FAQ

I removed mod from Koikatu/mods/ directory, but it still appears in patchwork

Zipped mods compatibility works by extracting those, and converting back to canonical on-disk format equivalent to that of a hard mod in separate folder. In Koikatu/Patchwork/mod, you'll find folders named after zip files. Delete the folders of mods you don't want. Note that 'unzip' script unzips everything it finds in mod directory on each game launch, so you may need to keep it disabled if you want to handle extracted mods on your own.

Mods are kept on disk like this to conserve memory (roughly 2GB for heavily modded game).