/boot/overlays was recently added without belonging to a package. It's only used by bootloaders at the moment, so add it to the 'runtime' package to get added with ubldr and friends.
Fix distrib-dirs METALOG generation while we're here. I can't pin down the involved commits, but history elsewhere seems to indicate that bapt@ fixed this to pull in all attributes from mtrees while generating the METALOG. This fix got clobbered somewhere later, so restore it.