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Edit: Whoops, thought I got a step further but realised I just messed up copying pasting some stuff while playing with the code
Edit2: So I don't think it's a keyword cipher at all at this point, like Ipquarx says it's already in Base64 after a Rot13 cipher is performed. The result doesn't form an image even if reversed, the clue to blackbox level 1 I thought maybe referred to ELF but again if I decode the code forwards or backwards to ascii or utf-8 I don't get an ELF file. Blackbox level 1 was fairly easy for me, I just used objdump -s on the ELF file and in the ASCII section I could read the password for level 2 was "PassFor2". I wasn't able to solve level 2 because it requires assembly knowledge and how to use bufferoverflow to execute malicious code. At no point was anything like WaterCactus referenced so not sure how that helps.