When I download a form I don't think I get all the source.

I created a form and downloaded all of the source code. However, the source code references some JavaScript files that are not part of the download. e.g. it references jotform.forms.js and prototype.forms.js. However those aren't included in the JS folder when I downloaded the code.

You do get the source code of your form, but please do note that you will not get all of the files. The only files that are referenced and not part of the form code are those that require to be called from our side to have all work properly.

Having that said, it is possible that your current form might work if you downloaded those files manually, but then again you would need to test all features to make sure that everything works correctly, which is why it was not included in the code with the rest of the files.