Absolutely not a perfect solution, and maybe you're already using it within your Makefiles, but for anyone who doesn't yet know about it there's Latexmk[1] which is supposed to automate all of this hassle. I think at least on Debian it's included with texlive-full. In addition it has some nice flags like `-outdir` which lets you send all the crazy LaTeX intermediate build/aux files to a separate directory that's easy to gitignore.