Cordova's JS file should appear on top of all other JS files.
This will alleviate issues for people having issues with the InAppBrowser not opening for iOS devices when using the window.open('[url=http://mysite.com','blank]http://mysite.com','blank[/url]');
When the cordova javascript file is in the middle, the .ipa file does not produce a browser with the "done" button. Also, xCode produces this error message:
"Failed to load webpage with error: CDVWebViewDelegate: Navigation started when state=1"
When the cordova javascript is moved up towards the top (above underscore.js), it works correctly.
Can you please move that javascript to the top so that we do not need to modify our start html page manually (which contains all the other page code when using jQuery Multipage Template)