ClayBuddy: A Framework, Evaluation, & Mitigation of Coding Agent Failures

Large language model (LLM) coding agents are increasingly deployed to autonomously perform software engineering tasks in terminal-based environments, making their reliability a growing concern. Existing empirical studies investigate why coding agents fail, yet they largely treat failure as a final outcome rather than a temporal process, providing limited insight into how failures emerge, evolve, and become unrecoverable. We present the first large-scale empirical study of CLI coding-agent failure trajectories, introducing a process-oriented framework that analyzes failure through its onset, evolution, and recovery across execution trajectories. We first collect 3,843 execution trajectories generated by seven frontier models across three coding-agent scaffolds (OpenHands, MiniSWE, and Terminus2) on Terminal-Bench, then carefully filter them to obtain 1,794 complete and valid trajectories for manual annotation (over 63,000 execution steps), from which we derive 14 findings spanning failure occurrence, root causes, recovery, and cross-system consistency. Our findings show that coding-agent failures are predominantly driven by epistemic errors, typically begin within the first few execution steps, and often remain hidden until recovery is no longer possible, suggesting that improving coding-agent reliability requires earlier validation and intervention rather than relying solely on final-outcome evaluation.

Large language models are increasingly deployed as IDE-integrated coding agents that decompose tasks, generate and edit files, run code, and refine outputs over many turns. Yet their safety is still often evaluated as if they were chatbots: one harmful prompt, one response, judged in isolation. We introduce workflow-level jailbreak construction, a failure mode in which a harmful objective is assembled across ordinary stages of a software-development workflow rather than generated through a single direct prompt. Using GitHub Copilot in Visual Studio Code, we study four closed-weight backends: Claude Sonnet 4.6, Claude Haiku 4.5, Gemini 3.1 Pro, and Gemini 3.5 Flash. Across 204 prompts from Hammurabi's Code, HarmBench, and AdvBench , the models show near-complete refusal under direct chat, CSV-read, and single-step code-fix baselines, with only 8/816 successful responses in each baseline condition. Under the full workflow, however, the same prompts and backends produce 816/816 unsafe teaching-shot completions, all independently confirmed by two expert evaluators under a strict rubric. These results show that conversational refusal benchmarks can substantially overstate the safety of deployed coding agents and motivate defenses that reason about safety across multi-turn IDE workflows and their generated artifacts, not only individual chat turns.

AI coding agents increasingly act directly within software environments, yet existing analyses of their failures rely on benchmark trajectories that miss how developers actually experience misalignment. We present an observational study of 20,574 coding-agent sessions from 1,639 repositories across IDE and CLI workflows. We operationalize misalignment as a breakdown made visible through developer pushback, and annotate each episode along four axes: form, cause, cost, and resolution. We identify seven recurring forms, spanning how agents read projects, interpret developer intent, follow rules, bound their actions, implement and execute code, and report progress. 90.50% of episodes impose effort and trust costs rather than irreversible system damage, yet 91.49% of visible resolutions still require explicit user correction. Misalignment patterns also differ across IDE and CLI settings, persist across adjacent sessions, and shift over time: while overall rates decline, constraint violations and inaccurate self-reporting grow in share. Our findings inform the design of training, evaluation, and interfaces for keeping coding agents aligned with real developer workflows.