Improve configuration management

[ekatef]

As discussed with @FabianHofmann and @davide-f in the context of #1053, the current configuration management can be improved:

1. Implement a modular structure of the configuration files.
2. Update the config in an automated way using the incremental update procedure temporally commented in Test routine: add Makefile; CI: consolidate ci.yaml files #1053.

A couple of comments to give a better overview.

1. Currently we have an incremental updates of the configuration files implemented as build_test_configs script which can be run with run_all_scenarios rule.
2. This issue mock_snakemake function to optionally include the config dictionary programmatically #751 gives a suggestion on a possible approach to deal with --configfile option by adjusting Snakemake.