I agree with the OP except for the web app part. I personally welcome a web app because it makes me platform independent which is important to me. There's one point I wanna expand on: I really believe the Paper files should be visible and accessible in Dropbox. In my view the perfect way would be to see the Paper documents as .md files in Dropbox, together with the ability to right click and "Open in Paper" which would then open them in the Paper app. Of course edits to the markdown should be possible through the md files directly and then be visible in the Paper web app as well. I'd also like the separate Paper app folder hierarchy to go away and move to Dropbox, which already does this well. I find it confusing that we have "two worlds" right now.
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