Sorting your shopping is a good example of how you should handle your scrap papers and notes.
It makes no sense to store ice cream and jeans together because they were bought from the same department store or on the same day. Then, why would you keep all the notes taken from reading the same book together despite the fact that they represent disparate ideas?
Organise things by purpose, not by their content.
Food in the fridge, clothes in the wardrobe. Context is the only criterion. If you want to eat, you peek at the fridge and decide what you can cook. You don’t try hard to remember what ingredients you’ve bought over the last three months. This applies to dealing with your notes, too. You store them by contexts, not by which book they are from, or which day they were taken.