Automatically determine/override config settings when loading from checkpoint

[jstjohn]

Currently checkpoint loading flow requires options to be specified in a list in sub-packages/bionemo-llm/src/bionemo/llm/model/biobert/model.py, specifically OVERRIDE_BIONEMO_CONFIG_DEFAULTS. We should come up with a CLI that "knows" what a user wants to change and applies those changes over the config in some easy to explain precedence procedure.

[jstjohn]

@skothenhill-nv let's include this as something we demonstrate we can improve on in our future CLI. Something where the runner is "smart" about which settings a user wants to override. Some kind of sane precedence rules. Maybe a case for something like a config with user-defined CLI overrides.