Agent4cs: A Multi-agent System for Code Summarization in Large Hierarchical Codebases

Understanding large, complex codebases, especially those with obfuscated structures and incomplete documentation, remains a significant challenge. Existing code summarization solutions often rely on a single language model or coding assistant like Claude Code, and treat source code as flat text, underutilizing the rich interdependencies and hierarchical information within a repository. To address these shortcomings, we propose Agent4cs - a multi-agent framework that summarizes large codebases in a bottom-up fashion, where a summarization agent focuses on producing robust summaries; a keyword-extraction agent proactively identifies critical information from subfolders; and a quality-assurance agent iteratively refines the outputs for readability, coherence, and completeness. Evaluated on 7 frontier models, Agent4cs improves semantic consistency across all folder levels by average 8% compared to two structured prompting baselines with code segments. Furthermore, extensive evaluation on real-world datasets demonstrates up to 38% gains in normalized keyword coverage rate over the same baselines.

SWE-Doctor: Guiding Software Engineering Agents with Runtime Diagnosis from Multi-Faceted Bug Reproduction Tests

Large language model (LLM)-based software engineering agents are increasingly developed to resolve software issues by generating patches from issue reports and code repositories. Bug reproduction tests (BRTs) are an important building block for such agents and have been shown useful for patch validation. However, it remains unclear whether BRTs can also help the more central stage of patch generation. We first conduct a preliminary study and find that directly using advanced BRT generators to guide patch generation is not beneficial: fail-to-fail BRTs can mislead agents, while even fail-to-pass BRTs bring limited or negative gains. Our analysis reveals two reasons: fail-to-pass BRTs may cover only one manifestation of the reported issue, leading to partial patches, whereas fail-to-fail BRTs are unreliable as direct patch-generation targets. Motivated by these insights, we propose SWE-Doctor, a software issue resolution agent that guides patch generation with runtime diagnoses derived from multi-faceted BRT executions. SWE-Doctor first generates multi-faceted BRTs for different behavioral requirements stated in the issue, then executes and debugs these BRTs to construct runtime-grounded diagnosis records, and finally uses the diagnoses together with localization information inferred during BRT generation to guide patch generation and reduce partial patches. We evaluate SWE-Doctor on Python bug-fixing issues from the widely adopted SWE-bench Verified and SWE-bench Pro across five LLM backends. SWE-Doctor consistently outperforms existing agents across all 10 LLM-benchmark combinations, achieving average resolution rates of 75.7% on SWE-bench Verified and 59.4% on SWE-bench Pro. In particular, on the more challenging SWE-bench Pro, SWE-Doctor improves the average resolution rate by 8.0-8.9 percentage points over the baseline agents.

The Impact of Configuring Agentic AI Coding Tools on Build-vs-Buy Decisions: A Study Protocol

Agentic AI coding tools write code with increasing autonomy and in doing so decide when to import a library and when to implement functionality from scratch. These decisions, whether to build functionality from scratch or buy into an external library, hereafter build-versus-buy, carry direct consequences for software security, licensing compliance, performance, and long-term maintainability. Yet no controlled experimental study has examined what governs build-versus-buy decisions in agentic AI coding tools. Configuration mechanisms, i.e., the means by which developers tailor agentic AI coding tool behavior to a project or workflow, are one of the primary means by which practitioners can influence these decisions. However, it is unclear which configuration mechanisms influence build-versus-buy decisions most effectively. We present a pre-registered protocol to study how configuration mechanisms alter build-versus-buy behavior in two popular agentic AI coding tools: Claude Code and OpenAI Codex. We will execute controlled programming tasks drawn from a benchmark of staged projects, each constructed around identifiable build-versus-buy points, and will manipulate the configuration supplied to each tool, ranging from no configuration, through context files with soft preferences and explicit prohibitions, to Skills (instructions that can be autonomously discovered), MCP-enabled library discovery tools, and permission controls, measuring which libraries the tool selects, whether it discloses newly introduced libraries, and whether those disclosures are complete and accurate. Nine pre-registered hypotheses structure the protocol. The resulting benchmark dataset and analysis pipeline will be released as a reusable artifact for evaluating build-versus-buy behavior in agentic AI coding tools.

