It's very versatile — it's got great image handling, for example, so you can use it for collecting visual materials, and easily browse as a gallery or as full-sized images. And I particularly love the built-in PDF support, which has everything you need — multiple reader views, annotations, table of contents, rotation, conversion, OCR, etc. Search is fast, multiple database support is great. And it's a very nice touch that you can combine the local database file support with cloud sync, although the mobile app could be better there.
It's worth noting that Devonthink does not have citation/reference management, so for scientists/adademics it's probably not an adequate replacement as Zotero, Endnote, Papers, etc.
Annotations become part of the PDF file on disk. But they're stored as separate editable objects in the PDF that remain editable; for example, if you open an annotated PDF in Preview (on macOS) or in Adobe Reader, they are still editable. And so you can remove them.
Devonthink also lets you remove all the annotations. With your PDF(s), select Data > Convert > "to PDF without Annotations", and it will make a copy that has all the annotations removed.
I agree that it would be nice to keep the annotations separate. But fortunately the PDF format is flexible enough that it can preserve the annotations and not "hard code" them into the visual tree.
You can’t even export pdfs or notes from it anymore to send to others. Only some snippets via some bad Elsevier platform which is a headache. They will lock you in, and they specifically updated Mendeley such that the database is encrypted towards you yourself. I lost my whole Years worth of papers and research to it.
Do not use Mendeley.
Do not use anything made by Elsevier.
It's very versatile — it's got great image handling, for example, so you can use it for collecting visual materials, and easily browse as a gallery or as full-sized images. And I particularly love the built-in PDF support, which has everything you need — multiple reader views, annotations, table of contents, rotation, conversion, OCR, etc. Search is fast, multiple database support is great. And it's a very nice touch that you can combine the local database file support with cloud sync, although the mobile app could be better there.
It's worth noting that Devonthink does not have citation/reference management, so for scientists/adademics it's probably not an adequate replacement as Zotero, Endnote, Papers, etc.