The Core plugin is different. It is being loaded by name before other plugins are loaded. It might have been a library instead.
Sharing my experience (I wasn't responsible for this terrible architecture, nevertheless I couldn't find a way to untie this Gordian Knot without totally rewriting the system) I strongly advise you to decide apriori which functionality goes where and what depends on what and then stick to what you designed. Splitting or merging as you go will lead you exactly where we landed.That's another worry, but I think by careful segregation of functionality into a set of well-defined plugins, I can hopefully avoid this.
Well... it depends. My problem was that I was the only one fully understanding the plugin architecture so I was being asked a lot of questions how to do things with it.This is the hope, isn't it?
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