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Papers2 does not integrate with external iPad applications in the way I expected. I use iPad applications like GoodReader, iAnnotatePDF, and PDFExpert to read and annotate papers.

The functionality I expected was:

• Export from Papers to an external PDF annotation application
• When I reopen Papers, the annotated PDF is shown in my library

However, here is what happens:

• Export from Papers to an external PDF annotation application. It renames the file, using a random string as the filename.
• When I reopen Papers, only the original (unannotated) PDF is in my library.
• Alternately when I export from the external application, the annotated file is imported as a *new* PDF, unconnected to the original, with a random string used for the filename.

I started using Papers because managing filenames in iAnnotate wasn’t working: I couldn’t figure out which files were which. So this is absolutely key for me.

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This is a bug report to Papers2, copied here since bug reports are private. Any workarounds or suggestions for alternate annotation/reference management workflows would be very welcome.

This annotation environment completely failed to meet my expectations: I expected to ‘Open In’ an annotation application; in fact there’s just ‘Export’ and ‘Import’, meaning that the annotated file isn’t automatically stored in the Papers2 library.