So I am someone who LOVES games like this (type-help, the roottrees are dead) so this was right up my alley and I was SUPER excited to see a game like this submitted! I think it's an interesting spin on the theme, and I appreciated how accessible it was for someone that doesn't know a lot about computer "shells" like I do. I was really enjoying it, and will definitely come back to it later!
SPOILERS
I got as far as decoding the binary in diary6.txt and then got a little stuck. I agree that the hint system isn't super helpful -- the only hint I ever got was "you may need to use outside websites," which I felt like I understood after the first time I went to a cipher translator. Unless, of course, it's referring to a different website I just didn't find.