CMake - Multiple subdirectories without multiple CMakeLists - cmake

Question

Description
I'm currently creating a program that would turn a model from simulink and matlab into an FMU.
As I want to automate the process as much as possible I want to also automate the build process for both an EXE, to extract information in the C-API supplied, and later a DLL for the FMU. My plan was to do this with CMake, which is why I'm here. As I know the layout of the code generation (See further down), I could go ahead and make multiple CMakeLists and just have a part of my python script paste them into their repsective folders. BUT, I wanted to make sure this was the only way of doing it (Multiple CMakeLists) before going ahead.
Question
Is there anyway to only have one CMakeLists with many multiple categories? Do I just include all subfolders that include files with target_include_directories() or have I understood that completely wrong? Is there a way to make target_include_directories() to also include subfolders?
My current directory looks like this:
\---CMakeListExperiment
| main.c
| CMakeLists.txt <--- Is it possible to make this the only CMakeLists?
|
+---R2017b
| |
| |
| +---extern
| | \---include
| | tmwtypes.h
| |
| +---rtw
| | \---c
| | \---src
| | | rt_logging.h
| | | rtw_capi.h
| | | rtw_modelmap_logging.h
| | | rt_logging.c
| | | rt_mxclassid.h
| | | rt_logging_mmi.c
| | | rtw_modelmap.h
| | | rt_logging_mmi.h
| | | rtw_modelmap_utils.c
| | |
| | +---common
| | | rt_main.c
| | |
| | \---ext_mode
| | \---common
| | ext_work.h
| |
| \---simulink
| \---include
| rtw_matlogging.h
| sysran_types.h
| rtw_extmode.h
| sl_sample_time_defs.h
| simstruc_types.h
| sl_types_def.h
| rtw_solver.h
| rtw_continuous.h
|
+---multi_grt_rtw
| rtGetInf.c
| rtwtypes.h
| rt_nonfinite.h
| multiword_types.h
| multi_capi.h
| rtmodel.h
| buildInfo.mat
| defines.txt
| rtGetNaN.h
| builtin_typeid_types.h
| rt_nonfinite.c
| multi_capi.c
| rtGetNaN.c
| multi.h
| multi_capi_host.h
| rtGetInf.h
| multi_private.h
| multi_types.h
| multi_data.c
| multi.c
I'm usually very bad at explaining things, so if there's any confusion let me know. I'm also new to posting at SO, which is why I would love feedback. Cheers
EDIT 1:
I have tried the following CMakeLists. I can get this working if I move all sourcefiles inside "/multi_grt_rtw/, but will fail if these files are in their folders that comes produced by matlab. Fail as in "can't find files".
cmake_minimum_required(VERSION 3.0)
project(hello-vsc C)
file(GLOB_RECURSE SOURCES_NORMAL RELATIVE ${CMAKE_SOURCE_DIR} "multi_grt_rtw/*.c")
file(GLOB_RECURSE SOURCES_MATLAB RELATIVE ${CMAKE_SOURCE_DIR} "R2017b/*.c")
set(SOURCE main.c)
include_directories(${CMAKE_SOURCE_DIR}/multi_grt_rtw)
include_directories(${CMAKE_SOURCE_DIR}/R2017b)
add_executable(main ${SOURCE} ${SOURCES_NORMAL} ${SOURCES_MATLAB})
My guess is that include_directories is not recursive (Not searching subdirectories for sourcefiles), so my question is if there's any way to do that? Make include_directories recursive?
The other two, in theory?, working options are
A) As everything is always produced the same, write all CMakeLists needed and copy them, with a script, to correct folder during execution.
B) Add multiple include_directories() to main directory CMakeLists
Now when I have had some time away from work, I guess my question is a bit weird. But it would still be intresting finding out if include_directories() could be used in the way I want it to be, as I can't find much information about it.