Yes, I was thinking specifically about mixing stowed and non-stowed files in directories, that's why I chose the fontconfig example: it's likely that I will want to add files there that I don't want to stow/sync to other machines. I also find it cleaner using --no-folding and easier to reason about. I remember feeling surprised and not understanding what stow did the first time I used it without --no-folding. Some people might actually prefer the folding behavior, I just wanted to highlight that the default behavior might not be what one would expect.