A very important feature in jabref-3.8.2 is broken, unfortunately:
It is not possible to add papers by using a doi.
There are two solution for the gentoo users:
a) a very small patch (server URL changed) for a source based jabref version
b) a bump to the app-text/jabref-bin-4.x version.
Unfortunately 4.x is still beta and has still many open issues.
For the latest Java dependencies read http://help.jabref.org/en/FAQlinux
JabRef is released https://github.com/JabRef/jabref/releases/tag/v4.0.
So we can make version bump for app-text/jabref-bin
I added jabref-bin-4.0 to tree.
Please open another ticket if this is still an issue.