Change CMakeLists.txt to closer match VisualStudio dependency structure

There have been several cases where a CMake user (myself) broke Visual Studio builds (e.g. by moving headers around), while CMake build still worked. This is partly because Visual Studio projects specify much more precisely which headers can be included in each project, while in CMake all headers are currently available for all targets.

The goal of this issue is to make the CMake build more similar in structure to our Visual Studio solution, so that both build systems behave more consistently.