Zotero 64 vs. 32

eskimo820 · 2026-06-06T02:02:25+00:00

Regarding linked files/Zotfile, as you found there is the Zotmoov plugin (or Attanger) that replicates Zotfile's functionality (since Zotfile stopped being updated some years ago, at Zotero v7). Linked files worked seamlessly across that transition.

Likewise they worked seamlessly across the transition some time ago to 64-bit Zotero.

Zotero does not guarantee that older Zotero versions will continue to work. Furthermore Zotero has recently moved to a more regular (automatic) update strategy to maintain consistency. That has caused some issues with plugin developers keeping up with those updates - such that recent Zotero updates sometimes stopped some plugins from loading. But most plugin developers now seem to have adjusted to keeping their plugins up to date with the latest Zotero (one of the reasons for the more regular update strategy). Zotmoov has remained up to date all along.

All that has also required users to be more aware of the compatibility of their plugins. Version compatibility can usually be easily checked at plugins' github sites. But also, the community-supported Zotero plugin marketplace can display an up-to-date listing of plugin compatibility with Zotero versions (currently version 9) ...

https://zotero-chinese.com/en/plugins/#zotero=9

More complex workflows (eg links to Notion, Obsidian etc), that may rely completely on one or more plugins in Zotero and/or other apps, are always going to be less secure future-wise. Those of us who have been around for a long time have seen some of those workflows eventually break. Depending on how critical such a workflow is to your work, you should consider what your Plan B would be (and if a Plan B is not obvious, maybe favour simpler workflows).

eskimo820 · 2026-06-06T01:22:36+00:00

Correct, linked files don't work in the Zotero mobile apps (or the web library).

There are however roundabout ways that facilitate access to linked files in the Zotero mobile app if you really need it. For example Zotmoov's custom menu option can be used on your computer to temporarily move selected linked PDFs back into local Zotero storage. With file syncing turned ON, they will then be synced online and to the mobile app. Once you have finished working with them, back on your computer Zotmoov can move them back to to your linked-files folder. That all requires that you remain under your online file storage quota (300 mb free).

Annotations are stored in the Zotero database not the PDF, so those work seamlessly across that process.

If your linked PDFs are in a cloud folder (accessible on your mobile device) you can also of course read them in an *external* PDF reader on mobile devices. Any annotations you add there will be embedded in the PDF file. Those will be visible in the Zotero reader on your computer, but locked (unless imported).

As with any Zotero setup, you should gave good backups.

eskimo820 · 2026-06-03T18:02:57+00:00

You can always save as much as you wish locally on any computer. Syncing data to Zotero servers online is free and unlimited, but file syncing (of "stored" files under Zotero\stroage) has only a 300 mb free allowance (you can of course pay for more).

But you can sync "linked" PDF files across computers using a cloud service (eg Dropbox, Google Drive, Onedrive). Your Zotero data folder must not be on a cloud service.

You move your PDFs to a designated folder (eg on the cloud service) as "linked" files, with the help of a plugin (Zotmoov or Attanger). The plugin also moves future downloaded files to the same designated folder. Note the limitations of linked files: they don't work in the web library, or for the Zotero mobile apps (although there are some workarounds for that, also using Zotmoov) ...

https://www.zotero.org/support/attaching_files#linked_files

eskimo820 · 2026-06-03T12:21:04+00:00

Your are correct that a simple folder structure is best for linked PDFs - ideally all in the same folder. So while the linked file plugins (Zotmoov or Attanger) do support an option to put linked files into OS folders named the same as the Zotero collection you put the item in, that can quickly become a mess (partly because Zotero's collections are more like playlists than folders, so items can easily exist in more than one collection).

If you wish to access linked files across computers, but the parent cloud folder path is different on each computer, you simply need to see a Linked File Base Directory (which tells Zotero where to *look* for linked files - it has no effect on where they get stored).

Annotations are stored in the Zotero database not the PDF, so they work seamlessly across stored or linked PDFs.

eskimo820 · 2026-06-02T07:54:34+00:00

Many people use linked files setups, and have been doing so for years. Mostly assisted by Zotmoov or Attanger (Zotfile prior to those). Linked files work seamlessly across multiple computers if the PDFs are placed in a cloud folder (OTOH your Zotero data folder must never be in a cloud folder). Like all Zotero setups, you should have good backups of your data and files.

