general: More 3.12.0 packages and dependencies for gnome-core-<apps/libs> + various fixes.

IIRC I had to work around issues similar to  #138, #137 and #135 so this might work around/fix some of those.

**media-libs/grilo** was removed since it exists in gentoo now.

**gnome-extra/gnome-contacts** was removed as a dependency to **net-im/empathy** to avoid #124.