Currently when you want to select a query to run you choose it from a drop down. But these do not appear to be sorted in any way and finding the right one can be time consuming. It has type-ahead which is good, but requires another trip from the mouse to the keyboard (and I’m a bad typist 
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Two suggestions. 1. Drag and drop from the query manager. 2. Sort the list the same as your query manager, folders and all. Doing folders would require a new component so if you flattened the structure and kept the order you could still use the standard dropdown and move the ball further down the field.