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I recently noticed that emerging world does not upgrade packages obtained with layman. I have been syncing with layman, and in fact many of the overlay packages currently installed are no longer in the tree. I suppose I could emerge each package individually to upgrade it, but there has got to be a better way. Here's the relevant part of my current upgrade process:

layman --sync-all
emerge --update --deep --with-bdeps=y --newuse --keep-going --complete-graph --verbose-conflicts @world

I would think that running emerge like that would at least raise a warning that atoms are in my world file yet not in the portage tree, but I've never seen one.

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The problem is that the overlay packages are never stabilized (the ~ is never removed from the arch KEYWORDS in the ebuilds). I'm not sure why this isn't being done -- at least in any of the overlay packages I use.

The solution, found in this gentoo-user mailing list thread, is to allow unstable packages from each overlay in package.accept_keywords:

*/*::overlay-name ~amd64

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