A Foreword on AGENTS.md#One aspect of agents I hadn’t researched but knew was necessary to getting good results from agents was the concept of the AGENTS.md file: a file which can control specific behaviors of the agents such as code formatting. If the file is present in the project root, the agent will automatically read the file and in theory obey all the rules within. This is analogous to system prompts for normal LLM calls and if you’ve been following my writing, I have an unhealthy addiction to highly nuanced system prompts with additional shenanigans such as ALL CAPS for increased adherence to more important rules (yes, that’s still effective). I could not find a good starting point for a Python-oriented AGENTS.md I liked, so I asked Opus 4.5 to make one:
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Even though my dataset is very small, I think it's sufficient to conclude that LLMs can't consistently reason. Also their reasoning performance gets worse as the SAT instance grows, which may be due to the context window becoming too large as the model reasoning progresses, and it gets harder to remember original clauses at the top of the context. A friend of mine made an observation that how complex SAT instances are similar to working with many rules in large codebases. As we add more rules, it gets more and more likely for LLMs to forget some of them, which can be insidious. Of course that doesn't mean LLMs are useless. They can be definitely useful without being able to reason, but due to lack of reasoning, we can't just write down the rules and expect that LLMs will always follow them. For critical requirements there needs to be some other process in place to ensure that these are met.
A few years later, in 2024, researchers in multiple labs were horrified to notice toxic batches of agar for reasons as yet unclear. After they observed a worrying lack of microbial growth (impeding their ability to carry out basic experiments), they switched to different agar suppliers, and their results improved.