single GPU
• I have tested the changes on multiple GPUs / multi-node setups
• I have run the Benchmark Profiler against the old version of the code
• If the new feature introduces modifications at the config level, I have made sure to update Pydantic Schemas and default configs accordingly

Dependencies

• I have ensured that the code is still pip-installable after the changes and runs
• I have tested that new dependencies themselves are pip-installable.
• I have not introduced new dependencies in the inference portion of the pipeline

Documentation

• My code follows the style guidelines of this project
• I have updated the documentation and docstrings to reflect the changes
• I have added comments to my code, particularly in hard-to-understand areas

Additional Notes

[FussyDuck]

All committers have signed the CLA.