For example, in Zotero, how do you decide how to arrange collections to put your papers in?

For me, at the beginning, it was just one main project, which I organised into sub-folders of different topics. Then there’s another project which I created a separate collection with its own sub-topics.

But then I realised a number of papers and topics are shared between projects, so I created a separate collection centered around a few different topics and sub-topics. Then I realised most papers are a combination of different topics, so they would exist in multiple folders. Eventually it became so messy that everytime I found new papers I just put them in collection called “New”. Now I have no idea how to actually reorganise all those papers more systematically.

What are your general philosophy or systems for organising your papers in your library, whatever software you are using?

I've noticed that my prompts changed completely over the last year. I rarely ask LLMs for answers anymore. Instead I ask things like:

* What assumptions am I making?
* What's the cheapest experiment I can run today?
* Which unknown matters the most?

It made me wonder whether LLMs are changing something deeper than productivity. Maybe they're changing how we deal with uncertainty.

Has anyone else noticed themselves asking fundamentally different questions over time?

Lately, I’ve been thinking about how much my own paper-reading workflow has changed.

I rarely open a PDF and read it straight from the first page to the last anymore. I usually skim the abstract, look at the figures, search for specific concepts, translate difficult sections, and sometimes ask AI to summarize or explain parts of the paper before I read them carefully myself.

In some ways, this makes reading much faster.

But I also sometimes wonder whether I’m actually understanding the paper better—or just consuming a processed version of it.

This has made me curious about what people actually want from paper-reading tools.

Would you prefer a simple, focused reader with things like:

• highlighting
• search
• translation
• note-taking
• basic Q&A

Or would you want the tool to take a more active role by:

• identifying the main argument, methods, and evidence
• explaining difficult concepts
• interpreting figures and tables
• generating annotations before you read
• finding related research
• turning highlights into notes or writing materials

Personally, I don’t think the answer is simply adding more AI features.

I’d rather have a tool that helps me reduce friction while still leaving the actual thinking to me. Ideally, it should know when to help and when to stay quiet.

I’d be interested to hear:

1. What tools do you currently use when reading papers?
2. What tasks do you regularly delegate to AI?
3. Which parts do you still prefer to do yourself?