My current workflow has me writing first drafts of academic work in Ulysses or Scrivner (depending on the scope of the project). I like writing in Ulysses for its simple markdown environment that is distraction free. I love not having to have a web browser open to write so Google docs isn't my first choice. For writing clinical trial protocols I use a special web app called protocol builder. I currently use Papers which allows me to "cite as a write," searching for papers I have in my library and add them as unformatted references in Ulysses, Scrivner and protocol builder (really any text editor).
To totally commit to Paperpile I need flexibility to do my writing in places either than just Google docs, meaning I need to be able to search for and add unformatted references in a variety of applications. I'd be quite happy leaving references unformatted and not formatting them until I paste into google docs (or word potentially). But, I need to be able to actually do the writing in another place. Is there any way some kind of desktop app that would enable this functionality might ever be created?