I had made simple bash script which helps to merge *.pac* files in /etc. It uses vimdiff as tool to merge two files. You can play with it absolutely safe. Script doesn't make any chenges untill you push w (write) command. Push p (pretend) command to watch what script will do after pushing write command.
You can get my script here:
looks like pacdiffviewer which belongs to yaourt, which offers a bit more options.