For Mac there is this nice shiny aplication called skim, that looks very nice. You can add notes, highlight (two-column does not work) and export the notes. The notes appear as a list in a sidebar as you work. Importantly skim stores the annotations in the file itself. So why am I not using smim yet? Unfortunately the annotations seem to be in a skim specific format, so that preview can not pick it up (and so acrobat reader might not either). Skim is not available for windows, so I'm not sure if I should lock myself in.
e.g. before submitting a MS, or hand manipulating some formatting because Word does things (like cross-references) so half-assed [from here ] Select all the text (CTRL-A) Press Ctrl+Shift+F9 Editing to remove anonymous comments that only contain thanks. I really appreciate the thanks, but it makes it harder to find comments that carry pertinent information. I'm also going to try and paste informative comments in the body of the post to make them easier to find.
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