I think you simply have to create your own .war file without the sc folder. The .war can then be manually uploaded as detailed in the Google App Engine documentation:
http://code.google.com/appengine/docs/java/gettingstarted/uploading.html
Let us know how you go! :)
http://code.google.com/appengine/docs/java/gettingstarted/uploading.html
Let us know how you go! :)
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