"Steve's still on the transfer list, there's still a long, long way to go with him," said Jones.
"If he has any sense, and I know he has, he will know he has got a fight on his hands and his future will lie wherever he wants it to be.
"I have said before that just because he is on the transfer list it doesn't mean that is it. Things change very quickly in football.
"As long as there is no animosity between us, which there isn't, then it remains a football decision.
"We've had to up Thommo's progress here and we've worked very hard with him on things like his sharpness, quick feet and that, and he has looked good in training, like we have been looking for from him.
"That goal at Plymouth will be a massive boost for him.
"It was a good goal and one I don't think he would have scored last season. He would have put that over the bar or in the side netting to be honest."
Thompson is likely to be on the bench again tonight as City face Watford.