The automatic prototype generation works with a simple regular expression to try to detect function definitions, and then just ignores setup() and loop(). It doesn't work all that well (it gets confused if your return type is multiple words like "unsigned int" or is on a different line than the rest of your function header). Still, it's been okay for most things.
In fact, here it is: ^(\w+)\s+(\w+)\s*\(([^)]*)\)\s*{