(In respone to this)
Yes, by topic would be OK. Topics like: math related, working with strings, working with arrays, etc.
The lists don't have to provide links to the sub dirs of the repo. Their purpose is just to provide a general overview of what's inside the repo. Without such an overview, the visitor has to go through the list of sub dirs one-by-one which is not very effective.
So, I think an overview in the README file would make this repo significantly more user friendly.