It seems that when compile_commands.json is used then VSCode will only use include paths specified in that file, and will fail to use the clang compilers built in include paths. My understanding is that compile_commands.json should only contain the flags that are passed to the compiler though, and there should be no need for it to contain compiler built-in include paths, defines, etc.

This issues causes includes such as:

#include <new>

to fail. That header file should be found under:

/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1

I'm on macOS 10.13.1 using VSCode 1.19.0-insider with C/C++ Tools 0.14.2.