I think that falls into a class of tradeoffs that using various tools involves. With a higher level of functionality the designer of the tool must make decision

I think that falls into a class of tradeoffs that using various tools involves. With a higher level of functionality the designer of the tool must make decisions about how to implement the functionality. They can provide options or configuration to tailor behavior to an individuals preferences but that increases friction when getting started with the tool. I'm using a a much less capable tool for managing my notes called `mkdocs`. It converts a collection of markdown pages to HTML that I serve from a script running on a Raspberry Pi (`python3 -m http.server 8100`) `mkdocs` provides Github integration but I keep the repo on a private server so I don;t have to worry about private information leaking. Point is, It does nothing with directories so that is completely under my control. It links the pages hierarchically but I can insert links between pages and to images. Manually.