> Surprisingly, we observe that developer-provided files only marginally improve performance compared to omitting them entirely (an increase of 4% on average), while LLM- generated context files have a small negative effect on agent performance (a decrease of 3% on average).
This "surprisingly", and the framing seems misplaced.
For the developer-made ones: 4% improvement is massive! 4% improvement from a simple markdown file means it's a must-have.
> while LLM- generated context files have a small negative effect on agent performance (a decrease of 3% on average)
This should really be "while the prompts used to generate AGENTS files in our dataset..". It's a proxy for prompts, who knows if the ones generated through a better prompt show improvement.
The biggest usecase for AGENTS.md files is domain knowledge that the model is not aware of and cannot instantly infer from the project. That is gained slowly over time from seeing the agents struggle due to this deficiency. Exactly the kind of thing very common in closed-source, yet incredibly rare in public Github projects that have an AGENTS.md file - the huge majority of which are recent small vibecoded projects centered around LLMs. If 4% gains are seen on the latter kind of project, which will have a very mixed quality of AGENTS files in the first place, then for bigger projects with high-quality .md's they're invaluable when working with agents.
Regarding the 4% improvement for human written AGENTS.md: this would be huge indeed if it were a _consistent_ improvement. However, for example on Sonnet 4.5, performance _drops_ by over 2%. Qwen3 benefits most and GPT-5.2 improves by 1-2%.
The LLM-generated prompts follow the coding agent recommendations. We also show an ablation over different prompt types, and none have consistently better performance.
But ultimately I agree with your post. In fact we do recommend writing good AGENTS.md, manually and targetedly. This is emphasized for example at the end of our abstract and conclusion.
My use of CLAUDE.md is to get Claude to avoid making stupid mistakes that will require subsequent refactoring or cleanup passes.
Performance is not a consideration.
If anything, beyond CLAUDE.md I add agent harnesses that often increase the time and tokens used many times over, because my time is more expensive than the agents.
Ok so that's interesting in itself. Apologies if you go into this in the paper, not had time to read it yet, but does this tell us something about the models themselves? Is there a benchmark lurking here? It feels like this is revealing something about the training, but I'm not sure exactly what.
> The LLM-generated prompts follow the coding agent recommendations. We also show an ablation over different prompt types, and none have consistently better performance.
I think the coding agent recommended LLM-generated AGENTS.md files are almost without exception really bad. Because the AGENTS.md, to perform well, needs to point out the _non_-obvious. Every single LLM-generated AGENTS.md I've seen - including by certain vendors who at one point in time out-of-the-box included automatic AGENTS.md generation - wrote about the obvious things! The literal opposite of what you want. Indeed a complete and utter waste of tokens that does nothing but induce context rot.
I believe this is because creating a good one consumes a massive amount of resources and some engineering for any non-trivial codebase. You'd need multiple full-context iterations, and a large number of thinking tokens.
On top of that, and I've said this elsewhere, most of the best stuff to put in AGENTS.md is things that can't be inferred from the repo. Things like "Is this intentional?", "Why is this the case?" and so on. Obviously, the LLM nor a new-to-the-project human could know this or add them to the file. And the gains from this are also hard to capture by your performance metric, because they're not really about the solving of issues, they're often about direction, or about the how rather than the what.
As for the extra tokens, the right AGENTS.md can save lots of tokens, but it requires thinking hard about them. Which system/business logic would take the agent 5 different file reads to properly understand, but can we summarize in 3 sentences?
In large projects, having a specific AGENTS.md makes the difference between the agent spending half of its context window searching for the right commands, navigating the repo, understanding what is what, etc., and being extremely useful. The larger the repository, the more things it needs to be aware of and the more important the AGENTS.md is. At least that's what I have observed in practice.
This. I have Claude write about the codebase because I get tired of it grepping files constantly. I rather it just know “these files are for x, these files have y methods” and I even have it breakdown larger files so it fits the entire context window several times over.
Funnily enough this makes it easier for humans to parse.
Large orchestration package without any tests that relies on a bunch of microservices to work? Claude Code will be as confused as our SDEs.
This in turns lead to broader effort to refactor our antiquated packages in the name of "making it compatible with AI" which actually means compatible with humans.
