Adding config creation features

[meyerkm]

What

• addresses issue Expose additional configuration options #131 via an update_defaults function, allowing complete overwrite of any parameters as noted in deeprvat/deeprvat/base_configurations.yaml if included in the respective deeprvat_input_config.yaml
• addresses issue MAF thresholds above 0.01 won't work #132
• updates create_main_config to be more readable and efficient
• updates docs relating to configuration file generation

Testing

Involved running the create_main_config function from various DeepRVAT pipelines with the example input config files.