Nix(OS) solved this problem by hashing all packages based on their inputs (including other package hashes) all the way down in a merkle tree. You would have one

Nix(OS) solved this problem by hashing all packages based on their inputs (including other package hashes) all the way down in a merkle tree. You would have one copy of the icon pack, for example. But if any common libraries are built with different inputs for a particular program it will be duplicated instead of shared. Nix can then go through your store and hard-link any duplicate files between similar packages to save some more space.