There is an issue with installing N9QT when MyDocs is on an ext4 filesystem. In that scenario root can not create/delete files and directories under ~user/MyDocs because standard root credentials won't allow it. The fix is trivial... simply use `aegis-exec -u user <shell-command>' throughout your deb control scripts (preinst postinst etc). I haven't checked the tweak scripts, but you should probably audit them for the same thing as well. Thanks very much for the awesome work you have put into these tweaks and scripts.
chown -R user:users /home/user/MyDocs