I use Obsidian. I make my notes atomic, and if I want to centralize notes, I treat the master note as a table of contents to the atomic notes. I use tags, and

I use Obsidian. I make my notes atomic, and if I want to centralize notes, I treat the master note as a table of contents to the atomic notes. I use tags, and I use the map that shows an SVG visual of how the notes are connected.