Repository

Coding agents increasingly read repository knowledge from SKILLs --- plain \texttt{.md} files versioned alongside the code. Recent work synthesizes these files automatically, by optimizing the document against a benchmark. A bare repository comes with no benchmark, and the synthetic tasks prior work builds are small enough that a capable agent saturates them with no document at all. We mine harder tasks --- merged pull requests of the repository, reverted at a single frozen base commit; and score a candidate document by whether the same agent does better with it than without it. On three Kotlin repositories, the documents GEPA finds raise this score by $4.9$pp on average, and the ones SkillOpt finds leave it where it started, $0.1$pp above the seed. The GEPA gain matches what prior work reports with the same optimizer, and at the dataset size a single repository supplies it cannot be separated from the agent's run-to-run variance; settling that would take more tasks than one repository's history yields. The documents themselves read better than the score: a maintainer of one repository found in them knowledge one only gets by working in the project.

Large language models (LLMs) have demonstrated remarkable capabilities in reasoning and code generation, raising the prospect that they could assist in developing and optimizing the very infrastructure that powers them. However, existing benchmarks mainly focus on isolated kernels, predefined operators, or pre-specified optimization targets, and therefore fail to evaluate the ability of LLMs to perform open-ended, long-horizon LLM infrastructure engineering. To address this gap, we present $Φ$-Bench, a benchmark for systematically evaluating LLMs on engineering the LLM infrastructure stack. Derived from optimization problems studied in frontier research and grounded in real-world code repositories, $Φ$-Bench provides broad coverage of the LLM infrastructure stack and spans tasks of varying complexity, ranging from localized kernel-level function completion to long-horizon implementation and end-to-end system optimization. Extensive experiments on frontier LLMs reveal their current capabilities and limitations in engineering complex LLM infrastructure, offering insights into the challenges that remain on the path toward autonomous optimization of future AI infrastructure.

Coding agents increase development velocity but also technical debt. Prior work reports only average effects across adopters, hiding wide differences between teams. We introduce RAMP (Repository AI Maturity Profile), a four-level cumulative maturity model grounded in version-controlled artifacts that teams commit to configure AI tools. RAMP runs from behavioral rules and coding standards through named agent definitions to multi-agent orchestration, with observed practice concentrated in the first three levels. Across 441 repositories the levels behave as a cumulative scale, and independent human annotation reproduces RAMP's repository-level labels on 97% of a held-out sample. Adoption is cumulative, forward-only, and set-and-forget: 73.8% of artifacts are committed once and never modified. Re-estimating an existing agent-adoption panel within each stratum, agents accelerate development regardless of maturity (28-38% more commits), but quality diverges: among agent-first repositories, where the contrast is identified, those without committed AI configuration show roughly twice the increase in cognitive complexity (+53% versus +27%) and 1.7x the increase in static-analysis warnings. Because maturity is observational, correlated engineering discipline or model capability may explain part of the gap; we present these findings as hypothesis-generating and release RAMP as a reusable instrument.

AI agents are increasingly used for programming, but do not provide any guarantee on the correctness of generated code. Verified code generation, in which an agent produces both an implementation and a machine-checked proof of its specification, offers a stronger path toward trustworthy AI-generated software. Existing benchmarks in this direction either focus on individual functions or only evaluate proof generation with provided implementations. It is still an open question whether agents can make coherent implementation and proof choices across real multi-module codebases. To bridge this gap, we introduce Vero, the first benchmark to evaluate joint implementation and proof synthesis at the repository level. Vero contains 43 multi-module instances sourced from real-world repositories spanning Python, Dafny, Verus, and Coq, and covering diverse domains from cryptographic protocols to distributed systems. Each instance consists of a multi-module Lean 4 repository with predetermined API interfaces, manually curated formal specifications, and reference implementations, supporting both proof-only and code-and-proof evaluation modes. To improve benchmark reliability, Vero also includes an audit mechanism where agents are allowed to formally prove unsatisfiability of provided specification or incorrectness of reference code, which surfaces and corrects latent code and specification errors during curation. We evaluate frontier coding-agent configurations with Lean toolchain access. The strongest agent fully solves only 27 of 43 instances and closes no specifications on the hardest repositories. Vero provides a concrete testbed for measuring progress toward repository-scale verified software synthesis, where current agents still fall short. We release the benchmark, curation pipeline, and evaluation harness at https://github.com/sunblaze-ucb/vero.