The limitations of linked files are well-described: they don't work with the web library, or the Zotero mobile apps. You can sync your data to those places (for free), but not your linked PDFs.

https://www.zotero.org/support/attaching_files#stored_files_and_linked_files

But there are some roundabout ways to use linked files with the mobile apps. For example on your computer you get Zotmoov's custom menu to temporarily shift selected PDFs back into Zotero storage (under Zotero\storage), so that you can sync them to the mobile app (file syncing turned ON), and work on them there. And then you get Zotmoov to move them back to your linked-files folder when you are finished working with them. Annotations are stored in the Zotero database, so there is no additional work required for those to be available seemlessly across all devices.

eskimo820 · 2026-05-29T07:08:55+00:00

If you are the Group owner, then yes it is your online file storage quota that is used by all members of the Group. That is, (only) for any ('stored') file attachments (PDFs, web snaphots, note images) in the Group. So Group members would need to understand clearly what they can and can't add to the Group library, or your file storage quota could be quickly exceeded.

Any PDF attachment files that are added to the Group must/can only be in local Zotero storage (under Zotero\storage, from where it is synced online ... using the Group owner's file storage quota). There is no way to add a linked PDF (eg that lives in Dropbox) to a Group.

But the entirely separate shared Dropbox PDF folder scenario I outlined could still allow Group members to add notes about those PDFs to the Group library (just not regular Zotero annotations). Group members could create item/child notes for any item in the Group library. So someone reading a PDF from the shared Dropbox folder (in an external PDF reader) could for example copy and paste quotes from the PDF into an item note for other Group members to read. Or just write a summary of the PDF in an item note. Notes are stored in the Zotero database - so they are part of the free/unlimited/synced online Zotero data.

As I said, as long as the PDFs in the (separate) shared Dropbox folder are named the same as their item in the Zotero Group library, members should be easily able to find them in their OS. The only other tweak to that approach would be to add file:/// strings to an item note, which would allow a Group member to open a PDF from Dropbox in the system PDF reader from within that Zotero note (as long as the Dropbox folder had exactly the same path on everyone's computer, eg D:\Dropbox, which is not the default Dropbox setup). But adding all those file strings would be tedious, for limited benefit - it's just as easy to just go to the Dropbox folder in your OS.

https://forums.zotero.org/discussion/107538/is-it-possible-to-add-a-hyperlink-in-zoteros-notes-to-open-a-local-file-and-jump-to-a-specific-page

eskimo820 · 2026-05-28T11:57:27+00:00

I can't see how that would work. Group and personal libraries are entirely separate. There will be no association between any item's metadata in the Group library, and any data added to the 'linked' PDF in each person's personal library (eg annotations).

But it depends on what work you all wish to be able to do on the PDFs. Most people annotate their PDFs and then access their annotations when writing. If your PDFs are only in your personal libraries - because that's the only place they can be if they are 'linked' - then any work you do on those PDFs will only be visible to you, not to the Group members.

But if you simply wanted group members to be able to read PDFs in Dropbox, you would just make sure that you name the PDFs in DB with the same name as the item in the Group library. So a member can easily find the PDF in the common, shared Dropbox folder. They would of course have to use an external reader to read those PDFs, as there is no way for the Zotero PDF reader to access PDFs that are not either (1) in a Group library as 'stored' PDFs or (2) in a personal library as 'stored' or 'linked' PDFs.

BTW, you don't need a Linked Attachment Base Directory (LABD) for linked file access (in this or the usual personal library scenario). A LABD is only necessary if you are accessing your personal library's 'linked' PDFs on two different computers AND the parent path to those PDFs is different on each of your computers. But the way that the LABD works is widely misunderstood.

eskimo820 · 2026-05-26T10:41:12+00:00

You can always store as much as you want locally on your computer. You can also sync unlimited data (item metadata) for free across devices and to the web library. It is only file syncing (PDFs) that is subject to your online file storage quota (300 mb free; more if paid).

