joe-3.2 installs: /etc/joe/doc/ChangeLog /etc/joe/doc/HACKING /etc/joe/doc/HINTS /etc/joe/doc/LIST /etc/joe/doc/NEWS /etc/joe/doc/README which are also put in /usr/share/doc/joe-3.2/ (with the exception of HACKING). I suggest adding to the end of src_install(): rm -rf ${D}etc/joe/doc
I've fixed this in the joe 3.4 ebuild. I've just checked it in to CVS so give it up to an hour before syncing.