In the past 8 months, I’ve probably worked on close to 10 different projects. While half of these consists of not more than a few Jupyter notebooks, the others consist of intermediate data and different notebooks for preprocessing and modelling.
Cookiecutter seems to be a good solution and framework: https://drivendata.github.io/cookiecutter-data-science/
Refactoring those projects will take some effort, but I believe it will be well worth the time to do so.