Structural changes

[BenSiv]

Summary

Reordering repo and simplifying the config

Details

removing default values from config.py and keeping all configs in config.yaml
moving all source files from the main dir to 'src'

[Linbreux]

Hi @BenSiv

Thanks for your contribution!

Cleaning up the configs is a good idea.

@Jerakin was already working on moving everything to a separate src folder in MR #146.