But it's then trivial to read them on my iPad when I just want to read or if I'm doing searches I just use Spotlight on my Mac. Unfortunately Files on iOS does't really leverage tags well - hopefully with iOS12. I just put them in a shared iCloud folder so they are synced to all my devices. I have a ton of academic ebooks and papers. If this is more casual academic use then I'd advocate just skipping using anything but the Finder and occasionally iBooks. I know you mentioned academic papers but is this just for casual reading or is this for specific research for writing a paper? There's a pretty big difference between organizing invoices, bills and notices and say organizing scientific papers for citations. It'd help if you explained your workflow. We are currently considering going back to EndNote, as much as this pains me, but there has been so much instability with other PDF/reference managers. We used to use Mendeley, but they got rid of their team plans (that we paid a lot for) so we had no choice to but to find a new solution. Finally, Readcube was supposed to take their citation manager out of beta in October and is still in beta an very unreliable. There are also some major bugs in how certain references are matched up and are nearly impossible to fix in a library once they start. They were supposed to release a Papers -> readcube conversion tool to preserve tags and collections, but have not released it (was supposed to be out by November). Specifically, the group collaboration features are browser only, and really only supported in Chrome. Readcube has missed 3 promised deadlines for improved features and bugfixes so our license has been extended each time for free. We have a license in my lab group for both Papers3 and Readcube. They are only issuing minor bug fixes to address major problems and are working to transition Papers3 over to the Readcube platform. As a FYI, Readcube purchased Papers about a year ago, and all development (aside from bug fixes) for Papers3 has ceased so currently there are no plans for future improvements or versions of Papers on any of the OSes.
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