Removed the hellish overhead that automake had... Time for a new build
system.
Reverted back to makefile-based system for now...

Updated various source files to play nicely with the Makefile again.
Repalced some bitwise addition with bitwise ORs because it can be
dangerous. (Courtesy of StackExchange)
http://programmers.stackexchange.com/questions/23852/bitwise-or-vs-adding-flags