It's designed to be as simple as possible.
Open a Romfs folder, or check the Pre-built box and select a pre-built decrypted Romfs binary.
Open an Exefs folder, or check the Pre-built box and select a pre-built decrypted Exefs binary.
Open the decrypted exheader for the game you're rebuilding. If the game in question was released before today, 3DS Builder should recognize the...
[Release] 3DS Builder
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