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Some pdf readers for windows allow you to highlight and type notes into PDF files. The pdf readers that I've seen for Linux only allow you to read pdfs. Are there any that allow you to highlight text and add notes?

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You can use okular for that purpose. Be aware that it doesn't actually change the PDF. The annotations are stored in a separate file and can (only?) be displayed by okular.

screenshots

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Have you had a look at Jarnal as a rather cool general note taking tool (and its cross platform)?

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Are annotations stored into the PDF? –  Nicolas Raoul Dec 22 '12 at 23:32
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