the migration to debian means that from now on all our releases will be based on Debian instead of Ubuntu. I am referring here to the target release, e.g. what runs on the board. Not what is used to create the images (which is irrelevant, and in fact we still use Ubuntu on our build servers).
Our images are based on Debian, which means that 99% of the packages that we assemble into the images come straight from Debian (we picked Debian jessie version). Then we add a few custom packages that come from our overlays, as you noticed. Most of what we have in our overlays are backport from more recent Debian release, and there are a few things that we add which don't exist in Debian/Ubuntu (mostly a few boot scripts). Then of course we use a custom kernel, not the main Debian kernel.
Effectively, we are no longer building our overlays for Ubuntu, so you won't be able to install anything from our overlays. And if you must use Ubuntu, you might have to rebuild what we push in the overlay for the specific version of Ubuntu that you are using. If you are ok with using Debian instead of Ubuntu, it should be fairly straight forward to update your build system to build Debian images. This is the exact same process as building Ubuntu images, you just point the tools to the Debian archive, instead of the Ubuntu archive.
Let me know if you have more questions.