I agree with Eric.
At the moment in-text citations automatically link to a Paperpile app page for that document.
Full citations in the reference list also link to that same Paperpile page, however some references will include a DOI or URL that is linked directly to the relevant DOI or URL.
I can see the use of having a single Paperpile page that lists all references within a document, but it isn't something I want in my document as it makes it harder for readers to get directly to the referenced paper.
As Eric suggested I think in-text citations should link to an anchor in the document for the full reference in the reference list (if this is even possible in GDocs), a la Wikipedia. Then the full references in the reference list shouldn't link anywhere unless a URL or DOI is included, in those cases link to the URL or DOI.
There could be an option to provide a link at the top or bottom of the reference list taking the user to the Paperpile app page for that document.
I'm not interested myself in the SEO side of things, but can see what Eric is saying. If people are publishing these documents on their websites search engines will rate their documents higher if they are found to include links to other respected webpages.
Actually, as i write this i think i understand what Stefan is saying. The Paperpile app needs an 'ID' for each reference in the document to know which ones have been included, so they can generate the full Reference list. This explains the links for the in-text citations, but would it be possible to add a bookmark for each one and use that as a unique identifier (are bookmarks available to the API?). Then the full references in the reference list just wouldn't need the links in them as they are reformatted each time so shouldn't need an ID.
Maybe that is possible?
Other that this small issue I find Paperpile to be a brilliant app that does a lot more than other referencing software, thanks for making it.