Apache Cordova deals poorly with html, since native html does not allow partial files nor templates.
I solved that with standard Handlebars because it allowed me to structure my html, but still having a full complete single html file produced after cordova prepare and before cordova compile. That is, contrary to jQuery with load, the html partial files are not loaded in runtime, but assembled before cordova compile. I did not want to use Handlebar templates in the browser either for the same reason. I wanted everything to be assembled before being compiled.
The html/handlebars file structure will be something like this inside your www dir: