> and for some reason the yubikey-neo-manager ebuild and package is gone...
Ah you mean https://bugs.gentoo.org/show_bug.cgi?id=620830 ("app-crypt/yubikey-neo-manager depends on dev-qt/qtwebkit:4 via dev-python/pyside[webkit]"). Read the comment, there is a reference to some other "manager" thingy.
