dev-vcs/git-annex-5.20141125 does not install a /etc/xdg/autostart/git-annex.desktop file, as e.g. Ubuntu does. This file seems to be created in Assistant/Install/AutoStart.hs.
dev-vcs/git-annex-5.20141125 is no longer in the tree. Is the bug present in current versions too? Can we close this ticket?
I have not used git-annex in ages. Updating the Haskell packages has been a mess every single time (lots of conflicts slowing down portage, and e.g. bug #534194, which took 1.5 years to get fixed), and git-annex itself was iirc consuming huge amounts of CPU and I/O time, slowing down computer start-up significantly. I switched to net-p2p/syncthing. Package updates are timely and painless, and syncthing itself is blazingly fast.