Create a "Settings" class to support Pydantic validation

[toni-neurosc]

Currently the "Settings" object is a dictionary loaded from a JSON file. This has sometimes created problems for users when specifying pipeline settings (see #289). To provide a more robust interface for configuration and validation of settings, settings should be converted into a class with proper type hints to be validated by Pydantic at initialization and when loading a settings file or changing settings in code.