You need to understand when do you need to have a well-defined project folder structure. Also, do not focus on hyper parameter tuning in the early stage as it may spend too many resource and time. If a solution is confirmed then it should be a good time to finding a better hyper parameter before launching the prediction service. Modularized your processing, training, metrics evaluation functions are important steps to manage to tune. Focus on building a model but not make sure everything works well in an unexpected scenario.