MANIFEST.SKIP in my Syntax::Construct repository contains MANIFEST.SKIP on its first line from the beginning. I think it's the correct way to do it.

Update: It's in fact wrong. The line should be

MANIFEST\.SKIP
[download]

On the other hand, most of my other distributions ship with the file if it exists. I guess it's just laziness - I'm usually tired enough with fixing bugs in the actual code, so I don't spend much time on thinking about what goes where when no one complains and everything works.

Update 2: Note that Test::CheckManifest is broken at the moment.