Yes, the zipped version is number four. It’s not great for the reason you noted. Some people come up with smudge/clean filters that handle the (de)compression,

Yes, the zipped version is number four. It’s not great for the reason you noted. Some people come up with smudge/clean filters that handle the (de)compression, letting Git store the more structured version of the data even though your working directory contains the compressed files your software can read and write—but I don’t know how portable these things are. I agree with you in general, and it is also why my number one example is that you might not need a single-file format at all. macOS app bundles is a great example of this approach in the wild. One question I was hoping to ask anyone who thought about these matters: what accepted approaches do exist out there when it comes to documenting/speccing out file formats? Ideally, including the cases where the “file” is in fact a directory with a specific layout.