Ideally your app shouldn't be navigating away from index.html -- instead it should be rendering content within the same DOM (either via bundling or loading content with XHR/Ajax).
Double check your content security policy meta tag -- that can get in the way of the PhoneGap Developer app recognizing gestures. If you're not sure yours will work (if you have one), paste it here.
Hmmm- I don't see a content security policy tag anywhere.
FWIW: a single index.html bundle or Ajax is not an option in this case- though that was part of the appeal of PhoneGap for me. I can package up an entire self-contained website as an app. Navigation between pages is working fine. The only part broken is the gestures.
I'm not sure then -- it may be down to how the gesture detection is handled in the PhoneGap Developer app. Since most of us will be operating under the SPA architecture, it just may not have been discovered as an issue yet. You might want to file an issue: Issues · phonegap/phonegap-app-developer · GitHub
Thanks for the suggestion- I just did.