But the whole problem is frameworks always decide against code colocation, and also they don't tell you what to do with all the functions that don't fit their d

But the whole problem is frameworks always decide against code colocation, and also they don't tell you what to do with all the functions that don't fit their directory scheme. People who don't use a framework will naturally tend toward fewer subdirectories and code colocation just because, e.g., there's no reason to elevate the importance of a models/views/controllers pattern.