I know that this is a clean working copy as I deleted the entire repo and started over 
cd modules/photon/system-part2
make clean all COMPILE_LTO=n program-dfu
arm-none-eabi-g++: fatal error: /usr/bin/../lib/gcc/arm-none-eabi/4.9.3/../../../../arm-none-eabi/lib/nano.specs: attempt to rename spec 'link' to already defined spec 'nano_link'
compilation terminated.
make: *** [../../../build/target/system-part2/platform-0-m/system-part2.elf] Error 1
Looking at the error and this dup of it, I have no information other than my g++ version is
arm-none-eabi-g++ --version
arm-none-eabi-g++ (GNU Tools for ARM Embedded Processors) 4.9.3 20150303 (release) [ARM/embedded-4_9-branch revision 221220]
Also, I’m using a Particle Core, not a Photon. Is the path correct?