In the case of it's gone. the 's could stand for 'has' or 'is' depending on the context. 'Where's the bus?' 'It has gone. (just left).' 'When money is spent, it is gone. (finished, no longer here). In the case of it's done you would need more words for the phrase to make sense with 'has'. It is done = finished, completed.

It is gone. It is done. There's your answer.

As far as i know ,''s' nerver short for 'has'.

Nope not has..it is short for it is!