backend/
module1
module2
module3
frontend/
module1
module2
module3
or
modules/
module1/
frontend
backend
module2/
frontend
backend
module3/
frontend
backend
This is purely personal choice really. I have constructed my system to isolate the back-end code from the front-end so that I can maintain strict and precise control over when and where website data is being edited, but that was just my approach. Personally, I don't feel that one way is necessarily better than the other; whichever you prefer is perfectly fine so long as you're consistent.
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