I want to add my compiz settings to a git repo but I'm having a hard time isolating the relevant files. My home directory is a bit of a mess here. I see gnome, compiz, and gconf everywhere. Which are the right ones? :)
It depends on your set-up. They are stored in several locations. The best way for you to find them is to open your Terminal
On my machine, which appears to be Ubuntu 14.10:
compiz settings turn out to be stored in
If you're planning to back up your Compiz settings, you might just want to back up the entire parent directory of your compiz settings - you're more likely to end up in a familiar desktop environment that way.