To be more specific:
As I asked before - What is this "template override system" that CraftZombie mentioned we SHOULD be using (see the top of the 1.3.9 upgrade announcement/ddirections)? A bunch of the instructions for 1.3.8 had me change files inside my template-specific folders, and I noticed the 1.3.9 upgrade directions change files outside the template folders. If my code is looking for instructions inside the template-specific files, then I suspect those aren't fixed and my coding is screwed.