Doc: Fixup misplaced filelist.sgml entities and add some commentary

Hi.

Having been in filelist.sgml a bit recently I've noticed that the original
alphabetical ordering of the entities therein hasn't been adhered to.
Partly, I suspect, because there is no guidance about these files and how
they are organized. The attached puts things back into alphabetical order
(by section) and adds some commentary to this and related files, and the
manual.

I made the choice to move the special %allfiles; reference to the top since
placement doesn't matter and burying the one unique thing in the middle of
the file didn't seem helpful. Now both its immediate presence and the
comment point out the existence and purpose of ref/allfiles.sgml.

David J.