A Fundamental Observation: there will be no substitute for just plain knowing how everything works. Once we get to that point, the rest will be simple.
It may be the case that it is necessary to write bad programs before one can write good ones...
One starts to consider the effect of analyzing groups of cooperating objects, such as the collection hierarchy, or the MVC stuff, relative to outside objects.
Such groups could be:
This gets at the problem that work is done by informal "teams" of objects that taken together constitute a holon or discrete whole, and present a coherent subsect of their total protocol ot the world.
Protocols could be formalized as objects distinct from other Organizations in the system.