Until this week, JBoss Hybrid Mobile Tools were able to work with a single Cordova version. To add insult to injury that single version (which is Cordova 3.1.0) was embedded in and was not changeable. However, Santa was busy and just dropped an initial implementation of multiple Cordova engine support to nightly builds. Below is a video of it in action. If you are cool enough to get the nightlies, instructions are on the project's site .
A word of caution is needed though. This feature is still under development. If you really really need to use a different cordova version it will do the trick but for anything else I would wait for the release before moving my production code. Please do try the feature and provide feedback either on the related issue or create new ones.