How do you keep large scale model inputs organized over time?

Hi everyone, I have been working with increasingly larger datasets and models, and I have reached a point where keeping everything organized has become more challenging than running the simulations themselves. I am interested in learning how experienced users structure their workflow when a project evolves over several months. Do you usually separate scenarios into different workspaces, rely on a naming convention, or keep everything together and document changes elsewhere? I would also like to know whether there are any common mistakes that are easy to avoid when maintaining long term projects. I have read through some of the documentation, but I would really appreciate hearing how people manage this in practice. Thanks in advance for sharing your experience.