Changing a third-party script is something to avoid if possible! There are other ways to define a bundle's references.
This assumes that "jquery" is an alias for the CDN URL. i.e.
(You can just put the URL into the bundle.txt, but that'll make updating versions more work later.)
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Option 2) Call Bundle.AddReference
In CassetteConfiguration, try this:
bundles.Add<ScriptBundle>("path", b => b.AddReference("jquery"));
Or after the Add* calls, you can get to the bundle by its path:
bundles["path"].AddReference("jquery");
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If you do own the script file, then reference either the jquery CDN URL, or the alias:
/// <reference path="~/jquery"/>
I hope that helps. Please let me know if you have more questions.
Thanks,
Andrew