I'm not sure what you are suggesting exactly, but wanted to highlight this humongous "if".
The real value is exactly what you described: the tribal knowledge, the "we tried X and it broke because Y", the constraints that live in someone's head and nowhere in the code. LLM-generated files miss this because the LLM is just restating what it can already see. Of course that doesn't help.
It seems like the best students/people eventually end up doing CS research in their spare time while working as engineers. This is not the case for many other disciplines, where you need e.g. a lab to do research. But in CS, you can just do it from your basement, all you need is a laptop.
I do not do this for all repos, but I do it for the repos where I know that other developers will attempt very similar tasks, and I want them to be successful.
I then asked if there is anything I could do to prevent misinterpretations from producing wild results like this. So I got the advice to put an instruction in AGENTS.md that would urge agents to ask for clarification before proceeding. But I didn't add it. Out of the 25 lines of my AGENTS.md, many are already variations of that. The first three:
- Do not try to fill gaps in your knowledge with overzealous assumptions.
- When in doubt: Slow down, double-check context, and only touch what was explicitly asked for.
- If a task seems to require extra changes, pause and ask before proceeding.
If these are not enough to prevent stuff like that, I don't know what could.
I have a line there that says Codex should never use Node APIs where Bun APIs exist for the same thing. Routinely, Claude Code and now Codex would ignore this.
I just replaced that rule with a TypeScript-compiler-powered AST based deterministic rule. Now the agent can attempt to commit code with banned Node API usage and the pre-commit script will fail, so it is forced to get it right.
I've found myself migrating more and more of my AGENTS.md instructions to compiler-based checks like these - where possible. I feel as though this shouldn't be needed if the models were good, but it seems to be and I guess the deterministic nature of these checks is better than relying on the LLM's questionable respect of the rules.
We have pre-commit hooks to prevent people doing the wrong thing. We have all sorts of guardrails to help people.
And the “modern” approach when someone does something wrong is not to blame the person, but to ask “how did the system allow this mistake? What guardrails are missing?”
You may want to ask the next LLM versions the same question after they feed this paper through training.
Even the "thinking" blocks in newer models are an illusion. There is no functional difference between the text in a thought block and the final answer. To the model, they are just more tokens in a linear sequence. It isn't "thinking" before it speaks, the "thought" is the speech.
Treating those thoughts as internal reflection of some kind is a category error. There is no "privileged" layer of reasoning happening in the silicon that then gets translated into the thought block. It’s a specialized output where the model is forced to show its work because that process of feeding its own generated strings back into its context window statistically increases the probability of a correct result. The chatbot providers just package this in a neat little window to make the model's "thinking" part of the gimmick.
I also wouldn't be surprised if asking it stuff like this was actually counter productive, but for this I'm going off vibes. The logic being that by asking that, you're poisoning the context, similar to how if you try generate an image by saying "It should not have a crocodile in the image", it will put a crocodile into the image. By asking it why it did something wrong, it'll treat that as the ground truth and all future generation will have that snippet in it, nudging the output in such a way that the wrong thing itself will influence it to keep doing the wrong thing more and more.
That said it can still be useful because you have a some weird behavior and 199k tokens of context, with no idea where the info is that's nudging it to do the weird thing.
In this case you can think of it less as "why did you do this?" And more "what references to doing this exist in this pile of files and instructions?"
"Thinking meat! You're asking me to believe in thinking meat!"
While next-token prediction based on matrix math is certainly a literal, mechanistic truth, it is not a useful framing in the same sense that "synapses fire causing people to do things" is not a useful framing for human behaviour.
The "theory of mind" for LLMs sounds a bit silly, but taken in moderation it's also a genuine scientific framework in the sense of the scientific method. It allows one to form hypothesis, run experiments that can potentially disprove the hypothesis, and ultimately make skillful counterfactual predictions.
> By asking it why it did something wrong, it'll treat that as the ground truth and all future generation will have that snippet in it, nudging the output in such a way that the wrong thing itself will influence it to keep doing the wrong thing more and more.
In my limited experience, this is not the right use of introspection. Instead, the idea is to interrogate the model's chain of reasoning to understand the origins of a mistake (the 'theory of mind'), then adjust agents.md / documentation so that the mistake is avoided for future sessions, which start from an otherwise blank slate.
