I compiled and installed LLVM from trunk on debian wheezy some weeks ago (configure & make) and now tried to out of source compile the llvm-mutate pass.
AFAICC, llvm-mut
Just for the sake of completeness if someone will come across this error. This bug is meanwhile fixed in LLVM 3.8.0 so that you only have to include AddLLVM to build your plugin. The HandleLLVMOption include file is only helpful to get the right compiler flags as stated above in the post.