Need help understanding system design.

I feel lost where system design is concerned, I am aware of architectural patterns but still don’t fully grasp how developers decide on structuring their projects. I would see similar applications on GitHub written in the same language(i.e. Node js) but with almost entirely different folder structures contained in the source(src) directory. Where are the libs, command, core, api, utils, helpers, models, ui, components etc. directory naming schemes from? Are there patterns in design I’m not aware of or is the design of the system mostly influenced by the developer(s) creativity? Are there any books, articles or lectures that I can go through which covers this topic? Should note that I am a self taught developer.