One question (and complaint) that has been raised after the release of multiple cargo version support is "How to use custom Cordova engines together with JBoss Hybrid Mobile tools?" Well, we heard you and we are already on it. In the next release, JBoss Tools 4.2.0 Beta 1, we are adding the ability to search Cordova engines from local directories and use them. Here is a video showing how this works, which is still subject to changes of course.
There are some caveats with this feature though. Unfortunately, we are not able to use "any" Cordova based distribution. In this release, tools are only able to recognize Cordova compatible directory structures. For instance, we rely on files such as VERSION, that is found on Cordova distributions, to recognize Cordova versions. However, If you have a Cordova based distribution that has a significantly different layout, it will be possible to introduce them through an Eclipse extension point. If you're interested in such an extension point, I would be happy to hear about your requirements.
If you wish to try it out, this feature is already part of nightly builds and you can get the information on nightly update site from jbostools-aerogear project site. I recommend updating the 4.2.0 Alpha2 with the nightly update site for best experience.