ROM Hack Encrypted CXI issue

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Pokéidiot

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Recently I was trying to obtain an ELF file from a firmware image, then I realized that each section of the file were CXIs. I tried to extract the ExeFS and exHeader from the image and everything went well. But when I tried to obtain the elf with patchrom (I use a fork called ctr-elf), it fails. Output below.
Code:
C:\Users\...\Documents\FIRMS\TWL_FIRM\0>C:\Python27\python exefs2elf.py
textBase: 00300000
textSize: 00047000
roSize:  00164000
rwSize:  00001000
bssSize:  00011000
WARNING: textBase mismatch, might be an encrypted exheader file.
arm-none-eabi-objcopy: error: the input file 'workdir/exefs/rw.bin' is empty
arm-none-eabi-ld: cannot find workdir/exefs/rw.o: No such file or directory
 

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