Zotero retaining deleted pdf bookmarks

realtime99
When I add a pdf attachment to a Zotero item, and highlight the pdf in the main panel, in the info panel I see the pdf's bookmarks.

The problem is that if I open the pdf, delete the bookmarks, and save it, Zotero still shows the bookmarks in the info panel for the pdf. It shows them even after I close and re-open Zotero. If I copy the attachment file elsewhere, delete the attachment in Zotero, and re-add the attachment (without the bookmarks), the bookmarks do not reappear.

Why/where does Zotero retain this bookmark data that is not in the actual file? Is there a way to delete the bookmarks without this workaround? Thanks.
  • adamsmith
    That's Zotfile functionality. I think you should be able to disable it entirely if you're not interested.
    As for the rest, ZotFIle doesn't really store bookmarks: it just extracts the bookmark structure to a Zotero note belonging to the PDF. It does so only once on importing the file, which is why deleting them in the PDF does nothing . You can of course just delete the contents of the note (e.g., ctrl+a and then delete) should you you want to.
  • Gurdas_Sandhu
    @adamsmith I could not find that setting in ZotFile's GUI. Maybe I missed it or it could be a hidden pref?
  • bwiernik
    I don't think there is a GUI option. The hidden pref is extensions.zotfile.pdfOutline.getToc
  • adamsmith
    (listed in the documentation on zotfile.com)
  • realtime99
    I see, thanks. I didn't realize I could delete the bookmarks in the pdf info panel b/c I didn't see that it was an editable note.
  • Gurdas_Sandhu
    Just curious, why are such settings in hidden pref and not upfront in the GUI? I know some settings are more complex and even damaging so they are hidden away, but something like this could have been in the GUI. I'm sure there's a good reason, so curious.
  • adamsmith
    I don't think Joscha spends a _ton_ of time thinking about UI/UX. He probably put it in the hidden prefs because relatively few people have asked about changing it.
  • Gurdas_Sandhu
    Thanks, and those are good reasons. BTW, I recall reading something about a future version of Zotero natively having many of Zotfile's features. Is that near-/mid-/far-term?
  • adamsmith
    I don't know. Dan has mentioned several times that they're planning on making the folder structure more human-readable in Zotero itself using some of the same ideas that attract people to Zotfile. I'm not aware of any activity on annotations, though.

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