path magic feature and bug

[benj919]

Currently there is quite some magic going on trying to divine the config, input, and output paths from partial info when running a simulation. Currently it is a bit inconsistent and intransparent on what is going on. Should we remove all/most of it and instead expect all three to be provided when calling a simulation?

The only part I'd keep is creating a subfolder with the config name in the output path.

(config_handling.R, prepare_directories, lines 16-81)

[ohagen]

I agree. We should think first on how to organize the outputs... now, if using config object I take the path from the input, while if using aconfig file it takes the path from the input. I added some additional printis to help the user a bit, but only informs after launched. Maybe just let's keep landscape (specious input) as the folder structure. I will git it a try