Yeah, seems he isn't around people who know git. E.g.:

  Me: Why?  I already added them before, why do I need to add them again?

  They: You just do, OK?

The answer isn't "You just do," neither is it complicated. You need to re-add files after you've further modified them, because you aren't adding files, you're adding changes to files at the time you added it.

After all, why should your VCS assume that your file layout consistently and meaningfully aligns with your changes? I've found it's much more meaningful to cut up a body of work into several commits after the fact using a tool like GitX.