cjdns/doc/autostart-at-login.md

Autostart cjdns when you log-in

You can configure your session to autostart cjdroute when you log-in to your computer. Just add a file in ~/.config/autostart/cjdoute.desktop containing:

[Desktop Entry]
Comment=
Terminal=false
Name=cjdroute
Exec=xterm -class cjdroute -e bash -c '...path/to/cjdns/cjdroute <~/.config/cjdns/cjdroute.conf; echo "Terminated ($?)"; read'
Categories=Network
Keywords=cjdns
StartupWMClass=cjdroute
Type=Application
Icon=modem
Version=1.0

As you can see, you should put your cjdroute configuration in ~/.config/cjdns/cjdroute.conf.