Comment by bballer

I try not to over think it, just:

  ~/$MAJOR_TOPIC
  |
  |--- ./$MORE_SPECIFIC
      |
      |--- ./$MORE_SPECIFIC
          |
          |--- ./general-file.type
      |
      | ./general-file.type
  |
  |--- ./$MORE_SPECIFIC
  |
  |--- ./general-file.type

etc

As you find yourself collecting more general files under a directory that can be logically grouped, create a new directory and move them to it.

Also keep all your directories in the same naming convention (idk maybe I'm just OCD)