Hi Greg!
I have been very busy with TypeScript 2 and Angular 2 support development and I was able to look into your issue only now. Apologies for such a delay!
First problem is that for some reason “.project” file in folder “.metadata/.plugins/com.genuitec.eclipse.javascript.debug.core/JavaScript Debug Target Source” has been removed. The fix will be released this week with the release of Webclipse CI 8.
I have filed a separate bug for the problem with opening TS files from source maps in JS editor. I hope to get it in for CI 9. However, I would recommend you to properly set up source mapping root, so that you can benefit from placing breakpoints directly in your TS source files in the workspace, which is the biggest advantage of debugging from within the IDE. Please have a look at https://www.genuitec.com/tech/javascript-debugging-with-source-maps/ on details of supported configurations. Unfortunately I don’t have any experience with Webpack, so I am not able to assist you where exactly you should put source maps root property.
Best regards,
Piotr Tomiak