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.