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.
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 plugins Better BibTex for Zotero, which lets you customize the citation keys; and ZotFile, which automatically renames the PDFs and saves them on a custom folder, which you can sync with the cloud or else.
Another cool and useful plugin is the 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.
You can edit the automatic citation keys by going to Tools, Better BibTex, Open Better BibTex preferences, 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.
To automatically move your pdfs with ZotFile to a custom folder (to sync it, etc), go to Tools, ZotFile Preferences, General Settings, Location of Files, Custom Location and select your desired folder. This same folder should also be specified at Edit, Preferences, Advanced, Files and Folders, Linked Attachment Base Directory.
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}.
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 only seems to work fine with one attachment per reference.