Also, as my unenlightened colleagues insist on using ridiculous tools like MS Word to author papers in, it's useful to have Zotero installed for the ability to link a BibTeX file to a WYSIWYG word processor when collaborating. Zotero helps you play well with others.

I don't think Zotero is perfect by any stretch, but I'm glad that at least it allowed academia to reject both Endnote and Mendeley. Anything that punches Elsevier in the face gets a tick in my book.

Zotero integrates well with various online services. This I think is Zotero's most valuable feature. The simple fact is that not everything exports BibTeX. Can you get a library catalog to export BibTeX? Perhaps in CS, most publications provide good BibTeX, but a lot of journals I (a mechanical engineer) deal with don't provide BibTeX at all to my knowledge. But I can simply press a button in Firefox and import the bibliographic data embedded in the web page into Zotero. (No, Google Scholar is not a good solution here because it's frequently inaccurate and incomplete.)

I'm a technical guy who can handle BibTeX fine, but I still prefer the Zotero UI over using BibTeX files in a text editor and shell, even if I'm only generating BibTeX files.

The author discusses using non-standard fields like keywords to store extra data. I would recommend that to store additional context about the document. Zotero can store even more than that, including web pages, files, and additional notes. I like that Zotero saves a snapshot of the journal article web page in most instances. Journals sometimes do go offline, so it can be nice to have the web page. I often have detailed notes about particular documents in notes in Zotero. Yes, you can do that with BibTeX, but I could see the extra fields cluttering the BibTeX file. (Contrary to what the author states, the note field probably should not be used as they describe because it's printed in some/most? bibliography styles.)

The search in Zotero is more powerful than grep. Try returning bibliographic entries where one field contains X and another field contains Y. I think you can probably come up with a grep solution for that, but it's so convoluted that it's probably never used in practice. You could use a BibTeX searching program like biblook to get around this problem.

Don't get me wrong. Zotero is far from perfect. It can be slow, and at this point I would prefer a TUI reference manager. But overall, it's the best option I've tried.

I like me some cli, but if I was to do something similar it would be with csl-json and jq/nushell. I cannot see the advantage of grepping a bibtex file, let alone having to manually manage the related articles.

A friend and I have been working (slowly, over the past few years, since we are both academics) on an abstraction layer over BibTeX called Autobib: https://github.com/autobib/autobib

Broadly speaking, Autobib is a CLI around SQLite database of BibTeX records. But in addition to plain BibTeX, Autobib is aware of 'external data providers' (like DOI, MathSciNet, OpenLibrary, arXiv, zbMath, etc.) and will automatically retrieve data bibliographic data from these data providers. The provenance of the data is stored alongside the record itself, and this can be used to retrieve updates, prevent duplication of data, etc.

The killer feature is: if you have a file (say `file.tex`) and the keys are in a format which Autobib can automatically recognize (say, you use citation keys like `doi:my/weird/doi`, and there is support for custom formats and aliases) you can run `autobib source file.tex` and it will write to standard output a sorted BibTeX bibliography for your file. This lets you trivially maintain a per-project bibliography which you can check into source control locally and which exactly corresponds to the paper itself.

But otherwise, Autobib is "just a wrapper over a BibTeX bibliography"! When you edit an existing record, you are just editing a BibTeX record. There is integrated search, directly on the BibTeX fields themselves.

There are some extra features, like support for attachments, fuzzy search, undo-tree support, headless edit, auto-normalization, soft deletion, replacement, merging, etc. The database format is relatively simple and open (currently not particularly well documented, but this will change when it stabilizes) to allow introspection by other tools.

The tool also strives to play nicely with other tools (structured output, composable, etc.)

The rest of the interface is ok.

These frontends are necessary however because researchers in non-computer related fields are not trained/proficient at command line tools. Many of them need help installing software. Many of them don’t use raw text files much either. They use MS word files instead etc.

The reason I like Zotero is because I can use it offline, have my all documents synced (the backup feature is one of the best things) when needed and I can organize my papers according to project/paper I'm working on. Actually one thing I do wish Zotero would add is tab groups which will allow me have papers open but grouped by project. It's based on Firefox which does support this so I hope it's a matter of time.