When linking with libraries the libraries has to be placed after the source/object files.
So you need something like
clang++ -O3 -g -Wall -std=c++11 -I./src \
`llvm-config --cppflags --ldflags core jit native` \
objectfile1.o objectfile2.o \
`llvm-config --libs core jit native` \
-o outputfile
It's because the linker looks for symbols in the order they are given on the command line.