For this tool, you need all file because the tool creates a new archive with files found in the folder « extract ». It doesn’t replace files on the original cfsi file. So if it misses any files, the game crash.
My patcher is different. It doesn’t replace files, it adds the new files at the end of the archive, and changes the address of the position of the new file. So at each patch apply, the archive size grows up because all files are kept.
I made for you a new tool here : http://teamzero.last-dreamer.fr/patch/softRepack.zip
It add in the 00000000.cfsi file only the files located in « gameFiles » folder. Be carefull, you need for each files, to keep the same path ! For exemple : « system/cinema/cinema_c_en.std.orb » -> « gameFiles/system/cinema/cinema_c_en.std.orb » and not « gameFiles/cinema_c_en.std.orb ». it is very important !
I didn’t test this tool, but I think it works. Say me if you have a problem.