Duplicate files

This is possibly a really silly question, but are there any occasions where Paperpile creates a duplicate copy of a file, eg for annotations or notes?

I’m asking because I’m reaching the limits of my Google Drive storage and while looking for files that I can delete I have come across a significant number of apparent duplicate pdfs in the Paperpile folders. They may well be the result of syncing issues, which I have had at some point, but I’d rather be safe than sorry.

In principle, Paperpile should not create duplicates. If you see files with duplicate names the reason can be that you imported from sources like your hard-drive or Mendeley that contained duplicates. In that case Paperpile attaches all files it finds to one reference (as we don’t know which one you want to keep).

Also the use of some third party Google Drive sync programs may mess things up.

But in general if you want to clean up space going after your PDFs is typically not the most primising. Often there is a video file somewhere which is as big as your whole paper collection. But that’s just a personal experience, your situation could be different of course.

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I have a load of these in my drive from Mendeley import and they add up across my files.

It seems to be that if you delete from Google Drive directly on the desktop (by targeting all those with brackets after their name) then they just get added back, which I assume is Paperpile. So you have to ‘remove’ them from Paperpile.

It would be useful to have a ‘has multiple PDFs’ filter - there is already a ‘has no pdf’ and ‘has pdf’ so could be extended to flag those with more than one.

I am finding two cases: (1) multiple files because these were imported as duplicates; or (2) multiples files were all the chapters from a book have been associated with the same reference.

Having a ‘has multiple pdfs’ filter would help me narrow this down and correct for either case.

The latter case is more difficult as you can’t extract a PDF from one reference into a new reference so I’ll need to create new references and then upload the file and remove the original.

@James, the Has Attachment filter will do just that - display papers which have more than one file attached (PDF or otherwise).


The permissions we get from Google make our sync to Drive a one-way street, so we’re not able to import or read changes made there.

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Is there a way to merge duplicates that I’ve identified and select, but that Paperpile has not identified as a duplicate?

@anna There isn’t a way to do this, but you can force Paperpile to detect the duplicates by making identifier fields like DOI, ISBN and URL the same in each of the duplicate references. Then you can go to the Duplicates Filter on the right-hand side column of your library, select the references, and click the “Merge Selected” button to merge them.