I do agree, however, that the 'theory of mind' is very close to the more blatantly incorrect kind of misapprehension about LLMs, that since they sound humanlike they have long-term memory like humans. This is why LLM apologies are a useless sycophancy trap.
Asking it why it did something isn’t useless, it just isn’t fullproof. If you really think it’s useless, you are way too heavily into binary thinking to be using AI.
Perfect is the enemy of useful in this case.
I once had an agent come up with what seemed like a pointlessly convoluted solution as it tried to fit its initial approach (likely sourced from framework documentation overemphasizing the importance of doing it "the <framework> way" when possible) to a problem for which it to me didn't really seem like a good fit. It kept reassuring me that this was the way to go and my concerns were invalid.
When I described the solution and the original problem to another agent running the same model, it would instantly dismiss it and point out the same concerns I had raised - and it would insist on those being deal breakers the same way the other agent had dimissed them as invalid.
In the past I've often found LLMs to be extremely opinionated while also flipping their positions on a dime once met with any doubt or resistance. It feels like I'm now seeing the opposite: the LLM just running with whatever it picked up first from the initial prompt and then being extremely stubborn and insisting on rationalizing its choice no matter how much time it wastes trying to make it work. It's sometimes better to start a conversation over than to try and steer it in the right direction at that point.
"You're absolutely correct. I should have checked my skills before doing that. I'll make sure I do it in the future."
- How to build.
- How to run tests.
- How to work around the incredible crappiness of the codex-rs sandbox.
I also like to put in basic style-guide things like “the minimum Python version is 3.12.” Sadly I seem to also need “if you find yourself writing TypeVar, think again” because (unscientifically) it seems that putting the actual keyword that the agent should try not to use makes it more likely to remember the instructions.
I can only assume that everyone reporting amazing success with agent swarms and very long running tasks are using a different harness than I am :)
The papers conclusions align with my personal experiments at managing a small knowledge base with LLM rules. The application of rules was inconsistent, the execution of them fickle, and fundamental changes in processing would happen from week-to-week as the model usage was tweaked. But, rule tweaking always felt good. The LLM said it would work better, and the LLM said it had read and understood the instructions and the LLM said it would apply them… I felt like I understoood how best to deliver data to the LLMs, only to see recurrent failures.
LLMs lie. They have no idea, no data, and no insights into specific areas, but they’ll make pleasant reality-adjacent fiction. Since chatting is seductive, and our time sense is impacted by talking, I think the normal time versus productivity sense is further pulled out of ehack. Devs are notoriously bad at estimating where they’re using time, long feedback loops filled with phone time and slow ass conversation don’t help.
Languages == Python only
Libraries (um looks like other LLM generated libraries -- I mean definitely not pure human: like Ragas, FastMCP, etc)
So seems like a highly skewed sample and who knows what can / can't be generalized. Does make for a compelling research paper though!
If you feel strongly about the topic, you are free to write your own article.
How does this invalidate the result? Aren't AGENTS.md files put exactly into those repos that are partly generated using LLMs?
Maybe I’m wrong but sure feels like we might soon drop all of this extra cruft for more rationale practices
Or create it in some other way
{
"hookSpecificOutput": {
"hookEventName": "SessionStart",
"additionalContext": "<contents of your file here>"
}
}
https://gist.github.com/lawless-m/fa5d261337dfd4b5daad4ac964...
#!/bin/bash
# ~/.claude/hooks/inject-readme.sh
README="$(pwd)/README.md"
if [ -f "$README" ]; then
CONTENT=$(jq -Rs . < "$README")
echo "{\"hookSpecificOutput\" :{\"hookEventName\":\"SessionStart\",\"additionalContext\":${CONTENT}}}"
exit 0
else
echo "README.md not found" >&2
exit 1
fi
{
"hooks": {
"SessionStart": [
{
"matcher": "startup|clear|compact",
"hooks": [
{
"type": "command",
"command": "~/.claude/hooks/inject-readme.sh"
}
]
}
]
}
} If there’s a nugget of knowledge learned at any point in this conversation (not limited to the most recent exchange), please tersely update AGENTS.md so future agents can access it. If nothing durable was learned, no changes are needed. Do not add memories just to add memories.
