if you don't have a air intake different than standard factory you are not quite to stage I... you have the exhaust, which doesn't require a new tune... your next step would be the air intake if you go factory it will come with a code card that your dealer will use to re-tune your bike... if you go aftermarket you will have to buy such a tune..
The exhaust pipes are definitely Indian stage one because the tips will only fit on these pipes. (I had mine recently installed.) The air cleaner mentioned above is the other half of “stage one” and may or may not have been done. You can tell just by comparing your air cleaner to the factory air cleaner. I only added the pipes and still have the factory air cleaner. The factory stage one pipes also come with a reflash of the ecm which the dealer will install if you have them install the pipes. General consensus seems to be that the reflash is not really necessary
for the pipes only - nevertheless Indian does do it. The dealer will have to hook your bike up and tell you whether the reflash was done.