Easy update from v2.1 to v2.2: No need to create a clean save-file. Just update and continue playing. (But only if updating from v2.1) Info about updating from the earlier versions is in the mod description.
Easy update from v2.1 to v3: No need to create a clean save-file. Just update and continue playing. After his death/resurrection Jesus will have the items from the new update in his inventory.