r189150 - Add note about following two commands are no longer equivalent.

[Rafael Espíndola]

This is a more user facing document, so it is probably a good idea to
say when each should be used. Also, -O3 is irrelevant here, -ftto and
-emit-llvm are now different, with any -O level.

I would suggest something on the lines of "-emit-llvm no longer
implies LTO, users should use -flto instead".

Cheers,
Rafael