Now, the problem is that Designer takes it upon itself to rename the subdirectories under the project to whatever you put in "appFolder" which completely defeats the bug fix (you can read my previous example above to see why this won't work). Is there any way to separate what the output directories are for the project from the value of appFolder to get this to work correctly?
In your case you should be using Deploy to do what you'd like. Preview is coming soon which would break based on your suggestion.
What you need is a way to set appFolder to something different for when you deploy. Expect deploy to have lots of features added to it as we move forward.
PS - I do use the deploy functionality but it basically just copies over the contents of the development directory to the deployment directory which still makes this same issue come up (with the appFolder because it changes subdirectories). The only way I see this not being an issue (if you don't hand edit the index file as you suggested) is if the application was on the root level of the webserver. Maybe it's just me, but that seems like a rare case in many development scenarios. I have a few different applications I've written with Sencha tools that I need to keep in different directories (like the /scripts directory, for example). If every application looks to the root of the webserver for the Sencha "app" folder, nothing works correctly.
If there is something I am missing about using the deploy button to make this work (how I've described before in previous posts), please feel free to let me know. I've changed just about every variable I can find in the tool to get it to work and am now stuck except for the hand edit change you suggested.