.dependencies file in skeletons

With skeletons is the .dependencies file just for reference, or is it of functional importance – i.e. is it necessary for the site to run?

They are functionally important, as they are necessary for installation of skeletons with proper dependent plugins, themes, or vendor libraries. Take for example the Blog Skeleton:

Plugins and themes are not hard-linked, ie they are not included with the skeleton itself as this would make updating its repository much more time-intensive (replacing plugins, themes, etc). Rather, the .dependencies file is read by Grav and the necessary plugins and themes gathered in the installation.

That said, downloading from the Skeleton-page gives you a pre-assembled package, where everything is included.