SGML is a good example of "groups of files". In the I-D on sgml the
proposal is to use Multipart/SGML, have the first part be the main
document, use a Content-reference: header to match body parts to
internally referenced file names. It is not clear to me that
headerset or references is a simplification.
I tend not to draw on SGML for examples because I know relatively little about
it. I had things like TeX in mind here. Defining a TeX packaging would be an
interesting exercise to undertake. The big problem with TeX, however, is that
you have to be very careful to plug all the security holes. For example, TeX is
capable of writing arbitrary files, which can be very bad news indeed. This may
be an issue in SGML as well, for all I know.
Ned