Well the explanations for each choice doesn't exactly match up to what it does. It would be great if there was a preview tree and an undo/redo button somewhere so that you didn't have to close the program, check output.mdl0 and then restart.
I have to make a change and if it works, rename the old input to input1 as a backup and rename output to input. Then by the time I'm done rearranging the whole top of the tree (which I'm doing), I have around 20 or more mdl0s as progress backups. It takes a long time this way