No, eix doesn't do any harm and does not cause the change in the location of the sources. (I think
the change is due to a re-design by the Gentoo devs of the way portage works.) But you'll find that eix won't give you the correct information any more (and neither will "emerge -s") once the location of the sources changes, until you change the sources line in /etc/make.conf. I don't know which specific package or packages caused the change in my case, but I expect in the Gentoo forums somewhere there's an explanation of the reason for the change and what causes it.
EDIT: Just had a quick look in the Gentoo forums and, sure enough, found the following post: http://forums.gentoo.org/viewtopic-p-51 ... ml#5167335
"the source directory in layman.cfg changed a while ago to /usr/local/portage/layman, so you probably blindly updated that configuration file.
You also have to check that the source line in your make.conf points to the correct destination."
So the design change was to the layman
Didn't bother to search further, but I expect there's something about it in the Gentoo Handbook and the Gentoo Wiki.
(Also, current latest version of layman in portage is 1.2.0-r1
, so when you merge that version, you will probably find things have changed.)