[candiddevmike]

After working with these types of systems, I'm convinced we need a new type of package manager that works with overlays and merges package databases somehow. That way you can update the underlying image (at your own peril, maybe) and have the overlay package manager see the new versions. Constantly rebuilding everything when the underlying changes is a waste.

[colordrops]

Nix?

[candiddevmike]

AFAIK Nix wouldn't solve this as it has the same issue (/nix/var/nix/db). Here's a scenario to better illustrate:

I'm using systemd nspawn with my host root as a lowerdir overlay. In this container I install some packages not present on the host. The overlay upperdir now includes the new packages and the new package database. I upgrade my host, and now the nspawn package database is wildly out of date because overlay doesn't track line-level file changes.

OverlayFS is really handy but it causes a ton of churn from rebuilding everything.