I was thinking about why we need to merge all packages on the root filesystem is this is not a requirement of POSIX. Posix uses PATH to determine where the executable files are, lib directories are setted on /etc/ld.so.conf, others directiories of packages are not important to the system at all, only to the package, so, it can be on the "package directory" inside stow. The unique directory that I think that will need to be merged is /include. So, instead a translator that merges all the filesystem, what we realy need is a translator to change PATH and emulates ld.so.conf, so, you will have a very organized directory structure without break POSIX compatibility.
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