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My method requires some file manipulation, but it works fairly well for several projects I've worked on.
I use a Livescribe digital pen for all my handwritten notes.
I have a Kindle eink reader, and write notes at the document level on the device.
Everything ends up in MS Word.
Livescribe has an OCR app that converts the notes into text.
I pull in the clippings.txt file from the Kindle that contains all the notes and annotations from the books.
With everything in Word, it is then easy to search and organize the material. I'll even use the Send to Kindle app to send the Word doc back to the Kindle to have the document available when away from the computer.
Bob
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