The main tree now uses virtual/pkgconfig. Please modify packages in the prefix overlay to depend on it instead of dev-util/pkgconfig. dev-lang/python needs to be changed. Others probably do too, although I have not grepped the overlay to check.
It will happen eventually, but it is not a major issue (everything still works now). In other words, there bug report is not helpful to anyone. We know that minor changes lag, we know that major breakage needs to be fixed. This report does not describe major breakage.
fyi: this is the list of packages that need a sync app-antivirus/clamav app-editors/scite app-misc/pal app-office/gnumeric app-shells/dash app-text/ghostscript-gpl app-text/stardict app-text/texlive-core app-text/xdvipdfmx app-text/xpdf dev-haskell/gtk2hs dev-lang/R dev-lang/mono dev-libs/confuse dev-libs/glib dev-libs/libIDL dev-libs/libcdio dev-libs/libcroco dev-libs/libgweather dev-python/wxpython dev-tex/luatex.mine dev-tex/luatex gnome-base/gconf gnome-base/gnome-vfs gnome-base/libglade gnome-base/libgtop gnome-base/orbit media-gfx/exiv2 media-gfx/gimp media-gfx/gthumb media-gfx/xsane media-libs/flac media-libs/fontconfig media-libs/gst-plugins-good media-libs/libart_lgpl media-libs/libcanberra media-libs/libdv media-libs/libexif media-libs/libgphoto2 media-libs/libopenraw media-libs/libsndfile media-libs/libtheora media-libs/libvorbis media-libs/libxspf media-libs/openexr media-libs/xine-lib media-libs/phonon media-sound/esound media-sound/herrie media-sound/jack-audio-connection-kit media-sound/rhythmbox media-video/ffmpeg net-ftp/filezilla net-ftp/lftp net-im/mcabber net-im/pidgin net-libs/libproxy net-libs/libtorrent net-libs/libwww net-misc/aria2 net-misc/openssh net-p2p/rtorrent net-p2p/transmission sys-apps/dbus sys-apps/preload sys-apps/usbutils sys-devel/distcc sys-devel/llvm sys-libs/e2fsprogs-libs www-servers/lighttpd x11-libs/vte
