You can export a copy of the PDF with annotations embedded by using File → “Export PDF…” from the library view or “Save As…” from the PDF reader. (To export the original file, drag the attachment item from the items list to your filesystem or use right-click → Show File and copy the file from there.) When exporting metadata (e.g., BibTeX or RIS) from your library, there's an “Include Annotations” option under “Export Files” that will embed annotations in all exported PDFs. We plan to support other ways to export annotations in future updates.
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