Vanilla added the ability to swap slots with 0-9. If you open a GUI and then hover over another item in the inventory and push the button with the same slot number as the item you interacted with it will switch spots.

Knapping can be done for free by opening the interface, working it and then swapping the stack or the initial item stack can be duped by moving the stack before interacting.

Vessel inventories can be duped by moving the vessel out of the protected slot and then dropped by picking it up or pushing Q.

Thanks to Alas for pointing this out.