Port over Hashim/Gulzar's changes from the application-specialization branch on google code.
Use the -pthread flag, do not pass -lpthread to the linker directly, as per FreeBSD Handbook:

https://www.freebsd.org/doc/en/books/porters-handbook/dads-pthread.html
Fix whitespace
Update llvmLDWrapper and bundle to work with llvm 3.5
Update support for .bc.a files, apache port now builds successfully.