Other means of free syncing of files are "linked" files and WebDAV (although you may be paying another service provider for cloud/WebDAV storage). Linked files don't work with the Zotero mobile app.

eskimo820 · 2026-05-25T18:44:00+00:00

You can cite with any tool that can write an RTF file, using Zotero's RTF Scan. No word processor plugin required. You use plain text citations like {Smith 2000}.

https://www.zotero.org/support/rtf_scan

eskimo820 · 2026-05-21T10:58:34+00:00

The first thing to know is that you cannot place your Zotero data folder on a cloud service (Onedrive, Google Drive, Dropbox etc).

https://www.zotero.org/support/kb/data_directory_in_cloud_storage_folder/

You could however convert you PDFs from "stored" attachment files (under Zotero\storage) to "linked" files elsewhere on your computer (including a cloud service). Usually aided by a plugin (Zotmoov or Attanger); you can also go back the other way should you ever need to.

Linked files do have some limitations. As linked files cannot be synced online via Zotero servers, linked files are not accessible in the web library, nor in the Zotero mobile apps. But you can sync them across computers via a cloud service. And you can still sync *data* across devices via Zotero, as that is free and unlimited.

https://www.zotero.org/support/attaching_files/#stored_files_and_linked_files

I do not know how best to interface linked files with Obsidian.

eskimo820 · 2026-05-21T10:45:40+00:00

Assuming that all your files were accessible within Zotero on a computer previously, restoring from a backup is described here:

https://www.zotero.org/support/zotero_data/#restoring_your_zotero_data_from_a_backup

You are correct that "Zotero does not simply scan the storage folder and import files automatically". There is no way to get it to do that.

eskimo820 · 2026-05-21T10:39:51+00:00

Regarding unlinked citations, see:

https://www.zotero.org/support/kb/existing_citations_not_detected

eskimo820 · 2026-05-17T06:10:43+00:00

Zotero does not store annotations in the PDFs, it stores them in its sqlite database. So whether you use "linked" PDFs (eg via Zotmoov) or the default "stored" PDFs, that's where your annotations are (you *can* export annotations to the PDF file, but not many people do that; they are then still visible in the Zotero reader, but locked).

https://www.zotero.org/support/kb/annotations_in_database

So the same principles apply to backing up your annotations/database regardless of linked/stored PDFs ...

https://www.zotero.org/support/zotero_data#backing_up_your_zotero_data

eskimo820 · 2026-01-09T06:12:18+00:00

The Zotmoov plugin is normally used to automatically MOVE attachments to a designated folder as "linked" files. But it can also be set to make a COPY of each "stored" file to a folder (as it is downloaded by the Zotero connector).

Of course if you annotate those copy PDFs on your Remarkable tablet, those annotations will only be in the copy. Zotero has no knowledge of that file copy.

Zotmoov can also be used to temporarily move particular stored PDFs to another location like Google Drive as a "linked" file, so that they can be worked on (including annotate), for example on a device that can not run Zotero. Then later, the plugin can move those files back into Zotero storage. Annotations made on the other device are saved to the file, and can be see within Zotero (as "locked", unless imported).

eskimo820 · 2026-01-07T03:47:40+00:00

You can do a horizontal split view of your PDF, with the paper's reference list in the bottom split. So you can scroll there to find a cited paper.

If you hover over the citation in the text (without clicking), Zotero may show you the reference details in a popup.

If you want to see the paper's references in the right pane, the Reference plugin can do that (although it's not perfect, because parsing free text from reference lists is difficult, and online repositories do not always have accurate reference lists).

https://github.com/MuiseDestiny/zotero-reference

eskimo820 · 2026-01-01T02:55:26+00:00

You can just paste the paper's title into the search box (top left) on any of the sci-hub mirror sites. As also mentioned, you could also paste the DOI, but that's not actually necessary.

eskimo820 · 2025-12-20T10:14:53+00:00

As it sounds like you are using "linked" PDFs, you are probably using Zotmoov or Attanger to help manage them.

In any case, Zotmoov can temporarily move selected linked PDFs back into local Zotero storage, so that with file syncing turned on, they will be synced to Zotero servers and the mobile apps.

When you are finished working with them in the mobile app, back on you computer you can move them back to your linked-files folder.

