I'm not sure how the stuff in the Sources tab of Google Chrome Developer Tools is generated. The tree there does not show every file in a topmost folder. Instead, I am betting that links are crawled from an entry point, perhaps main.js in a dojox/app application. This would explains why controllers such as /app/foo/Bar.js are not showing up by default as "foo,Bar" would be called as a route to reach this item and the app would not have a hardcoded reference to this .js file anywhere. I am still too green to these tools to know if you can add a file to the tree at Sources. I could not figure that out. What you can do to hack around the problem is to put...
debugger;
...in the controller. If your app makes it to that line of code, the controller will suddenly be a part of the file tree and stop at a breakpoint at that line of code within the Sources tab.
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