When you include all files for every version of your app, wyBuild compares the files and see what needs to be patched, what needs to be added, what needs to be delete, and what needs to be left alone.
I other words, wyBuild is smart enough to know how to get from version "A" to version "B" by making the smallest possible update. Does this make sense?
In other words, follow what we wrote in the step-by-step walkthrough. Include all files for every version and let wyBuild worry about what has changed.