You'll have to use the latest master branch version of crosstool-ng. on Arch linux you can install crosstool-ng-git from the AUR, on other distros you'll have to clone, make and make install it according to the official instructions.
ct-ng defconfig DEFCONFIG=configs/uefi_[GCCARCH]_defconfig
ct-ng menuconfig
Now navigate to C-Library > Target CFLAGS for newlib and extend it like this to add the required directories to the include path:
-I /home/builduser/edk2/MdePkg/Include -I /home/builduser/edk2/MdePkg/Include/[EDKARCH] -I /home/builduser/EFIDroidLKLPkg/UEFIThreads/Include
/home/builduser/edk2 is the path to your EDK2 directory.
GCCARCH: See configs/ for a list of supported values
EDKARCH: Supported values:
- Arm
- X64
ct-ng build