I never thought to I'd say this about an open-source project, but if I wanted to single out an unbeatable case of "Bad Design", and the manifestation of the term "Redundancy Hell", It is definitely Calibre.

Single job: To keep some e-book files + some metadata.
What it does in brief: In a single dir as your library; From metadata stored IN each file; It generates subdirs <author_name>/<title_name>(<some_numerical_id>), copies the e-book file there, generates a jpg cover from the first page and also stores it there, generates an xml file to support legacy e-book formats (but it generates it anyway even for pdfs), which contains all the same metadata for the file, including title, author and href for the cover, and also stores it there. And then, all the same metadata for all books is stored in a metadata.db in the library root folder. I don't know if there is more data stored/used somewhere in a more obfuscated way.

Not too much to ask: Change some author/title/any single field.
What is done: 💩🌋

It is so helpful, it does all the stuff by itself or its plugins; you don't have to touch anything. But it also has this amazing ability to fuck everything up without even being touched. I mean WHAT THE FUCK WERE YOU THINKING? WHAT KIND OF A FUCKING DESIGN IS THIS? A FUCKING FRACTAL?

Literally, If I had listed all my books on physical papers with a real life pen, It would take me less time that I've already wasted on unfucking the regular disasters. Fuck you and your arrogant responses to issues.