Presumably with the KDK (if it ever gets released) you could write a kindle app that would update the collections.json file from info maintained on Calibre, and then programmatically cause a restart -- still clumsy, but almost practical. You could also have an app to deliver the collections.json file info to Calibre for storage and display -- I don't know yet whether kindle app invocation could be instituted from the pc-side of the usb connection or not.
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