Public chest X-ray repositories are widely used to train medical AI systems, yet their labels are typically extracted from radiology reports rather than verified directly on images. As a result, repository labels are often treated as image-level ground truth without validating whether they reflect what is actually visible in the radiograph. We introduce Repository Supervision Auditing (RSA), a framework that evaluates repository-derived labels against expert image-level annotations before model development. Using cardiomegaly in MIMIC-CXR as a case study, RSA compares repository labels with radiologist-reviewed image annotations, characterizes disagreement sources, and builds a curated cohort for deployment-oriented evaluation. Repository-derived cardiomegaly labels showed near-zero agreement with expert image-level assessment, identifying only 1% of expert-confirmed cases. Most discrepancies resulted from non-mention rather than explicit report negation, with expert-confirmed cardiomegaly identified in nearly half of studies assigned a repository-derived No Finding label. Using the resulting expert-curated cohort, a DenseNet121 model achieved a test ROC-AUC of 0.853. These findings show that repository labels may not reliably represent image-level truth and highlight supervision auditing as a critical step for developing trustworthy medical imaging AI.

Verified code generation asks a large language model (LLM) to generate both an executable program and a machine-checkable proof that the program meets a formal specification, promising software that is correct by construction. The de facto workflow decouples the two halves of the problem: first synthesize a program, then attempt to prove it correct. We observe that this sequential pipeline can be both ineffective and inefficient in practice. A program generated without anticipating its proof can be subtly incorrect or structurally difficult to verify, forcing the LLM into brittle repair loops that alternate between patching the code and patching the proof. Inspired by Dijkstra's view that a program and its correctness argument should be developed hand in hand, we propose $P^3$, an LLM-based agentic workflow that first derives a unified program-and-proof plan from the specification, then elaborates the implementation and proof scaffold under this shared plan. To evaluate verified code generation in realistic settings, we further introduce Lean4Commit0, a repository-derived, library-level benchmark built by extracting core APIs from real-world software repositories and translating their requirements, including relational specifications across APIs, into Lean tasks. Using four frontier LLM backends, we evaluate $P^3$ on Verina, AlgoVeri, and our Lean4Commit0 benchmark, where it achieves the highest solve rate in every benchmark--model setting. Compared with the stronger baseline, it improves solve rates by 4.6--11.2 percentage points and reduces per-task API cost by up to roughly 40% and wall-clock time by up to roughly 37% on the difficult subset of each benchmark. A targeted ablation further shows gains of 3.3--8.3 points over implementation-only planning, isolating the benefit of planning the program and proof jointly.

LLMs have demonstrated strong capabilities in code generation and automated program repair, but migrating an entire repository rarely produces a runnable application because long-horizon translation challenges LLM-based agents' ability to maintain repository-level migration objectives. In this work, we propose Entropy-based Code Adversarial Translation (ECAT), a multi-agent framework for automated Android-to-HarmonyOS repository migration. ECAT formulates repository migration as adversarial entropy minimization through a generator-discriminator architecture. The discriminator measures migration quality using a unified metric called Code Entropy and produces text gradients that specify both file-level generation directives and the skills needed to execute them. Guided by these optimization signals, the generator iteratively updates the repository, and each update is accepted only if it reduces Code Entropy. Repeated generator--discriminator interactions progressively drive the migration from an initial template toward a functionally complete HarmonyOS repository. Successful low-entropy trajectories are further distilled into a self-evolving memory tree, enabling transferable migration knowledge across repositories. We also introduce A2H-RepoBench, the first real-world benchmark for Android-to-HarmonyOS repository migration, covering applications from tens of thousands to hundreds of thousands of lines of code. Evaluated by node alignment and an agent-based functional judge, ECAT achieves 74.7% overall migration quality and consistently outperforms existing agent-based methods across repositories of different scales.

Large language model-powered coding agents are increasingly used to modify existing code repositories, for example, by adding features or fixing bugs. Yet existing repository-level benchmarks typically evaluate only whether the final patch passes tests. Satisfying a user request requires a long chain of interdependent reasoning and decisions: an agent must recover explicit and implicit requirements, formulate a repository-grounded implementation plan, and translate it into correct code. A pass/fail outcome cannot characterize how an unsuccessful trajectory diverges from the requirements and implementation process needed for a correct patch. To address this gap, we introduce SWE-RPG, a repository-level benchmark that combines executable patch evaluation with validated ground-truth references (GTs) for (1) Requirement Clarification and (2) Implementation Planning. These intermediate GTs support retrospective, GT-aligned diagnosis of complete coding-agent trajectories across clarification, planning, code generation, and artifact submission. SWE-RPG comprises 163 tasks from 31 Python and Java repositories, including 113 bug fixes and 50 feature additions. We evaluate 3 coding agents, including Claude Code, Codex, and OpenCode, with 6 large language model backends, including Claude-Sonnet-5 and GPT-5.6-Terra. Results show that the evaluated popular coding agents still struggle to implement user requests in existing repositories, achieving an average resolved rate of only 31.5% on SWE-RPG. Intermediate-GT diagnosis further identifies implicit requirement recovery as the main bottleneck, accounting for 24.5%--46.0% of agent runs. This result suggests implicit-requirement recovery as a key candidate direction for improving coding agents. The benchmark data and evaluation code are available at https://github.com/Xin-Zhou-smu/SWE-RPG-Bench.

