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The issue is one of clearly defining the system. For example, consider a
Stirling cycle. The analysis of its efficiency *changes* depending on
whether the regenerator is included inside or outside of the system
boundary. If it is inside, the heat output during the isochoric compression
is stored inside the system and re-input during the isochoric expansion. It
thus does not count into Q_in or Q_out, whereas it does if the regenerator
is outside the boundary.
From an engineering point of view, in a wide range of practicalsituations, if you care about high efficiency, you can do better