Here is an ebuild for ipsec-tools-0.5.2. It worked nicely on my system. The ipv6 bug reported in 87920 is fixed in this version of ipsec-tools so the patch is not needed.
Created attachment 58743 [details] ipsec-tools-0.5.2.ebuild
Created attachment 58751 [details] ipsec-tools-0.5.2.ebuild
Created attachment 58752 [details] racoon.conf.d for ipsec-tools-0.5.2.ebuild
Created attachment 58753 [details] racoon.init.d for ipsec-tools-0.5.2.ebuild
Created attachment 58754 [details] setkey.conf.sample for ipsec-tools-0.5.2.ebuild
Ok, I've just bumped this in portage. I'm going to stick with the ipsec.conf file for now, I'd prefer we make any config file location changes along with at least a minor version change, so when 0.6 is out I'd like to do it then. Marking this FIXED, if you disagree with the config file stuff, please feel free to re-open this bug for discussion (or open a new one).