After I open Zotero for a time, it can not attach new file through Zotfile. I need to restart the app to attach new file. BTW, I am using the Mac version.

Did the trick for me, ZotFile will extract the annotations fine.

I had a look on what ZotFile could do for me but stumbled upon 2 issues:

Is there a way to have an item permanently tagged after being retrieved from a mobile device?

I've followed the instructions for dowloading Zotfile and am using v. 5.0.25 of Zotero. I have pointed to the folder where I am dowloading PDFs but when I do this, Zotero doesn't seem to give me the p

You need to install Zotfile in the Zotero app, not Firefox. In Firefox, right-click on the download link and choose Save Link Target As and save the .xpi file to your computer. Then, in Zotero, click

Zotfile can't be downloaded and installed in Firefox?

Now I also understand that you're saying Zotfile reproduces the links in Zotero, even though they originally appear as bookmarks in the PDF file.

And if your note looks similar to the 2nd one I posted, that's absolutely Zotfile, which extracts the bookmarks in PDFs into a Zotero note for ease of access. Deleting them in Zotero doesn't delete th

I don't think Zotfile is generating these links, as the actual PDF file has all of them as bookmarks, as far a I can tell.

@dstillman ZotFile auto-extract PDF table of contents using PDF bookmarks.

It just has a large table of contents (generated by ZotFile, btw.) of the PDF/book -- correct?

If you are using Zotfile and you are saving files in another folder, you can just search for pdf files in the storage directory using software like directory opus and delete all the pdf or manually li

If they come on a USB, you get the metadata separately, and you want to use Zotfile to process them, there is no solution to get all of them into your library at once. You'd probably have to copy them

Interesting ! but I trust more isbn/doi retrieval to add the entry, then zotfile to attach the pdf. Most of my pdfs are preprint version with no metadata for zotero to retrieve. In my experience, star

I use zotfile to attach a document I just downloaded to a zotero entry. With my configuration, zotfile will move the document to a specific folder and rename it.

Yes, I'm pretty sure ZotFile handles the PDF link function entirely separately of Zotero settings, so you'd have to set that separately.

It still seems that, assuming one uses ZotFile, in order to open the pdf at links (e.g. imported chapter headings), one will need to adjust the ZotFile advanced settings.

No need for ZotFile — in the latest version of Zotero you can select the PDF viewer to use from the General preferences if you don't want to use the system default.

Zotfile advanced settings allow you to make Skim the default reader.