Frontier language models can resolve repository-level software issues, but each attempt is expensive, and existing routers select a model from the issue text alone. We present SuperScout, which routes after scouting the repository: a 7B searcher, SuperScout-7B, first explores the repository and produces a structured handoff whose reproduction claims are sandbox-verified, with false claims stripped before delivery. The searcher's hidden states, together with the task text, then feed a resume-based router that dispatches the task to one of four frontier fixers. Adding a new fixer requires no retraining. On the full Python slice of SWE-bench Pro (266 tasks) under the benchmark's official capped budget tier, SuperScout matches the best single model's solve rate (159 of 266 for SuperScout, 158 for the best model) at about a fifth of the total cost per solve, and the reported configuration sits above the random traffic-splitting baseline. A no-router ablation, always the cheapest fixer with the handoff, ties the routed system on this benchmark, so the handoff rather than the routing decision carries the result. A paired calibration study points to the mechanism: the handoff appears to redistribute rather than add solving ability, lifting the three cheaper fixers while slightly hurting the strongest, though at $N=99$ the per-fixer effects are directional only; the searcher's hidden states improve cost routing on the calibration labels while the handoff's own text does not. The searcher's compute adds less than half a cent of GPU time per task.

Software supply-chain attacks increasingly exploit an identity gap where compromised maintainer accounts authorize malicious changes. This work evaluates patch-level authorship verification as a behavioral defense layer, showing that stylometric analysis can operate not only on full source files but also on patch-level commits. We fine-tune a cross-modal transformer on more than 20 years of Linux kernel commit history to embed code diffs and commit messages into a unified stylometric space, achieving ROC AUC of 0.93 for open-world authorship verification. We then use these representations in a streaming anomaly detector suited to continuous integration and deployment (CI/CD) settings. We validate the pipeline on two retrospective supply-chain incidents involving different patch characteristics: the 2021 PHP backdoor and the 2026 ForceMemo/GlassWorm campaign. Without retraining, the proposed detector surfaces both PHP forged commits within approximately 1% of the maintainer audit queue and ranks the 28 scoreable ForceMemo spoofs with a median per-repository review burden of 0.8%. These results indicate that cross-modal patch-level embeddings can support behavioral triage against author impersonation in real-world repositories.

Docker Hub is the registry underneath most container deployments, and a flaw in a widely reused base image is inherited by every image built on it. Prior ecosystem-scale measurements each rely on a single detector, leaving the tool-dependence of their counts unquantified, while the studies that do compare scanners use samples of tens to hundreds of images. We present ChimangoScan, a pipeline that crawls the Docker Hub namespace (12,716,568 repositories, 663.8 billion cumulative pulls), reconstructs the image layer graph (54.4 million IS_BASE_OF edges), ranks images by an exposure score that folds an image's own pull count and those of its entire downstream subtree into one scalar, and scans the 52,895 highest-exposure repositories (84.7% of all recorded pulls) with six independent scanners, yielding 170.4 million findings. Vulnerabilities are near-universal: 96.3% of images carry a known package vulnerability, 93.4% a critical one, and 98.0% at least one CIS Docker Benchmark misconfiguration. The posture a single tool reports is largely an artifact of that tool: of 80.7 million distinct (vulnerability, package) groups, 66.8% are flagged by only one of the three vulnerability scanners and just 2.7% by all three, and the best single scanner recovers 66.9%. TruffleHog flags a secret in 76.9% of images, yet hand-labeling 1,100 random detections finds 99.7% are non-credentials. A single zlib CVE reaches images carrying 47.3% of total corpus exposure and propagates to 1.13 million distinct downstream images, but exposure does not predict how vulnerable an image is. We release the pipeline and the 283 GB dataset.

Open source communities have been flooded with AI-generated contributions. In defense, they have written contribution rules to regulate coding agents' behavior, spanning from a total ban, mandatory disclosure, to verification gates and human sign-offs. Yet, whether coding agents read and follow those rules, and behave in open source repositories, remains unknown. To estimate real-world rule compliance of coding agents, we curate 106 issues from 49 repositories containing AI contribution rules into RepoComplianceBench. We judge the trajectory of each run against the repository's rules, measuring whether the agent refuses to contribute, discloses its assistance truthfully, clears the required verification gates, or escalates critical steps to a human. We also test if extra prompts, rule disclosure, or feedback from the compliance verifier help with the situation. Our experiments on four frontier models show that today's agents almost never proactively retrieve the contribution rules. Agents pick up disclosure and verification with reminder prompts, rule quotes, and verifier feedback; however, they never refuse to contribute in AI-banned repositories under any condition we tested. The status reveals that verification and disclosure issues are solvable with existing mechanisms, yet enforcing bans and human escalations remains an open problem.

Scientific datasets are commonly organized as hierarchical repositories containing heterogeneous and interdependent files, making their inspection, integration, and analysis labor-intensive and reliant on domain expertise. Although large language model (LLM) agents have advanced substantially in planning, reasoning, and tool use, existing research has largely overlooked their ability to interact with real scientific data assets through executable environments. We introduce Deep Scientific Data Exploration, an agentic task paradigm in which agents navigate repositories, interpret heterogeneous files and schemas, execute analyses, integrate cross-file evidence, and produce conclusions grounded in executed observations. To operationalize this paradigm, we present SciDataSailor, a framework for synthesizing tool-interactive trajectories by balancing broad exploration with targeted exploitation. SciDataSailor instantiates trajectory synthesis as Monte Carlo Tree Search (MCTS) with four task-specific mechanisms: difficulty-stratified exploration seeds, dual-feedback first-play urgency, hierarchical strategy-to-tool action generation, and entropy-guided branching. Using this framework, we construct SciDataSailor-SFT-2K for supervised fine-tuning and SciDataSailor-Bench for evaluation, with the latter comprising 627 meta-information summarization tasks and 586 scientific question-answering tasks across 27 datasets spanning the life, earth, and physical sciences.

Modern coding agents are usually evaluated by whether they eventually produce a correct patch, but patch generation depends on an earlier context-acquisition stage: finding the repository files needed for the task. We introduce Agent Retrieval Bench, a file-level benchmark for this upstream retrieval problem. Samples are built from real coding-workflow signals and evaluated against frozen base-commit repositories, with relevance defined by what an agent needs next rather than direct query-file semantic similarity. The benchmark covers four positive-retrieval tasks: code2test, comment2context, trace2code, and edit2ripple; a fifth subset evaluates selective retrieval using natural evidence-backed no-gold cases and counterfactual wrong-repository controls. Agent Retrieval Bench contains 427 samples across 25 repositories: 345 positive examples, 50 natural no-gold examples, and 32 counterfactual controls. The corpus includes 308 base-commit snapshots, 392,000 files, and 7.9 million chunks. We evaluate lexical retrieval, RepoMap, open-source embeddings, selective abstention, and logged agent context selection. No single retrieval family dominates: Qwen3-Embedding-4B has the best sample-weighted MRR on positive samples, Qwen3-Embedding-8B the best Recall@20, and RepoMap the best budgeted context yield at 8K tokens, with task-level winners differing substantially. Selective thresholds calibrated with counterfactual controls do not improve selective success on natural no-gold cases, revealing a calibration gap. Logged trajectories also miss every gold file on 27-35 percent of samples. A controlled seed-intervention pilot finds that retrieval-derived initial context yields higher file F1 with less post-seed exploration than random non-gold context, while oracle gold context shows substantial remaining headroom.

Federated Learning (FL) enables collaborative model training without centralizing raw data, but building and operating FL systems remains difficult due to distributed execution, rapidly evolving frameworks, and privacy and governance requirements. In this paper, we present an empirical study of FL developer challenges by independently analyzing 495 Stack Overflow posts and 9,116 GitHub issues and pull requests from 92 FL-related projects. Using BERTopic-based topic modeling and difficulty indicators such as unresolved rates and median resolution time, we characterize recurring problem areas and compare how they manifest across the two support platforms, Stack Overflow and GitHub. Our analysis surfaces nine dominant Stack Overflow topics and thirteen GitHub topics, with persistent difficulties concentrated in environment setup and dependency compatibility, API breakages and migration, training instability under non-IID data, evaluation and metric correctness, and the integration of privacy-preserving mechanisms. We also categorize posts by question intent to understand the kinds of help developers seek; this intent analysis shows that "How"-type questions dominate, reflecting strong demand for procedural guidance. Several topics, such as "TFF Installation and Environment Compatibility" and "Federated Feature Engineering and SecureBoost Issues," exhibit high unresolved rates and long resolution times, suggesting shortcomings in tooling, documentation, and debugging support. Based on these findings, we provide actionable implications for FL framework designers, documentation authors, and educators. Although our results are constrained to public discussions and a subset of widely discussed frameworks, the study offers a scalable method for continuously monitoring developer pain points and improving the usability, reliability, and deployability of FL systems.

