Add custom input.nml field-value pairs

Currently only some fields are populated through the config.yaml file. The user might want to toggle some options or specifify more values in the input.nml file, so we should add a dedicated section in the config file where the user can overwrite any option of the input.nml (for advanced users).

Start by tracing how config.yaml is read and how input.nml is populated. Determine the configuration shape needed for advanced users to override input.nml options, then verify that those field-value pairs are applied without breaking existing configuration behavior.

Written by the indexing model from the issue text.