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The app makes use of the fact that Action Tools are not activated during regular workflow runs. This means that whatever they are configured to do only takes effect when the workflow is run as an app:
As evident above, the "DetourRight" value of the Detour Tool is set to True, so when you run it as a workflow it will divert the stream to the right. This stream has our Run Command on it, so you'll get a pop-up asking you to run it as an app.
If you oblige and do run it as an app (after all it did ask nicely), then the Action Tool will kick in, replacing the value for True with the value for False. This means the stream goes left, harmlessly past the Run Command Tool, and does not produce the pop-up window.
N.B. "True" and "False" are Boolean types, which are interchangeable with values 1 and 0, respectively.