I am flying Etihad SFO-AUH-KTM on a single ticket. I have a very short layover.
Will I go through Customs at Abu Dhabi or Kathmandu?
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Assuming it's on one ticket, you will go through customs only upon landing in Nepal and will not actually enter the UAE officially (you remain in a transit lounge).
In some situations you might have to also go through customs in the UAE, but in any case you definitely will be dealing with Nepalese customs.