I am extremely frustrated by the lack of a web app that will simply store PDFs and let you annotate them. For example, a simple navigation sidebar and a display to the right would be sufficient. I have tried googling for this to no avail. Are there any recommendations for something like this? As a sidenote, I currently use Dynalist for all of my notes and if there is something similar to this that can store and annotate PDFs, that would be ideal.
Consider converting the PDF to HTML, and then annotate the HTML, <a href="http://web.hypothes.is" rel="nofollow">http://web.hypothes.is</a><p>Three years ago I faced this problem while creating a prototype to annotate research papers, and used a client side library by <a href="http://annotateit.org" rel="nofollow">http://annotateit.org</a> which posted annotations to my own server.<p>The conversion from HTML to PDF was handled by <a href="http://pdftron.com" rel="nofollow">http://pdftron.com</a> DocPub.