Something good did come out of all that testing though and I thought I should put it in a separate reply, so it does not get lost in the above. I now know why I made sure that the highlighted text was

As far as I can tell, no PDF editor is able to automatically delete all the notes from highlights, whilst keeping the highlights intact. I'm still holding out hope that there is a solution on Zotero's

When you move on to the next project in life, zotfile->rename&move. Store long term references in a cloud service.

To be clear, ZotFile is a plugin. It's something you installed.

Okay then... I didn't know what ZotFile was until a minute ago, but I see that it has a separate set of file rename settings that must work independently of the main setting, and it was set to rename

Does it happen with ZotFile disabled?

I think I used to believe that the "copy selected text into highlight..." feature of Acrobat, PDF X-Change, and Foxit was necessary for Zotfile to extract highlights. Looking into it now, I cannot fin

I agree @dmvalmadre - the more you work with it, the more you realise it is a different workflow, but a much better workflow than Zotfile (and I say that as a huge Zotfile fan). @astroHao - I agree th

- Zotfile

@cenktaskin: I wasn't commenting on this feature. You mentioned "zotfile+system pdf reader", and I was just pointing out that you no longer use ZotFile in Zotero 6 to extract annotations. You can cont

Thank you for your reply. I'm very glad to hear there is a planned workaround. As you suggested, I have turned that feature in PDF-Xchange off, as it was only necessary for Zotfile's now defunct annot

I have downloaded the Zotfile, however, after I take notes and/or highlight, I am not getting the option for 'Extract Annotations' under Manage Attachments. any insights?

For me, the greatest hurdle for now is the note extracting changes between Zotfile and Z6.

I would also recommend using tablet only for reading and annotating PDFs. For this purpose, "Zotfile + tablet" seems to be an efficient workflow. Just google it a little.

Can someone provide instructions on how to extract annotations from an external PDF reader (Adobe) now that Zotero has the embedded PDF reader and Zotfile no longer has the extract annotations option.

I've reinstalled those add-ons (Zutilo and Zotfile) as they are important to my "desktop > writing tablet for annotations > desktop" workflow and the sync is working fine now.

Regarding the minimum nesting level, I'd probably not offer a choice for that, for the sake of simplicity. I think ZotFile also just always extracted the entire Table of Contents. Anyway, if people wa

ZotFile was using that field — and possibly not doing anything else, which is why your ZotFile examples just show an offset from Pages when it was set and numbers starting from when 1 when it was blan

Just sent you the pdfs. I understand your focus is Add Note from Annotations, it’s part of Zotero 6, after all. I am using a modified version of Zotfile, and I only used it for comparison purposes. (I

Extract Annotations also isn't relevant — we're just debugging Zotero's PDF page detection here, and Extract Annotations was removed in ZotFile. (I assume you're running a modified version of ZotFile,