Set output directory in conf

[felixleopoldo]

The benchmark_setup section of the config file should have a key called output_dir specifying where the output of the evaluation modules should be saved. Thus everything currently saved in output should instead be saved in output/config["benchmark_setup"]["output_directory"]. When running a config file, the config file itself should also be saved here.
One would basically just have to change the output part of the rules.smk in the evaluation modules. For example this line and the ones below.