Being a tourist attraction, commuting within the city is not an issue. Both Olacabs and Uber are available in Jodhpur at very reasonable rates, so you can use the app to conveniently hop from one location to another. However, these cabs don't enter a part of city which has narrow alleys. So it is better to ask the driver before boarding!
Local autos are available as well - you'll need to bargain with them a little but they generally don't charge exorbitant prices. You can also talk to the auto drivers to stay with you the whole day - that's another convenient option.
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