I am running through the Unix Bootcamp section of Biostar handbook and it was working perfectly up until I got to the command section saying to input

ls -l 
ls -R 
ls -l -t -r 
ls -lh

My computer was running all sorts of craxy codes for a few minutes, it asked me to allow Terminal access to a few applications. Now when I try to type in ls it does not pull up my files/directory, it only shows the word Shared highlighted in green followed by my home name. When I try to type mkdir it says permission denied. Clearly, I made a mistake in the above step when the computer coded a ton of stuff. Is there a way to fix this? Undo what I did?