I had the same problem.
My project directory was like this:
--project
---Classes
----Application
-----.h and .c files
----OtherFolders
--main.cpp
And what I used to include the files in all those folders:
file(GLOB source_files
"*.h"
"*.cpp"
"Classes/*/*.cpp"
"Classes/*/*.h"
)
add_executable(Server ${source_files})
And it totally worked.