When I wrote my PhD thesis 25 years ago there were no DT, Scrievener or Bookends. Paper books and journals, libraries, a special system of paper workflow and Word at the end of it 
Even then I already used hierarchical method with sharp pencil, eraser and tons of A4 paper lists.
I even write lecture drafts using short hierarchy of topics. Never write full texts until it’s time to write a textbook )