As to classes, there are some places where they make sense, but for the most part, your code really represents workflows against objects (not necessarily classes) as your code/flow really doesn't care if it's a duck as long as it quack()'s.

As to the second part of your comment regarding imports... import really isn't any different than require, and in that vein is easy enough to reason against, and work through. For the most part, your discrete modules should be hierarchical in nature, and exposed as collections/wrappers via directory/index structures... this will make it easier to avoid spaghetti.