I was a Mac developer for a long time. In the end we were using Code Warrior and their PowerPlant c++ application framework. If you are familiar with this, it'll give you a good idea for what I am used to.
From what I recall, from a "user" point of view was that the code included in your build was in a project file list that was editable. Also your code had to list, in the source files, what it needed using the standard #include statements. Easy to use, easy to control.
What I've run into here, for example, is writing code for two processors. Master/Slave I have both sides (classes) in the same library folder because they are a pair, and they also need common .h files so that you know things will match. But, one processor is bigger and has more responsibility and there is more leeway on how you write its code. The other is small and you need to be more careful with the code. (Being very careful of RAM) The Arduino IDE Dumps ALL of the code into both processors. Completely overfilling the poor little one.
So I have a hard time with the auto selection of source code. I understand why its done that way because for a new coder it makes things a LOT easier. But in certain situations, like this, it wold be nice to be able to specify what goes in what sketch.
-jim lee