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The shapes.graffleshapes file in the app package is now in Contents/Frameworks/GraffleShapes.framework/Resources.*

I'm not sure about your stencil-editing problem. Are you talking about the mapping between the file's extension (.gstencil) and its actual format? The file is, in fact, an XML text file. It will be zipped if "Compress on disk" is checked in the Document:Document inspector.

*I recommend Devon Technology's EasyFind for searching in app packages. It's free in the App Store or on their site.