Trouble debugging complex node-webkit app

I have setup a nw.js debug configuration for a complex node-webkit app I have been tasked to work on. Breakpoints set in the app.js file work fine, but break points set in any of the other application files are never hit. Also, if I step into a function from the app.js file a new instance of the target file is opened for edit even if I already have the target file open. The tab for this new version includes the full path to the target file instead of just the file name.

The working directory is set in the nw.js debug configuration to the default value set when the new configuration window is opened.

Has anyone else seen this behavior? It only happens with node-webkit. Straight up node,js apps work fine.

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