Hi,
Yes, indeed your correct! A command line prompt is the same as your terminal application. Just a different way of expressing the same thing. "Navigate to the folder where Jav-It exists" simply means to make your current directory the folder where you installed Jav-It. Conisdering your getting program output, I assume you've done this already!
In regards to your folder path, I noted that it contains spaces. Did you remember to include quotes around it? For example:
./jav-it catalog -d "/Library/Documentation/User Information/Vuze/system library/maintenance"
You will notice that the entire path is surrounded in quotes. This is done to protect the spaces you have, since otherwise MacOS has no idea how to understand what part is your path and which part is a new command option.
Let me know if this helps!