Reddit reviews Large-Scale C++ Volume I: Process and Architecture (Addison-Wesley Professional Computing Series)
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"Large-Scale C++ Software Design" by John Lakos is pretty much about that and far more (definitely beyond structuring directories, but rather the entire codebase architecture). However, it's from 1996 -- and the update isn't out, yet: https://www.amazon.com/Large-Scale-Architecture-Addison-Wesley-Professional-Computing/dp/0201717069
That being said, I believe BDE follows these principles (given John's role) and may be somewhat more recent:
For more, watch his conference talks -- in particular "Large-Scale C++: Advanced Levelization Techniques" (C++Now 2015):
While John Lakos is working on the new version of his book, it may be a good idea to look at what he's talking about at various conferences today (whether you agree or not, it's something to know if you're in this space).
For example, "Applied Hierarchical Reuse" talk from C++Now 2013 is fairly representative: https://github.com/boostcon/cppnow_presentations_2013#wednesday (slides)
https://www.youtube.com/watch?v=ASPj9-4yHO0 (video)