Versions used:
Hammer.js v1.0.5 (jQuery version) Ember v1.0.0 RC 1
No conflict. These guys play well together. I'm using hammer.js in the jquery plugin version since jQuery is required by ember and gives extra support for old IE's.
The test-project is build in the style of an app and they've been tested both on my Nexus 4 as a webpage as well as packed in a cordova app without conflict.



















