It depends on what your prototype is trying to prove. Do you prototype the user interface for ease of use and demonstrate to customers or use prototypes of architecture?
If I prototype the user interface, then I will throw away everything as soon as the concept goes through iterations and is proven.
If I prototype the architecture, then the final code will be in line with best practices and will be used.
However, it is surprising the number of prototypes of hacking workers that end in full production due to lack of time or budget. If your intention is to ensure that the code does not end in production (i.e. the prototype user interface), then a screenshot layout may be useful, rather than their code.
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