don't want Zotero duplicating my files

Hello! I am new to Zotero.

I like that it retrieves metadata from .pdfs so I like having it linked to my files.

But, I have been researching for many years now and I have my own file organization system, and I do not want to use Zotero's.

Right now, Zotero has copied all my .pdfs to put it inside its own storage system, the one with the folders with the letters and numbers. I don't like this and I want it to just use my "Readings" folder.

I downloaded Zotfile. The General Settings for Zotfile has the Location of Files set to my "Readings" folder, instead of "attach stored copy of file(s)". I then deleted the Storage folder in my Zotero folder, to get rid of the copy. But Zotero just made a new Storage folder with new copies to replace it.

I am still confused about how to make this happen. Please help. Thank you!
  • (First, let me re-iterate what I said on Twitter: I think this is a mistake. By keeping your file organization on your harddisk, you're effectively duplicating the places where you organize things: you now have a Zotero library and a folder structure. For example, if you delete an item in Zotero, it does _not_ delete linked files, so you need to perform the same operation in two places. When you move a file on your harddisk, Zotero doesn't know about that, so the link breaks. There's also functionality that's not available with links, e.g. you won't be able to access files online on nor will you be able to share them via groups.)

    With that out of the way, if you still want to go this way, here's what you'd do:
    This is assuming a blank library.

    1. You probably will want to disable auto-sync while you're figuring this out. (I think e.g. that's why your storage folder mysteriously returned)

    2. Getting links into Zotero: Instead of dragging files to Zotero, you want to either use the "Link to File" option under the green plus sign or use ctrl+shift+drag (cmd+opt+drag on Mac).

    3. You can then retrieve metadata on all the files -- as you've already noted, if you do a lot of this quickly, google scholar will lock you out. Improvement on that are planned, but currently the only way to deal with this is to go in small-ish steps.

    4. You can now set up ZotFile with a custom location for files. This will affect any newly added files, not the old ones. Note that ZotFile only move files once they're attached to metadata. If you regularly drag or otherwise save a file to Zotero by itself, it will still go into storage until attached to metadata and moved by Zotfile.
  • (I get what you're saying, but I use my Readings folder for a lot of things on a lot of devices and having to change that up would be a huuuuuge pain for me. I don't delete files much—mostly just stockpile them—so not concerned about the deleting files issue.)

    #2—okay, so me dragging my files in made the duplicates, I think. So what I want to do is delete my existing Zotero stuff that I dragged in, then re-import the stuff with "Link to file" instead of dragging-and-dropping?
  • To keep your PDFs organized your way, use the "Attach Link to File" option. You still get the full text search from the PDF. If you set up a "base" directory, then only the folder structure inside the directory matters. In Zotero 5, you can define the base folder in Edit>Preferences>Advanced>Files and Folders

    You could do this manually, but if there are too many items, maybe ZotFile can do this (I do not know).

    My attachments are organized using this schema. With a base directory setup, you can move the PDFs between computers and drives as long as everything inside the base directory is consistent. For example:
    let's say your base directory is set to C:\Users\username\Documents\Articles\

    Inside this base directory, you might have sub-folders, such as "Conference", "Journal Article", or "A" "B", "C". Later, if you wish to move everything to another drive (D:\MyData\), or maybe an online storage folder (C:\Users\username\Documents\Dropbox\), you just need to go to Preferences and point to the new base folder.

    - Before you make any major changes, please take a full backup
    - If you use "Attach Link to File", the attachments cannot be synced via Zotero's storage. But then, they can be synced via Dropbox/OneDrive/Google Drive. However, you cannot open attachments from Zotero's web interface (because they are not on Zotero's storage server).
  • I think the easiest would be to drag everything to the Zotero trash, empty it, and make sure sync goes through. This may take some time. Then restart.

    All of gurdas's advice is good, btw., but I'd recommend you to first get everything set up the way you want and _then_ deal with the base directory etc.
  • I agree with adamsmith. My response was posted to an older version of the thread and I had not seen other responses. If all your PDFs are in "Readings", then just proceed with attach to file link, and when you have everything set up and working, switch to the base directory option. Note that the base directory option is just an additional feature and is not required to meet your prime objective.
  • Thanks all. I think adding everything with "link to file" instead of dragging and dropping was the key to achieving what I wanted. I already had the rest of this stuff set up as you both suggested but I had dragged-and-dropped the files in, causing the duplicates. I believe everything is working now.
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