Update AGENTS.md **only** if you learned a durable, generalizable lesson about how to work in this repo (e.g., a principle, process, debugging heuristic, or coding convention). Do **not** add bug- or component-specific notes (for example, “set .foo color in bar.css”) unless they reflect a broader rule.
If the lesson cannot be stated without referencing a specific selector or file, skip the memory and make no changes. Keep it to **one short bullet** under an appropriate existing section, or add a new short section only if absolutely necessary.
Another common mistake is to have very long AGENTS.md files. The file should not be long. If it's longer than 200 lines, you're certainly doing it wrong.
Off topic, but oh my god if you don't do this, it will always do the thing you conditionally requested it to do. Not sure what to call this but it's my one big annoyance with LLMs.
It's like going to a sub shop and asking for just a tiny bit of extra mayo and they heap it on.
I don't think the instruction following benches test for this much and I don't know how you'd measure it well
AI crushes structured data like package.json but struggles with free-form markdown. Two developers describe the same repo completely differently. There's no schema, no validation, no scoring.
Our paper on CERN's Zenodo proposes FAF — a structured YAML format (IANA-registered as application/vnd.faf+yaml) that replaces prose with validated fields. One .faf file generates native outputs for CLAUDE.md, AGENTS.md, .cursorrules, and GEMINI.md. The instruction files stay — they just sit on top of a structured foundation instead of floating independently.
Also, I bet the quality of these docs vary widely across both human and AI generated ones. Good Agents.md files should have progressive disclosure so only the items required by the task are pulled in (e.g. for DB schema related topics, see such and such a file).
Then there's the choice of pulling things into Agents.md vs skills which the article doesn't explore.
I do feel for the authors, since the article already feels old. The models and tooling around them are changing very quickly.
> (e.g. for DB schema related topics, see such and such a file).
Rather than doing this, put another AGENTS.md file in a DB-related subfolder. It will be automatically pulled into context when the agent reads any files in the file. This is supported out of the box by any agent worth its salt, including OpenCode and CC.
IMO static instructions referring an LLM to other files are an anti-pattern, at least with current models. This is a flaw of the skills spec, which refers to creating a "references" folder and such. I think initial skills demos from Anthropic also showed this. This doesn't work.
I thought Claude Code didn't support AGENTS.md? At least according to this open issue[0], it's still unsupported and has to be symlinked to CLAUDE.md to be automatically picked up.
Progressive disclosure is invaluable because it reduces context rot. Every single token in context influences future ones and degrades quality.
I'm also not sure how it reduces the benefit of token caching. They're still going to be cached, just later on.
Any well-maintained project should already have a CONTRIBUTING.md that has good information for both humans and agents.
Sometimes I actually start my sessions like this "please read the contributing.md file to understand how to build/test this project before making any code changes"
I understand the sentiment, but it is really strange that the people that are pushing for agents.md haven't seen https://contributing.md/
Is it even mentioned at GitHub docs https://docs.github.com/en/communities/setting-up-your-proje...
Think of the agent app store people's children man, it would be a sad Christmas.
Also important to note that human-written context did help according to them, if only a little bit.
Effectively what they're saying is that inputting an LLM generated summary of the codebase didn't help the agent. Which isn't that surprising.
I went through a couple of iterations of the CLAUDE.md file, first describing the problem domain and library intent (that helped target search better as it had keywords to go by; note a domain-trained human would know these in advance from the three words that comprise the library folder name) and finally adding a concise per-function doc of all the most frequently used bits. I find I can launch CC on a simple task now, without it spending minutes reading the codebase before getting started.
The article is interesting but I think it deviates from a common developer experience as many don't work on Python libraries, which likely heavily follow patterns that the model itself already contains.
> Their definition of context excludes prescriptive specs/requirements files.
Can you explain a bit what you mean here? If the context file specifies a desired behavior, we do check whether the LLM follows it, and this seems generally to work (Section 4.3).
- Don't state the obvious: I wouldn't hand a senior human dev a copy of "Clean Code" before every ticket and expect them to work faster.
- File vs. Prompt is a false dichotomy: The paper treats "Context Files" as a separate entity, but technically, an AGENTS.md is just a system prompt injection. The mechanism is identical. The study isn't proving that "files are bad," it's proving that "context stuffing" is bad. Whether I paste the rules manually or load them via a file, the transformer sees the same tokens.
