its recommended to use a tool that GUI i feel that cmd based tool are very "iffy" from OS version to spaces in the directory. props to the guys using CMD but i perfer GUI
anyway if you want that romFS.bin try what i do (or something similar)
decrypt your rom
i recommend rxtools and hit the decrypt rom on 3ds option. (you will need to make a nccinfo.bin and place it in your sd root prehand.
once you have a decrypted 3ds rom (how you decided to is up to you) download a app for PC called 3ds Rom Tools (gui ver)
and take the decrypted rom form your 3ds and put it in the 3ds Rom Tools folder then open the app and select the rom. then in order hit the buttons and it will completely decompile the game, if you want that RomFS.bin then stop at extract romfs button
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