I think we could have both:
- Graph UI could have the controls for temporarily hiding stuff. Basic users without advanced skills can use this.
- Have a meta option that can be written at the top of a file that should be hidden, like hide-from-graph or something. This would serve the purpose of permanently hiding individual files, and it would be out of the way of people who do not use it, because there is (maybe) no UI controls for this.
For the latter, I personally think that it would be a good feature because if I want to hide something permanently from the graph, I find it a bit annoying if I need to preserve it in the graph filter string. It Takes up space there and I might accidentally remove that filter. But if I have written that hiding mark into the hideable file, it stays there permanently.
@Soncro also had a good idea about showing a message “x files are hidden from the graph-view”. That should help to make users understand why some of the notes are not visible in the graph. Maybe make that message clickable so that it can then show which files were hidden.