alt Hacker NewsThe one piece of advice I give new PhD students is to maintain a list of your references for a bibliography ahead of time. For every paper you read, copy the citation in BibTeX format and write a couple of sentences to remind yourself what the paper was about. Do this for every source, even if it doesn't seem important at the time.
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Not within a PhD, but as a side project I work on a research project on wikiversity about grammatical gender in French. It does reference a bunch of books and academic works, like probably a hundred I guess. The most tedious work though is to check which nouns are used only in a single gender of do have some epicenic or specific inflection used in the wild and giving a reference that attest that when it's not already so consensual that most general public dictionary would already document the fact. For that the research refers to thousand of webpages. I'm glad that most of the time I just need to drop the DOI, ISBN, or page URL and MediaWiki will handle the filing of the most relevant fields. That's not perfect, it generates the output with many different models currently (some don't have an excerpt field), and some required fields might be left blank, url to pdf won't work, and so on. But all in all it make the process of taking note of the reference quick and not going too much in my way. Creating a structured database out of it can certainly be done later.
I have had some fun exhuming my old LaTeX skills and assembling a BibTeX bibliography from which I automatically extract the right entries presented in whichever style is needed for a given paper and for my own (HTML) site. I even publish the collection in Zenodo in case useful to others. I use the 'annote' field for the reminder you suggest.
The lack of good tools to have good research notes with good search is kind of mind-boggling. I have reverted to having a website for myself, a private one that I run on my machine, using mkdocs which comes close to what I would want.
Zotero and AI have this covered now. If there's one thing AI is good at it's summarising crappy formatted papers. Never understood the 2 and 3 column thing. Horrendous way to format something.
Use zotero and betterbibtex. By all means type a comment so you know which ideas came from where but I'm a big advocate of taking notes by hand when you really want to understand something, as opposed to reminding your future self about something you already understand.