I reverted this to draft because a little more work needs to be done to make it all consistent and useful.

I think this is probably where this needs to be to be consistent now.

but a naive version of me would probably try to type the command tutorial $ cycstub --type inst tutorial:TutorialLibrary:TutorialInstitution instead of the command cycstub --type inst tutorial:TutorialLibrary:TutorialInstitution in the tutorial folder

I think we've often wondered whether it makes sense to include the prompt in the samples. I'm torn on this. The only real benefit is that you can see the directory change and the user gets some clear feedback on which directory they should be in to run the command. The downside is that it looks like part of the command... we could try a different prompt separator... maybe:

(/home/tutorial) |> command here

I'm not sure the separator is really the problem, since ultimately this "issue" is with people who aren't that familiar with using the terminal. I wonder how other people handle this when writing documentation. I guess my personal preference is to change:

"""
You can add additional agents to this module by calling cycstub multiple times:

    tutorial $ python rename.py tutorial
    tutorial $ cycstub --type inst tutorial:TutorialLibrary:TutorialInstitution
    tutorial $ cycstub --type region tutorial:TutorialLibrary:TutorialRegion

"""

Into something like:

"""
You can add additional agents to this module by calling cycstub multiple times.

From the "tutorial" directory, run:

    python rename.py tutorial
    cycstub --type inst tutorial:TutorialLibrary:TutorialInstitution
    cycstub --type region tutorial:TutorialLibrary:TutorialRegion

"""

But perhaps that's too verbose/much overhead/easy to miss? Ultimately I don't think it matters much (except that actually this makes the commands really easy to copy form the markdown file and paste in your terminal since you don't have to remove the tutorial $ bit from every line), but wanted to point this out.

I just updated all the code-blocks to be type console instead of type bash to hopefully get syntax highlighting to help with this

All the bash code blocks now have sytnax highlighting that requires the prompt to be indicated with only a single $ (there may be other options, but indicating the directory name is definitely not allowed).