- Latent vs. Inferable Knowledge: This is the key missing variable. If I remove context files, my agents fail at tasks requiring specific process knowledge - like enforcing strict TDD or using internal wrapper APIs that aren't obvious from public docs. The agent can't "guess" our security protocols or architectural constraints. That's not a performance drag; it's a requirement. The paper seems to conflate "adding noise" with "adding constraints."
each role owns specific files. no overlap means zero merge conflicts across 1800+ autonomous PRs. planning happens in `.sys/plans/{role}/` as written contracts before execution starts. time is the mutex.
AGENTS.md defines the vision. agents read the gap between vision and reality, then pull toward it. no manager, no orchestration.
we wrote about it here: https://agnt.one/blog/black-hole-architecture
agents ship features autonomously. 90% of PRs are zero human in the loop. the one pain point is refactors. cross-cutting changes don't map cleanly to single-role ownership
AGENTS.md works when it encodes constraints that eliminate coordination. if it's just a roadmap, it won't help much.
"The system does not assign tasks.
It defines gravity."
Helios looks cool though!
Doesn't mean it's not worth studying this kind of stuff, but this conclusion is already so "old" that it's hard to say it's valid anymore with the latest batch of models.
The other part is fueled by brand recognition and promotion, since everyone wants to make their own contribution with the least amount of effort, and coming up with silly Markdown formats is an easy way to do that.
EDIT: It's amusing how sensitive the blue-pilled crowd is when confronted with reality. :)
What wasn't measured, probably because it's almost impossible to quantify, was the quality of the code produced. Did the context files help the LLMs produce code that matched the style of the rest of the project? Did the code produced end up reasonably maintainable in the long run, or was it slop that increased long-term tech debt? These are important questions, but as they are extremely difficult to assign numbers to and measure in an automated way, the paper didn't attempt to answer them.
I added these to that file because otherwise I will have to tell claude these things myself, repeatedly. But the science says... Respectfully, blow it out your ass.
But with LLMs, the internals are not well-documented, most are not open-source (and even if the model and weights are open-source, it's impossible for a human to read a grid of numbers and understand exactly how it will change its output for a given input), and there's also an element of randomness inherent to how the LLM behaves.
Given that fact, it's not surprising to find that developers trying to use LLMs end up adding certain inputs out of what amounts to superstition ("it seems to work better when I tell it to think before coding, so let's add that instruction and hopefully it'll help avoid bad code" but there's very little way to be sure that it did anything). It honestly reminds me of gambling fallacies, e.g. tabletop RPG players who have their "lucky" die that they bring out for important rolls. There's insufficient input to be sure that this line, which you add to all your prompts by putting it in AGENTS.md, is doing anything — but it makes you feel better to have it in there.
(None of which is intended as a criticism, BTW: that's just what you have to do when using an opaque, partly-random tool).
Even with the latest and greatest (because I know people will reflexively immediately jump down my throat if I don't specify that, yes, I've used Opus 4.6 and Gemini 3 Pro etc. etc. etc. etc., I have access to all of the models by way of work and use them regularly), my experience has been that it's basically a crapshoot that it'll listen to a single one of these files, especially in the long run with large chats. The amount of times I still have to tell these things to not generate React in my Vue codebase that has literally not a single line of JSX anywhere and instructions in every single possible file I can put it in to NOT GENERATE FUCKING REACT CODE makes me want to blow my brains out every time it happens. In fact it happened to me today with the supposed super intelligence known as Opus 4.6 that has 18 trillion TB of context or whatever in a fresh chat when I asked for a quick snippet I needed to experiment with.
I'm not even paying for this crap (work is) and I still feel scammed approximately half the time, and can't help but think all of these suggestions are just ways to inflate token usage and to move you into the usage limit territory faster.
No problem, x agents, hundreds/closed to one million token usage to add a line of code.
Gemini 3 : can you review the commit A (console.log one ) you have made the most significant change in your 200kloc code base, this key change will allow you to get great insight into your software.
Codex : I have reviewed your change, you are missing tests and integration tests.
But I fully agree, overall I feel there are a lot of tea leaves readers online and LinkedIn.