Unless I have somehow missed a setting, I cannot make folders affect my nodes. This is my current nodes setup, I have made my own text file that links all things together (so there is an overall contents page linked to a contents page for each topic which is linked to all the notes).
My suggestion is to add an option to remove the need for a page that links all my notes inside a folder, and makes the folder a node themselves.
P.S. I love this notes app, it is by far my favourite and the graph view is already an amazing addition! I love it <3