For what it’s worth, I don’t think breaking backward compatibility with the Atom link munging is a great idea. Two basic reasons:

1. preserving the convention that $item[‘link’] means the rel=”alternate” link, and thus the same thing that $item[‘link’] means in RSS feeds, would impose the need for some kind of sorting logic to guarantee that the first link element in the array is always the rel=”alternate” link. Breaking the convention would break virtually all Magpie software everywhere, and make normalizing with RSS a horrendous pain in the ass.

2. in practice, anyway, a generic Atom link element means absolutely nothing to a program consuming the feed; it is only in the context of being a link rel="alternate" or link rel="self" or link rel="enclosure" or whatever that it actually means anything that a feed consumer would be interested in understanding. I can’t think of any reason that I’d want to be able to search through a straight list of all the link elements without regard to their “rel” value; and if there is some reason that you’d want to, you can always store some special kludge element somewhere that will keep track of all the link rel values that are used in a particular item.