I could only assume jQuery is somewhat compiled into the obsfuscated file? Am I correct?
Yes. That is correct. Juicebox comes with its own version of jQuery bundled within the 'juicebox.js' file.
In doing so, we know that Juicebox will work.
Otherwise, we would have to rely on users including jQuery in their web pages (a further step in the embedding process) and we could not guarantee that the version of jQuery that the user uses does not have any bugs in it which would result in the Juicebox gallery failing to function correctly.
But on a page where I already have a copy of jQuery loaded it's a waist of filesize...
You might think that it would be OK to just use the the version of jQuery which comes bundled within the 'juicebox.js' file to save you from loading a separate version of jQuery in your web page.
However, if Juicebox ever changes its version of jQuery or strips out any jQuery functionality or changes its built-in JavaScript library completely, then your web page may break. Therefore, if your web page requires jQuery for anything other than Juicebox, I would recommend that you continue to load jQuery separately in your page.
Do you provide a juicebox.js without jQuery compiled?
No. There is no version of the 'juicebox.js' file available without jQuery included.