The biggest issue here is the difference how Waypoint plugin and Quartz resolves the links, I already had the perfect view for files locally in Obsidian. I ruined it when moving to the Quartz. I’m thinking about writing my own plugin to Quartz to solve it.

There are two issues:

  1. Quartz uses the files names as the folder files for the representations of the folders, not included in graph. To avoid it I have to use different names for these special files.
  2. Quartz is not including folder files in graph.

Solution is to separate the folder file from folder with the same name. Thenuse its links as regular links

I have to think about it, I’m not sure yet if it would work. If I seperate it, I will lose the Explorer navigation through folders.

My garden:
quartz-djn.pages.dev