Not using the package manager and copying files instead terrifies me
The patching part of the package manager will make changes to files only if none of the files that it needs to change are changed in the parts it needs to change. Whew, what a mouthful.
Otherwise it will tell you that the patch cannot be update because some file is modified.
(A pure php implementation of GNU patch for the technical ones)
The reason for doing this is because a simple copy could overwrite files changed by you or by other patches and this method won't.
We will never make changes to the skins. You will get instructions on what to change if needed and it's your duty to do it.
If you want to get the full file just redownload the latest Etano package and copy the files from there. Winmerge is your friend in this case. But be aware that the patches are also updating the database, something that Winmerge cannot show.
Maverick was one step ahead of you: he changed the files from the start and then asked for explanations (by email) on how to read/understand the update packages and how to apply the patches. I presume he started to enjoy doing this cause I didn't hear any complaint from him ever since
I guess we could add the explanation for Maverick to the technical docs for Etano in case there are other DIY hardcore users out there.