In order to install gnome-3.10 for a friend I cloned the gentoo gnome overlay and used its config files to get a quick start - I simply created symbolic links. Unforitnately eix ignores those files and still tells me e.g. net-libs/webkit-gtk-2.2.2 was masked, though it is not.
So far, eix never had problems to read symlinks in /etc/portage. I suppose that something else is wrong with your setup (wrong filename, wrong directory name, ...)
ls -l /etc/portage/package.unmask/gnome3 lrwxrwxrwx 1 root root 60 25. Jan 11:02 /etc/portage/package.unmask/gnome3 -> /root/src/gnome/status/portage-configs/package.unmask.gnome3 grep webkit-gtk /etc/portage/package.unmask/gnome3 >=net-libs/webkit-gtk-2 eix -eI webkit-gtk [D] net-libs/webkit-gtk Available versions: (2) 1.8.3-r200 1.8.3-r201 (3) 1.8.3-r300 (~)1.10.2-r300 2.0.4(3/25) [M](~)2.2.2(3/29) {aqua coverage debug doc +egl +geoloc gles2 +gstreamer +introspection +jit libsecret +opengl spell test +webgl webkit2} Installed versions: 2.2.2(3)(17:34:41 26.01.2014)(egl geoloc gstreamer introspection jit opengl spell webgl -aqua -coverage -debug -gles2 -libsecret -test) I think my config setup/naming is valid. webkit-gtk is just an example, any package that is unmasked in a symlinked file is not recognized by eix. Also package.accept_keywords is affected the same way.
I now moved the cloned overlay from /root/src to /var/repositories (where all my repos live) and now it seems to work. The remaining question is, why eix run as root did not "see" those files. A user is not able to see them - which I was fully aware of. It's only me who administrates that computer, logged in as root via ssh. So I expexted this setup to work.
(In reply to Franz Fellner from comment #3) > A user is not able to see them This would have been my next question after your example: By default, eix drops permissions to portage:portage (250:250) as soon as possible. So I suppose the issue is solved: You either have to change permissions or to configure eix (EIX_USER,EIX_GROUP,EIX_UID,EIX_GID) to keep/set corresponding permissions.