Had similar problems as the OP
cat hello.c
#include <stdlib.h>
int main() { exit(0); }
clang hello.c
/usr/local/include/stdint.h:2:10: error: #include nested too deeply
etc...
I installed the latest version of XCode, however, release notes indicated the file mentioned in the previous fix, from Jonathan here, was no longer available.
open /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg
Details here https://developer.apple.com/documentation/xcode_release_notes/xcode_10_release_notes , under the New Features section.
Using details in this comment, https://github.com/SOHU-Co/kafka-node/issues/881#issuecomment-396197724
I found that brew doctor reported I had unused includes in my /usr/local/ folder.
So to fix, I used the command provided by user HowCrazy , to find the unused includes and move them to a temporary folder.
Repeated here...
mkdir /tmp/includes
brew doctor 2>&1 | grep "/usr/local/include" | awk '{$1=$1;print}' | xargs -I _ mv _ /tmp/includes
After running the scripts, the include file issue was gone. nb: I commented on this issue here too.