cleanup pipeline and bin directory

[ismael-mendoza]

Following #96 we should also cleanup the pipeline to generate data. This might enable processing other sims in the future and make the input of the data generation clearer which could prevent bugs.

I propose getting rid of click (or using barebones parts of it, not the ctx object) and instead use a yaml config files (parsed with omegaconf).

For the rest of the bin directory we could have different yaml files (or a yaml file with a bunch of options) to avoid hard coding default values.

• avoid hard-coding paths make relative to repo.