Zotero

Zotero is a free & open source reference manager. With just a few tweaks, it is the perfect tool to help you organize all your messy pdfs.

Installing

First download Zotero for desktop, and the browser addon Zotero Connector. If you are on Linux, it is best to download the Flatpak desktop install from Flathub.

The browser addon Zotero Connector will automatically save the references from your browser with the click of a button: for example, if you are on the official webpage of a paper, it will automatically save all the related information, authors, DOI, etc.

You definitely should also install the following plugins:

• Better BibTex for Zotero, which lets you customize the citation keys
• ZotMoov to automatically rename the PDFs and save them on a custom folder, which you can sync with the cloud or else. ZotMoov works for all Zotero Versions. Note that ZotMoov is a replacement for ZotFile, an older and discontinued plugin which only works for Zotero versions lower than 7.

Another cool and useful plugin is:

• Inciteful Zotero Plugin, which helps you find related literature.

Finally, there is a native dark mode for the Linux Flatpak installation. But if you are on Windows and want a dark mode for Zotero, take a look at Zotero Shadow.

Some of these addons require a small configuration to work flawlessly, which is indicated below.

Automatic and custom citation keys

You can edit the automatic citation keys by going to Settings, Better BibTex, Citation keys. There you can modify the citation key formula, for example as auth.lower + year to have automatic citation keys such as druzbicki2023.

You can also create a custom citation key for any particular reference, by editing the Extra section of said reference with citation key: MyCustomKey.

Renaming rules

Zotero 7 has new and easier renaming rules. For example, you can rename your PDFs as:
{{ citationKey }} - {{ title }}

Zotero 6 had different rules, and also using ZotFile had a problem with subinexes; to fix those, check the appendix. If you are using ZotMoov on Zotero v7 you can skip it.

Saving files to a custom folder

You can automatically save your pdfs to a custom folder (to sync it, etc) with ZotMoov. Go to the Zotero 7 settings, to Settings, Advanced, Files and Folders, Linked Attachment Base Directory, and choose there your custom folder to save all tour PDFs. Now, you must set the same folder in ZotMoov. To do that, go to Settings, ZotMoov and write the same folder on Directory to Move Files To. Also in ZotMoov settings, leave empty the Source folder for Attaching New Files setting. On ZotMoov's Other Settings, set File Behavior to More, and check all checkboxes.

If you are using a Zotero version < 7, you can still use ZotMoov, or ZotFile instead (although it is discontinued). To automatically move your PDFs with ZotFile to a custom folder, go to Tools, ZotFile Preferences, General Settings, Location of Files, Custom Location and select your desired folder. This same folder should also be specified for Zotero itself, at Edit, Preferences, Advanced, Files and Folders, Linked Attachment Base Directory.

Supporting Information PDFs

It is recommended to save the Supporting Information (SI) of the papers by creating a copy of the corresponding reference (with a right click), adding _Supplementary at the end of the title, then attaching the supplementary pdf, and finally editing the citation key as CitationKey_SI. This prevents SI to be renamed incorrectly, since ZotFile and ZotMoov only seems to work fine with one attachment per reference.

Appendix

Renaming titles with subindexes via ZotFile

For Zotero < v.7 with ZotFile.
Some papers have subindexes on the title, such as in MAPbI₃. These subindexes are rendered in HTML, using the tags MAPbI<sub>3</sub>. This is useful when referencing, but instead of saving titles as MAPbI3, ZotFile will incorrectly introduce those "sub" tags on the renamed PDFs by default. To remove HTML tags such as <sub> from the renamed pdf files, you need to configure a custom ZotFile User Wildcard. (source)
To fix that, simply go to Edit, Preferences, Advanced, Config Editor and click on accept the risk (because if we are brave enough there is no risk). Search for zotfile.wildcards.user, and introduce the following text:

{"1": {"field": "title", "operations":[{"function": "replace", "regex": "<sub>", "replacement":"", "flags":"g"},{"function": "replace", "regex": "</sub>", "replacement":"", "flags":"g"}]}}

You have now configured a custom User Wildcard. You can now extract the title without the HTML tags by writting {%1} on the ZotFile renaming rules, located in Tools, ZotFile Preferences, Renaming Rules.
For example, to rename all PDFs as CitationKey - Title, you should configure ZotFile renaming rules as {%b - }{%1}.