There are other issues, too:
/usr/libexec (should not exist, files should be moved to /usr/sbin
/mnt (is reserved for administrator, subdirectories not allowed, mount
point for removable media is not yet standardized, will probably be
/home/httpd (/home is reserved for users, service home is not yet
standardized, will probably be /srv, currently /var/lib or /var is used
in other distros, too)
Causes big problem on AFS or NFS /home systems (unable to emerge update
on client machines; unable to have two webservers in one network,
because they are sharing data).
/usr/kde and /usr/qt (/usr should not have sub-trees, sub trees are
allowed in /opt, i. e. /opt/kde and /opt/kde).
/usr/games should be a directory for binaries, not subtree, (i. e.
/usr/games/bin -> /usr/games, /usr/games/lib -> /usr/lib,
/usr/games/share -> /usr/share/games).
/usr/X11R6/share is not in FHS (probably move --datadir to
Issues 1, 4 and 5 can "automagically" solve GNU-FHS:
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