I am currently working on a Console Based Game. Is is permissible to have games that run on the command prompt of the PC based on the rules? For example you might have to use commands like cd on the terminal/command prompt to get to the file to run it?

I'm guessing yes.  It would likely be a downloadable game and run on windows, but people will be much less likely to try it out -- downloaded games often get a bad reputation for virus potential and other dangers of course.

One of the rules for this jam is that it need to be able to be played on Itch.io

Thanks for the information. Well but it says to links to external downloads whereas what I would do is make it downloadable not any external links plus there are a few windows downloadable games in this game jam so how does that work anyways?