Unfortunately PhoneGap is more than just a JS-file and exentds the JS featureset with native platform features. Usually phonegap plugins are reduced to very simple operations, such as sending an SMS e.g. The Wikitude plugin uses sensors and even analyses cam-frames to apply ImageRecognition algorithms.
Although Wikitude's ARchitect technology also uses JS/HTML that does not mean you can combine them that easy. The AR-View runs in a completely different context and is a View on top of phoneGap's main Activity. Sole way to exchange data between cordova and Wikitude is using the "document.location = architectsdk://..." and architectView.callJavascript.
I recommend you to handle any file-readings in your Cordova environment and pass over all data to Wikitude's SDK using callJavaScript(EgAnyJSONObject).
Hope that helps.
Kind regards, Andreas