Updating application with C++ native library to NDK 18, cmake isn't including required sysroot platform include directory

Question

I have an Android application, developed with Android Studio, that is using a very old build system - NDK 14 with CMake 3.6 and AGP 3.5. I'm trying to update it to NDK 18 (I eventually want to update it to latest NDK, but baby steps) using CMake 3.18.1 and AGP 4.2.2 with Gradle 6.7.1, but the build fails due to errors finding a system include file asm/types.h.

Looking at the clang++ compile command that CMake generates, it is clearly missing the ${SYSROOT}/usr/include/<platform-abi> directory.

My CMake (which worked well for NDK 14 with CMake 3.6.1) has these lines:

if(${CMAKE_ANDROID_ARCH_ABI} STREQUAL arm64-v8a)
    include_directories(${ANDROID_SYSROOT}/usr/include/aarch64-linux-android)
elseif(${CMAKE_ANDROID_ARCH_ABI} STREQUAL x86_64)
    include_directories(${ANDROID_SYSROOT}/usr/include/x86_64-linux-android)
endif()

Running CMake with --trace-expand, I can see it correctly parses those lines:

…
… arm64Release|arm64-v8a :/home/…/myapp/mynativelib/CMakeLists.txt(5):
  if(arm64-v8a STREQUAL arm64-v8a )
… arm64Release|arm64-v8a :/home/…/myapp/mynativelib/CMakeLists.txt(6):  
include_directories(/home/…/Android/Sdk/ndk/18.1.5063045/sysroot/usr/include/aarch64-linux-android )
…

But the build.ninja file generated does not have this include directory - it contains compile directives that look like so:

build CMakeFiles/mynativelib.dir/home/…/mynativelib/MyClass.cpp.o: \
    CXX_COMPILER__mynativelib_Debug /home/…/mynativelib/MyClass.cpp || \
    cmake_object_order_depends_target_mynativelib
  DEFINES = -DANDROID -DCMAKE_BUILD_TYPE=Debug -DDEBUG -DMIXIT=0 -DNDEBUG -DRELEASE=0 … -D__GXX_EXPERIMENTAL_CXX0X__ -D__STDC_CONSTANT_MACROS
  DEP_FILE = CMakeFiles/mynativelib.dir/home/…/mynativelib/MyClass.cpp.o.d
  FLAGS = -std=c++14 -fno-stack-protector -ffor-scope -fexceptions -O0 -fno-limit-debug-info \
    -fPIC -fno-stack-protector -fpic -ffunction-sections -funwind-tables -no-canonical-prefixes \
    -Os -fomit-frame-pointer -fomit-frame-pointer -UNDEBUG -fno-omit-frame-pointer -Ijni -Wformat \
    -Wa,--noexecstack -fno-stack-protector -std=c++14
  INCLUDES = -I/home/…/Android/Sdk/ndk/18.1.5063045/sources/cxx-stl/llvm-libc++/libs/arm64-v8a/include \
    -I../../../../../../../some-custom-include-from-cmake \
    -isystem /home/…/Android/Sdk/ndk/18.1.5063045/sources/cxx-stl/llvm-libc++/include
    -isystem /home/…/Android/Sdk/ndk/18.1.5063045/sources/cxx-stl/llvm-libc++abi/include
  OBJECT_DIR = CMakeFiles/mynativelib.dir
  OBJECT_FILE_DIR = CMakeFiles/mynativelib.dir/home/…/mynativelib

I can see that the build command include the some-custom-include-from-cmake include directory, that is added in my CMakeLists.txt file, as well as all the cxx-stl/llvm-libc++ includes that are also added in the CMakeLists.txt file, but the /usr/include/<android-abi> platform include dir is missing.

Even if I use the include_directories(${ANDROID_SYSROOT}/usr/include/aarch64-linux-android) command without the if check, right near where the other include_directories() commands that do make it into the build file, it is still missing from the build file. I even tried to add the -I flag directly using set(CMAKE_CXX_FLAGS) and that didn't cause the required include dir to be listed.

OTOH, if I change the include_directories(${ANDROID_SYSROOT}…) to be something that doesn't start with ${ANDROID_SYSROOT}, or points to a non-existing directory - then whatever I put there does make it to the build.ninja file.

Looks like something is very purposefully removing include directories that are in ${ANDROID_SYSROOT} maybe?