Just to add another viewpoint on annotations: I tend to severely edit a PDF while I'm reading it. For example: crop the top and bottom margins off, expand the left and right margins and use them for text boxes with notes to myself, draw on figures, rearrange figures and text (like a collage) so they're in more convenient places, and add color-coded highlights depending on whether the highlighted text is fact, opinion, an open question, etc. I edit the PDF directly so my notes are available even if I have to use another PDF viewer/editor. If I need to preserve the original PDF I archive it separately. I think one of the key advantages of digital medial is that the user can rearrange and edit it to suit their needs (the other advantage being search / automated indexing). Not sure how many people take this approach, and you're of course free to make the feature work however you think best. Just sharing as a counterpoint to the general consensus for a standalone annotation file.