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Use jQuery Audit to debug your jQuery programs.
I ended up using an extension called jQuery Audit which adds extra info in but I hadn't considered getting an extension to the developer tools.
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To debug a Bootstrapper Application, you'll want both your Bundle .wixproj and BA .csproj (or .vcxproj if you're doing a native .dll) in the same solution and the Bundle project should be dependent on the BA project so rebuilds work correctly. The following steps should allow you to step into your code.
Note: Ensure you are not running Visual Studio elevated. If you have UAC disabled, re-enable it. These steps will not work correctly if Visual Studio is running elevated.
1.Rebuild the project. This ensures you have a Bundle created with an updated BA.dll inside it.
2.Right click on the BA .csproj in Solution explorer and select Set as StartUp Project. The BA .csproj should be bold.
3.Right click on the BA .csproj and choose Properties.
4.On the Properties for the BA .csproj select the Debug tab.
5.In the Debug tab, choose the radio button labeled Start external program
6.Browse to the path where your Bundle is built.
Now, you can press F5 and start debugging. Remember that any time you change the BA .csproj, you also need to ensure the Bundle .wixproj is rebuilt. Otherwise, the Bundle will launch with your old BA in it and the debugger will find the newly built BA's .pdbs don't match.