portage(5): improve layout.conf documentation

Signed-off-by: Mike Frysinger <vapier@gentoo.org>
removeFromContents: avoid KeyError, bug #454400

It's possible for two different paths to refer to the same
contents_key, due to directory symlinks. This could happen if a
directory was changed to a symlink after a package was merged, either
by the user or by a pkg_* phase from some random ebuild.
emerge-delta-webrsync: fix STATE_DIR for EPREFIX