Very strongly agree.
What I'm currently having to do is to download the PDF to outside of the Library (to get any annotations made on the web), edit the PDF locally (in Preview or Highlights), attach it to the reference, make it the primary attachment, and then finally delete the old attachment.
I think Papers is storing the annotations outside of the PDF so that it has a clean copy in case it needs one perhaps. There has to be a way to allow it to do that and still do end-to-end synchronisation of annotations.
same issue here. I already lost annotations and highlights on dozens of papers made by Preview while I didn't know it...
Please...this is one of the best aspects of papers!
I submitted a similar feature request but cannot find it. I think it got killed during the review process. I don't understand why such an intuitive behavior was not there from the very beginning. Only annotations that are made into the PDF files are permanent. Any annotations stored in third-party apps are not reliable in the long run, just like the legacy Paper 3 app. I hope this feature can be planned and implemented soon.
Strongly support that! It would at least be very helpful to export all PDFs including the annotations at once such that annotations don't get lost in case switching reference managers.
If using "Open file" from ReadCube Papers to read and add annotation a paper in Preview (Mac) (the location of that paper is in ~/Documents/Papers Library), hit save, and then close Preview, the change won't be reflected in ReadCube Papers, instead, it will try to recover the file to an earlier version, which led to the lost of all the annotation made by Preview. Please fixed that since not everyone like the internal PDF reader, and there do exist people have there preference over PDF readers.
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