Reasoning-Trace Collapse: Evaluating the Loss of Explicit Reasoning During Fine-Tuning

Explicit reasoning models are trained to produce intermediate reasoning traces before final answers, but downstream fine-tuning is often performed on ordinary instruction-response data that contains no such traces. We show that this mismatch can induce reasoning-trace collapse: a fine-tuned model continues to produce plausible final answers while losing the structurally valid explicit reasoning traces that made it a reasoning model in the first place. We introduce a structural evaluation framework that separates answer correctness from reasoning-trace validity, measuring valid, empty, missing, and truncated reasoning alongside reasoning-conditioned task performance. Using this framework, we study four open-weight reasoning models and find that standard supervised fine-tuning can rapidly suppress valid reasoning traces, and that answer-only metrics can substantially obscure this failure: in several settings, performance conditional on valid reasoning remains high while the rate of valid reasoning falls sharply. We further show that simple loss-masking strategies can substantially mitigate collapse without requiring teacher-generated reasoning traces. These results suggest that evaluations of fine-tuned reasoning models should report structural reasoning reliability metrics in addition to final-answer performance, especially when adaptation data does not contain explicit reasoning traces.

StepCodeReasoner: Aligning Code Reasoning with Stepwise Execution Traces via Reinforcement Learning

Existing code reasoning methods primarily supervise final code outputs, ignoring intermediate states, often leading to reward hacking where correct answers are obtained through inconsistent reasoning. We propose StepCodeReasoner, a framework that introduces explicit intermediate execution-state supervision. By automatically inserting structured print-based execution-trace anchors into code, the model is trained to predict runtime states at each step, transforming code reasoning into a verifiable, stepwise execution modeling problem. Building on this execution-aware method, we introduce Bi-Level GRPO, a reinforcement learning algorithm for structured credit assignment at two levels: inter-trajectory, comparing alternative execution paths, and intra-trajectory, rewarding intermediate accuracy based on its impact on downstream correctness. Extensive experiments demonstrate that StepCodeReasoner achieves SOTA performance in code reasoning. In particular, our 7B model achieves 91.1\% on CRUXEval and 86.5\% on LiveCodeBench, outperforming the CodeReasoner-7B baseline (86.0\% and 77.7\%) and GPT-4o (85.6\% and 75.1\%). Furthermore, on the execution-trace benchmark REval, our model scores 82.9\%, outperforming baseline CodeReasoner-7B (72.3\%), its 14B counterpart (81.1\%), and GPT-4o (77.3\%). Additionally, our approach also improves code generation performance, demonstrating that explicit execution modeling enhances both code reasoning and code generation.

SkillMOO: Multi-Objective Optimization of Agent Skills for Software Engineering

Agent skills provide modular, task-specific guidance for LLM- based coding agents, but manually tuning skill bundles to balance success rate, cost, and runtime is expensive and fragile. We present SkillMOO, a multi-objective optimization framework that automatically evolves skill bundles using LLM-proposed edits and NSGA-II survivor selection: a solver agent evaluates candidate skill bundles on coding tasks and an optimizer agent proposes bundle edits based on failure analysis. On three SkillsBench software engineering tasks, SkillMOO improves pass rate by up to 131% while reducing cost up to 32% relative to the best baseline per task at low optimization overhead. Pattern analysis reveals pruning and substitution as primary drivers of improvement, suggesting effective bundles favor minimal, focused content over accumulated instructions.

