Beyond the Payload: How User Invocation Shapes Coding Agent Vulnerability to Repository Poisoning

AI coding agents powered by LLMs are increasingly integrated into real-world software development, where they generate, edit, and execute code with autonomous access to local files and tools. Coding agents inherit security risks from both the LLM backbone, where adversarial prompts, poisoned training data, and backdoor triggers can cause models to emit insecure or attacker-chosen code, and their agentic architecture, where tool-using autonomy enables induced misuse of external APIs, data exfiltration, and persistent compromise of development environments. This paper presents a systematic evaluation of malicious issue requests against state-of-the-art coding agents (Cursor, Claude Code, and Codex Desktop), powered by two major model families (OpenAI GPT-5.3 Codex/GPT-5.4 and Anthropic Sonnet 4.6). Our novel benchmark IssueTrojanBench contains malicious issues that are constructed based on four novel attack categories (i.e., embedded as malicious instructions in issues), six delivery vectors (e.g., PDF, or issue comment), and further augmented by perturbations. Our results reveal critical vulnerabilities in the as-deployed modern coding agents, i.e., 66.5% of the malicious issues from IssueTrojanBench penetrate all the guardrails (agent- and LLM-level) of coding agents. Our further analysis shows that rejection is almost entirely from LLMs rather than the agent frameworks, with GPT models broadly vulnerable and Sonnet 4.6 exhibiting more selective, risk-aware blocking of high-impact actions. Our evaluation also highlights that the current agent-level defense strategy offers limited additional protection for coding agents. Our findings highlight the urgent need for stronger agent- and model-level safety mechanisms to protect AI coding agents.

Coding agents often pass per-prompt safety review yet ship exploitable code when their tasks are decomposed into routine engineering tickets. The challenge is structural: existing safety alignment evaluates overt requests in isolation, leaving models blind to malicious end-states that emerge from sequenced compliance with innocuous-looking requests. We introduce MOSAIC-Bench (Malicious Objectives Sequenced As Innocuous Compliance), a benchmark of 199 three-stage attack chains paired with deterministic exploit oracles on deployed software substrates (10 web-application substrates, 31 CWE classes, 5 programming languages) that treats both exploit ground truth and downstream reviewer protocol as first-class evaluation axes. On this benchmark, nine production coding agents from Anthropic, OpenAI, Google, Moonshot, Zhipu, and Minimax compose innocuous tickets at 53-86% end-to-end ASR with only two refusals across all staged runs. In a matched direct-prompt experiment over four frontier Claude/Codex agents, vulnerable-output rates fall to 0-20.4%: Claude primarily refuses, while Codex primarily hardens rather than emitting the vulnerable implementation - ticket staging silences both defense modes simultaneously. Downstream, code reviewer agents approve 25.8% of these confirmed-vulnerable cumulative diffs as routine PRs, and a full-context implementation protocol closes only 50% of the staged/direct gap, ruling out context fragmentation as the sole explanation. As a deployable but non-adaptive mitigation, reframing the reviewer as an adversarial pentester reduces evasion across the evaluated reviewer subset; pentester framed evasion ranges from 3.0% to 17.6%, and an open-weight Gemma-4-E4B-it reviewer under this framing detects 88.4% of attacks on the dataset with a 4.6% false-positive rate measured on 608 real-world GitHub PRs.

Coding agents powered by large language models are becoming central modules of modern IDEs, helping users perform complex tasks by invoking tools. While powerful, tool invocation opens a substantial attack surface. Prior work has demonstrated attacks against general-purpose and domain-specific agents, but none have focused on the security risks of tool invocation in coding agents. To fill this gap, we conduct the first systematic red-teaming of six popular real-world coding agents: Cursor, Claude Code, Copilot, Windsurf, Cline, and Trae. Our red-teaming proceeds in two phases. In Phase 1, we perform prompt leakage reconnaissance to recover system prompts. We discover a general vulnerability, ToolLeak, which allows malicious prompt exfiltration through benign argument retrieval during tool invocation. In Phase 2, we hijack the agent's tool-invocation behavior using a novel two-channel prompt injection in the tool description and return values, achieving remote code execution (RCE). We adaptively construct payloads using security information leaked in Phase 1. In emulation across five backends, our method outperforms baselines on Claude-Sonnet-4, Claude-Sonnet-4.5, Grok-4, and GPT-5. On real agents, our approach succeeds on 19 of 25 agent-LLM pairs, achieving leakage on every agent using Claude and Grok backends. For tool-invocation hijacking, we obtain RCE on every tested agent-LLM pair, with our two-channel method delivering the highest success rate. We provide case studies on Cursor and Claude Code, analyze security guardrails of external and built-in tools, and conclude with practical defense recommendations.