I didn't find in EBoard any way to automatically call
the flag when the opponent's time reaches 0.
If it exists, shame on me :-)
If it doesn't, here is a patch that adds this feature.
It is user-configurable with the menu item I added in
the "settings" menu.
It is not 100% clean because I used the user input to
send the command, so it pollutes the console a little
bit. But it works.
The patch is based on 0.9.5 version.
eboard-0.9.5# patch -p1 <
Congratulations for your work.