EffiSkill: Agent Skill Based Automated Code Efficiency Optimization

Code efficiency is a fundamental aspect of software quality, yet how to harness large language models (LLMs) to optimize programs remains challenging. Prior approaches have sought for one-shot rewriting, retrieved exemplars, or prompt-based search, but they do not explicitly distill reusable optimization knowledge, which limits generalization beyond individual instances. In this paper, we present EffiSkill, a framework for code-efficiency optimization that builds a portable optimization toolbox for LLM-based agents. The key idea is to model recurring slow-to-fast transformations as reusable agent skills that capture both concrete transformation mechanisms and higher-level optimization strategies. EffiSkill adopts a two-stage design: Stage I mines Operator and Meta Skills from large-scale slow/fast program pairs to build a skill library; Stage II applies this library to unseen programs through execution-free diagnosis, skill retrieval, plan composition, and candidate generation, without runtime feedback. Results on EffiBench-X show that EffiSkill achieves higher optimization success rates, improving over the strongest baseline by 3.69 to 12.52 percentage points across model and language settings. These findings suggest that mechanism-level skill reuse provides a useful foundation for execution-free code optimization, and that the resulting skill library can serve as a reusable resource for broader agent workflows.

Not All Code Is Equal: A Data-Centric Study of Code Complexity and LLM Reasoning

Large Language Models (LLMs) increasingly exhibit strong reasoning abilities, often attributed to their capacity to generate chain-of-thought-style intermediate reasoning. Recent work suggests that exposure to code can further enhance these skills, but existing studies largely treat code as a generic training signal, leaving open the question of which properties of code actually contribute to improved reasoning. To address this gap, we study the structural complexity of code, which captures control flow and compositional structure that may shape how models internalise multi-step reasoning during fine-tuning. We examine two complementary settings: solution-driven complexity, where complexity varies across multiple solutions to the same problem, and problem-driven complexity, where complexity reflects variation in the underlying tasks. Using cyclomatic complexity and logical lines of code to construct controlled fine-tuning datasets, we evaluate a range of open-weight LLMs on diverse reasoning benchmarks. Our findings show that although code can improve reasoning, structural properties strongly determine its usefulness. In 83% of experiments, restricting fine-tuning data to a specific structural complexity range outperforms training on structurally diverse code, pointing to a data-centric path for improving reasoning beyond scaling.

On the Impact of AGENTS.md Files on the Efficiency of AI Coding Agents

AI coding agents such as Codex and Claude Code are increasingly used to autonomously contribute to software repositories. However, little is known about how repository-level configuration artifacts affect operational efficiency of the agents. In this paper, we study the impact of AGENTS$.$md files on the runtime and token consumption of AI coding agents operating on GitHub pull requests. We analyze 10 repositories and 124 pull requests, executing agents under two conditions: with and without an AGENTS$.$md file. We measure wall-clock execution time and token usage during agent execution. Our results show that the presence of AGENTS$.$md is associated with a lower median runtime ($Δ28.64$%) and reduced output token consumption ($Δ16.58$%), while maintaining a comparable task completion behavior. Based on these results, we discuss immediate implications for the configuration and deployment of AI coding agents in practice, and outline a broader research agenda on the role of repository-level instructions in shaping the behavior, efficiency, and integration of AI coding agents in software development workflows.

Analyzing Message-Code Inconsistency in AI Coding Agent-Authored Pull Requests

Pull request (PR) descriptions generated by AI coding agents are the primary channel for communicating code changes to human reviewers. However, the alignment between these messages and the actual changes remains unexplored, raising concerns about the trustworthiness of AI agents. To fill this gap, we analyzed 23,247 agentic PRs across five agents using PR message-code inconsistency (PR-MCI). We contributed 974 manually annotated PRs, found 406 PRs (1.7%) exhibited high PR-MCI, and identified eight PR-MCI types, revealing that descriptions claiming unimplemented changes was the most common issue (45.4%). Statistical tests confirmed that high-MCI PRs had 51.7% lower acceptance rates (28.3% vs. 80.0%) and took 3.5x longer to merge (55.8 vs. 16.0 hours). Our findings suggest that unreliable PR descriptions undermine trust in AI agents, highlighting the need for PR-MCI verification mechanisms and improved PR generation to enable trustworthy human-AI collaboration.