Just put notes into multiple “notebooks”, but keep them flat. Somewhat like single-level folders. Then simply reference them as “Article number of Notebook title.”
All articles should have a title and a number. Numbers can be arbitrary, since notes need not be orderly, although it should help a lot. So one note will call another note from another notebook.
Simple structure. Can also be printed.
Inspired by the site: http://www.vicharasagara.com/2015/04/who-requires-which-sadhana.html