The generator terminal should not be shorted to ground, but it is connected to the generator windings which will only show a very low resistance to ground. If the poor machine were jumped with 12v direct to the battery the cut out relay is probably fried. Good news is it probably protected the generator.
Start the tractor and bring it up to about 3/4 throttle. I assume the ammeter at this point will show discharge. If that's the case, meter from the generator output terminal to ground. If you show a good voltage (might be as high as 9 or 10v) then your generator is fine. Short across the cutout relay terminals momentarily and the ammeter should show a reasonable charge and the voltage observed at gen. output term. should be roughly the battery voltage. If this is the case, replace cutout relay.
If, however, you see no appreciable voltage at the generator in the above test, things get more expensive. Third brush generators typically don't lose their polarization but it's possible espeically if the fellow that jumped her with the wrong voltage also didn't know a thing about polarity (sorry, I'm a 6v purist.) If that's the case, I recommend the motoring test:
Motoring test -- remove generator from tractor and set on test bench. Connect ground (POSITIVE for heaven's sake) to generator frame. Connect 6v negative to gen. output terminal. Be sure to brace generator well (a vise works nicely) as the whole point is to spin it like a motor. If at all possible, put an ammeter in the circuit. There are several possible outcomes -- 1) Generator motors fast and evenly -- good generator. 2) Gen. does not motor and ammeter goes off scale -- internal short, need to rebuild generator. 3) Gen does not motor and ammeter reads low or zero -- internal open or test connections bad. Verify test connections, if still bad, rebuild generator. (normally I'd say replace brushes and inspect for internal broken wires but in your case something may have melted.) 4) Motors slow and unvenly with low current or "jumpy" meter reading -- dirty commutator, clean and retest.
Hope this helps,