Absolute link pointers, able to work in another system

With the symlinks utility by Mark Lord (offered by many distributions; if yours doesn't have it, build it from source):

chroot /home/user/system symlinks -cr .

Alternatively, on systems that have a readlink command and a -lname predicate to find (warning: untested code):

cd /home/user/system &&
find . -lname '/*' -exec ksh -c '
  for link; do
    target=$(readlink "$link")
    link=${link#./}
    root=${link//+([!\/])/..}; root=${root#/}; root=${root%..}
    rm "$link"
    ln -s "$root${target#/}" "$link"
  done
' _ {} +

Symbolic link files take more space. Hard linked files share the same inode; but a symbolic file is a pointer to the original (location).

Despite that, there are two caveats for hard links:

• Not all file system support hard links.
• Hard links cannot be applied for folders.

I guess you do not need to consider about the storage issue since in most of the cases they are trivial. In addition, there might be some tools helping you organize genres virtually (they may take advantages of virtual file systems).