If I long a lot of futures in a particular commodity, say gold.and at the same time I long a lot of gold so that the price of gold goes up due to market shortage, is this considered market manipulation or arbitrage?
Market manipulation all depends on intention. In your case, I would say that it would be market manipulation because your intention is to pump up the price of gold to benefits from it. I do not see this as arbitrage. Arbitrage is related to the mis-pricing of identical securities in different markets. I do not think it applies here.