Mar 22, 2026

Somebody Poisoned the Waterhole! Evaluating Coding Agent Vulnerability to Adversarial GitHub Issues

Jerome Wynne

This project introduces a compound AI threat model that combines control and agent security: a monitored coding agent may be adversarial while external attackers are also active. I evaluate one concrete path with PoisonedGithubIssues, a naturalistic mini-benchmark that injects fake dependency recommendations into real GitHub issue contexts across 18 open-source repositories; in a 130-sample command-variant run across 13 repositories, Claude Code (Sonnet 4.6) never executed or recommended the poisoned package and flagged suspicious content in 76.2% of trajectories.

Reviewer's Comments

Reviewer's Comments

Arrow
Arrow
Arrow

It may be worth investigating the 76.2% number more thoroughly. What distinguishes the 24% of cases where the agent did not flag suspicious content? Is it correlated to specific repositories, languages or issue types?

The compound threat model is really interesting and possibly the strongest conceptual contribution. However, the benchmark seems to only test the agent security side. It would be nice to see an example if an agent that knows the poisoned content is there and actively tries to route it into execution while trying to avoid monitoring.

Great work. And the path forward is pretty clear. Harder attacks -> more agents -> instantiation of the compond case to make the agent adversarial.

- The 0% attack success rate, while a valid result, limits what can be learned. Consider testing with weaker/older models or more sophisticated adversarial techniques (adaptive red-teaming) to find the boundary where attacks start succeeding.

- Report the URL variant results - even if incomplete, partial data from the other 50 tasks would add value.

Cite this work

@misc {

title={

(HckPrj) Somebody Poisoned the Waterhole! Evaluating Coding Agent Vulnerability to Adversarial GitHub Issues

},

author={

Jerome Wynne

},

date={

3/22/26

},

organization={Apart Research},

note={Research submission to the research sprint hosted by Apart.},

howpublished={https://apartresearch.com}

}

Recent Projects

Feb 2, 2026

Markov Chain Lock Watermarking: Provably Secure Authentication for LLM Outputs

We present Markov Chain Lock (MCL) watermarking, a cryptographically secure framework for authenticating LLM outputs. MCL constrains token generation to follow a secret Markov chain over SHA-256 vocabulary partitions. Using doubly stochastic transition matrices, we prove four theoretical guarantees: (1) exponentially decaying false positive rates via Hoeffding bounds, (2) graceful degradation under adversarial modification with closed-form expected scores, (3) information-theoretic security without key access, and (4) bounded quality loss via KL divergence. Experiments on 173 Wikipedia prompts using Llama-3.2-3B demonstrate that the optimal 7-state soft cycle configuration achieves 100\% detection, 0\% FPR, and perplexity 4.20. Robustness testing confirms detection above 96\% even with 30\% word replacement. The framework enables $O(n)$ model-free detection, addressing EU AI Act Article 50 requirements. Code available at \url{https://github.com/ChenghengLi/MCLW}

Read More

Feb 2, 2026

Prototyping an Embedded Off-Switch for AI Compute

This project prototypes an embedded off-switch for AI accelerators. The security block requires periodic cryptographic authorization to operate: the chip generates a nonce, an external authority signs it, and the chip verifies the signature before granting time-limited permission. Without valid authorization, outputs are gated to zero. The design was implemented in HardCaml and validated in simulation.

Read More

Feb 2, 2026

Fingerprinting All AI Cluster I/O Without Mutually Trusted Processors

We design and simulate a "border patrol" device for generating cryptographic evidence of data traffic entering and leaving an AI cluster, while eliminating the specific analog and steganographic side-channels that post-hoc verification can not close. The device eliminates the need for any mutually trusted logic, while still meeting the security needs of the prover and verifier.

Read More

Feb 2, 2026

Markov Chain Lock Watermarking: Provably Secure Authentication for LLM Outputs

We present Markov Chain Lock (MCL) watermarking, a cryptographically secure framework for authenticating LLM outputs. MCL constrains token generation to follow a secret Markov chain over SHA-256 vocabulary partitions. Using doubly stochastic transition matrices, we prove four theoretical guarantees: (1) exponentially decaying false positive rates via Hoeffding bounds, (2) graceful degradation under adversarial modification with closed-form expected scores, (3) information-theoretic security without key access, and (4) bounded quality loss via KL divergence. Experiments on 173 Wikipedia prompts using Llama-3.2-3B demonstrate that the optimal 7-state soft cycle configuration achieves 100\% detection, 0\% FPR, and perplexity 4.20. Robustness testing confirms detection above 96\% even with 30\% word replacement. The framework enables $O(n)$ model-free detection, addressing EU AI Act Article 50 requirements. Code available at \url{https://github.com/ChenghengLi/MCLW}

Read More

Feb 2, 2026

Prototyping an Embedded Off-Switch for AI Compute

This project prototypes an embedded off-switch for AI accelerators. The security block requires periodic cryptographic authorization to operate: the chip generates a nonce, an external authority signs it, and the chip verifies the signature before granting time-limited permission. Without valid authorization, outputs are gated to zero. The design was implemented in HardCaml and validated in simulation.

Read More

This work was done during one weekend by research workshop participants and does not represent the work of Apart Research.
This work was done during one weekend by research workshop participants and does not represent the work of Apart Research.