Containers don't handle the case where two different versions (or otherwise conflicting variants) occur in the whole dependency tree. For instance, consider program A with direct dependencies B and C, where B needs version X of /usr/bin/D but C needs version Y of /usr/bin/D.
I just remembered that the thing I was talking about was SubUser [0]. You can read their manifesto since it better describes everything that they are looking for. Their solution is to keep file revisions so if you need an older version of a file it is still there.
