webstorm debugging with chrome, ripple and phone gap

I have a project setup in phonegap and have copied the www directory over to a web storm project.

We are using an HTML5 librarie named Kendo IU and specifically the Mobile portion.

I installed chrome along with the jetbrain and ripple emulator plug-ins to debug.

I am using a MAC so I am starting chrome from the command line as follows:  open /Applications/Google\ Chrome.app --args --allow-file-access-from-files --disable-web-security

For reference I have a team member using a Windows environment as well and has the same issue.

Our problem is that we cannot get web storm to stop at a break point on any javascript that is not in the initial html file (index.html) in this case.

We think the problem has to do with how either phonegap or kendo pushes the new html files into a singlel DOM using the app.navigate method they provide.

The application by the way works fine in chome with and without the emulator ripple.

Any help would be appreciated.

Shawn