zotero VS zotero-mdnotes

Maybe try Zotero[1]. There are many addons which can do what you need.

[1]https://www.zotero.org/

And next time, you use a real literature management program like zotero (some university libraries offer classes, there is a r/zotero, etc) or jabref to create a proper bibtex file with the references. It is not that difficult, and keeps you sane (esp. if a paper has to be formatted for a different publisher). See e.g. learnlatex.

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Zotero is an open-source project that develops software to help people collect, organize, annotate, cite, and share their research. Our software is recommended by most universities and used by millions of students, scholars, scientists, and researchers worldwide.

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Zotero is your answer, it even auto generates your citations.

https://www.zotero.org/

Apparently there are plugins for Logseq and Obsidian as well.

Zotero - Price: Free Free and open-source reference manager that helps you collect, organize, and cite your research sources.

I use the free and open source Zotero which I think you'd find very calibre-like and manage notes and concept linking with org-roam in emacs.

If you can't hold the urge to know, you can check on the Zotero web library if all of your things are still there

Resources: ZOTERO. Zotero is a free (you can pay to get more storage), open-source citation manager with optional browser plugins. IT WILL FORMAT CITATIONS FOR YOU. (sometimes you have to edit them, but most of the time it can pull metadata and format things correctly on its own). You can sort your references into folders or with tags, read and annotate PDF copies on your computer or in a mobile app, and make notes - which I used to keep track of specific quotations I wanted to use.

You can also use online resources like The Encyclopedia of Archaeological Sciences, that I think is mostly free or the Handbook of Archaeological Sciences which I think is also mostly free. If you can't get a hold of those things you can also email the authors/editors and they might send you a free copy or look them up on Academia.edu and see if they have a free version. Also, if you don't already, use Google Scholar, it's the best resource for finding free articles and topics to read. It's also never too early to start using something like Zotaro, Mendeley, or Endnote to keep track of your readings and help you with citations/references in papers. You can literally download the citation, import it into one of those systems and it automatically formats your referencing.

Hm, have you ever considered using Mdnotes and if so, would you be able to compare your workflow with the one it leads to?

I then extract these highlights and annotations using the Zotfile plug-in, and import them into my literature notes folder in Obsidian. I really liked the Mdnotes plugin for this, but it recently stopped working for me so I re-created the template, which I have to populate manually, and which is structured into three sections: metadata, summary, and key ideas.

If it's of interest I just found this zotero plugin, Zotero mdnotes, and the joplin plugin Hotfolder, work quite well together.

I recently installed the ZotFile and MdNotes plugins to Zotero as described here. The ability to export highlights and other annotations to a .md file is really useful, and makes me think that there must be a CLI out there which does something similar. I ask because ideally I would like to avoid having to go into Zotero, click on the pdf, extract annotations, then export to a .md file, selecting the project folder each time that I want to scrap export my annotations from a pdf. Rather, I'd like to integrate this process into Vim so that when there is some citation I have, I can use the Vimtex context feature to point the pdf-annotations-to-markdown-CLI that I hope exists at whatever pdf is included for that citation. My question is: does anyone know of such a piece of software which does something like this? Any pointers would be greatly appreciated!

Zotero mdnotes https://github.com/argenos/zotero-mdnotes