My main criticism is the ipynb files. I don't like that it stores input and output in the same file. Ideally I'd like at least an option for it to put the out

My main criticism is the ipynb files. I don't like that it stores input and output in the same file. Ideally I'd like at least an option for it to put the output in a directory, with images stored as normal, separate files. It's commonly known that the current approach is terrible for version control, for one thing.