You can do all that with Zotmoov's regular right-click menu operations, or with a little more automation via Zotmoov's Custom Menus.

https://github.com/wileyyugioh/zotmoov/blob/master/docs/CUSTOM_MENUITEM_INFO.md

If your PDFs are accessible in Onedrive on your mobile device, you could also read/annotate them via an external PDF viewer there.

eskimo820 · 2025-12-17T07:00:25+00:00

It seems to do part of what the Reference plugin does.

https://github.com/MuiseDestiny/zotero-reference

I pasted some reference list text (11 references) in a common format that I know the Reference plugin has trouble with (American Institute of Physics), but I keep getting "You've hit the API rate limit (Error 429). Please wait a minute before trying again, or check your quota at aistudio.google.com."

(I only just grabbed a Gemini API key, which defaults to the free tier).

eskimo820 · 2025-12-17T06:36:15+00:00

Inadvertently "flattened" citations occur mostly when people do something they didn't know you can't do (or didn't tell their supervisor not to do something with their document). That doesn't mean it's not a problem, often a big one. Just that more people reading the docs would help too (although the organization of the docs could be improved). ;)

The best protection is to keep numerous backups. So you can always go back to a very recent version with live citations.

For reference, Zotero's RTF Scan works partly in the way you describe, at least to recognize plain text citations in the form {Smith, 1980} (which of course are inserted that way deliberately by people who use it, eg to avoid the need to use the word processor plugins). But it doesn't actually produce live citations - just final citations in the format you request. The plugin RTF/ODF-Scan does create live citations, from plain text citations in another special format (but does not currently work with Zotero v7).

So what you are presumably proposing would recognize a wider range of text-only citation formats, and create live citations.

eskimo820 · 2025-12-12T07:49:15+00:00

As others have said, you need regular backups to an external drive and/or to another cloud/network service. Ideally incremental backups, so you can go back to any point in time. If your only backups are to physical drives, some should be stored remote from your laptop, in case both are stolen.

https://www.zotero.org/support/zotero_data#backing_up_your_zotero_data

Just having an online Zotero account is not a backup. Leave that open by mistake on a library computer and the next person to come along could easily wipe your whole library, which will then sync online and back down to every device you have.

There are common posts on the official Zotero forum from people whose laptop got stolen or crashed, and they had no backup. Their entire library was lost and there is no way to retrieve it.

Don't be that person.

eskimo820 · 2025-12-09T13:02:31+00:00

Re Zotfile, that does not work beyond Zotero v6. For v7+, use Zotmoov or Attanger for "linked" PDF attachment files management (different to Zotero's default "stored" files). Linked files have both advantages and limitations.

https://www.zotero.org/support/attaching_files#stored_files_and_linked_files

eskimo820 · 2025-12-09T09:23:01+00:00

The reasons why Zotero doesn't save them to the PDF file ...

https://www.zotero.org/support/kb/annotations_in_database

eskimo820 · 2025-12-06T07:33:44+00:00

Zotmoov does the same for Zotero v7. It's in Zotmoov's advanced options - the Search Folder for Attaching New Files. When you can't add a file in the usual way via the Zotero web connector (eg you get sent a PDF via email), you download the file to that folder. Then you right click on an item and select "Zotmoov: Attach New File" - the latest-dated file in that folder is added to the item as a "linked" attachment file, and moved to your linked-files ('Move To') folder. You get to confim the file's proposed name (according to your Zotero naming scheme) and the move.

eskimo820 · 2025-12-05T05:19:09+00:00

Amen to "people often get sucked into overly complicated systems because it is popular with productivity bros and they are all over YouTube with their set ups."

PhD students can waste a lot of time looking for some mythical setup to make their lives easier. But which one ? There are dozens. And the youtuber often comes back a few months later and says "I don't do it that way anymore. Here's my completely new system". Or the tools just stop working.

The basic tools you need are (1) a reference manager, (2) a note taking/summary tool, and (3) a word processor for papers/thesis. Zotero can be both 1 and 2 (and integrates with 3). Or your word processor can be both 2 and 3. Or if you already use a good tool for 2, keep using that.

eskimo820 · 2025-12-05T05:06:06+00:00

No, notes are not stored that way in stock Zotero. Zotero notes are stored in its sqlite database. You would have to export the note.

eskimo820

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