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Currently this are what the Zen js files are named and contained:
html5.js = html5shiv.js only
html5-respond.js = html5shiv.js AND respond.js
How Zen works right now only up one of the above files ever gets included, just depending on what options a developer chooses on the appearance admin page:
Choosing "Add Respond.js..." - will included the "html5-respond.js" file
Choosing "Add HTML5 shim" - will include the "html5.js" file only if the "Add respond.js" option is not also chosen
...now the problem...
Though the admin configuration options would suggest otherwise, it is currently impossible for Zen to enable only respond.js:
if a developer unchecks "Add HTML5 shim" but still has the "Add respond.js" option checked the html5-respond.js file is still added to the page. So even though the developer explicitly has chosen differently, and the admin interface indicates otherwise, the developer will still have html5shiv added to their pages since html5shiv is part of the "html5-respond.js" file.
Zen needs a separate respond.js file which is not combined with any other scripts for this use case.