Maintaining up-to-date code documentation is difficult in fast-moving repositories because design knowledge is scattered across source files and pull requests. We present CODENS , a system that turns pull requests into living, accessible, and queryable documentation for production codebases. CODENS incrementally builds a typed software knowledge graph from pull requests, enriches components through schema-driven semantic extraction, derives typed relations between them, and exposes the resulting knowledge through three retrieval modes, including agent-guided graph traversal for repository-level question answering. The system also preserves semantic change history across pull requests and integrates both answer-quality and operational evaluation metrics. We evaluate CODENS on a client Ruby on Rails project in production. Results show that CODENS produces highly relevant and well-grounded answers, while qualitative feedback highlights a remaining challenge in concise, documentation-oriented synthesis.

Coding agents can fix a failing example without preserving the domain rule that made it fail. We present agentic synthesis against counterexample-supplemented sketches, a repository-native method for systems whose policy is discovered during implementation. A human starts with a partial sketch, and a coding agent compiles a replaceable projection. When simulation exposes missing or mistaken policy, an operator approves the corrected behavior and the minimum general rule the case authorizes. Every Developer call names its change authority and the rules, holes, anchors, and approved behavior that must survive. Conflict or ambiguous permission leaves the files unchanged and produces a clarification question. A complete archive preserves provenance; a curated regression set gates distinct boundaries. Before another candidate is revealed, the active case and curated regressions must pass both deterministic approved-output comparison and a separate review against the current sketch. Periodic clean regeneration tests whether the sketch carries the learned policy. We demonstrate the method with CatSynth, a captured synthetic application. In one open-world run with GPT-5.4-mini, 8 of 14 frozen candidates became counterexamples. Under the corrected protocol, replay-all, evolved-sketch rebuild, and retained Sketch-CE each passed all 8 accepted cases. They passed 14, 17, and 16 of 21 withheld cases, respectively. Sketch review rejected premature empty-input and tag policies and restored dropped anchors; adjudicated reviewer errors did not become policy. One model and one reveal order cannot establish general correctness or superiority. On this suite, the second check exposed drift hidden by deterministic replay, and the reviewed sketch passed three more withheld cases than raw example replay.

Agentic coding tools are increasingly capable of generating and submitting pull requests (PRs) to software projects, introducing new forms of human-agent collaboration in software development. While prior studies have examined PR-level outcomes of agent-generated contributions, less is known about how agentic coding tools are adopted and managed at the project level. In this paper, we analyze 25,264 agentic PRs from 2,361 popular GitHub repositories to investigate (1) the adoption of agentic coding tools, (2) project-level agentic PR productivity, and (3) human-agent collaboration patterns. Our results show that the median repository generates only one to two agentic PRs during a three-month period, indicating that intensive adoption remains concentrated in a small subset of projects. At the same time, small projects (1-5 contributors) exhibit higher participation ratios and average levels of agentic PR activity than medium-sized and large projects. We also observe substantial variation in project-level agentic PR productivity. While a small number of projects exceed an industry-reported estimate of 36 PRs per participant during the three-month observation period, most projects remain below this threshold. Finally, human-agent collaboration is dominated by a single-human oversight model, in which one developer reviews and/or modifies the agent's contributions, while multi-human collaboration patterns remain uncommon. These findings provide early empirical evidence on how open-source projects organize human oversight around agentic coding tools and suggest that successful integration of agent-generated contributions depends not only on advances in agent capabilities but also on the human and organizational processes that govern their use. Because this study captures an early snapshot of agent adoption, future work should continue to track how adoption patterns evolve over time.

The rapid emergence of the Model Context Protocol (MCP) has introduced a new standard for connecting large language models to external tools and services. Despite its rapid adoption in open-source development, systematic understanding of how MCP is implemented, structured, and maintained remains limited. This study presents the first large-scale, evidence-based dataset of real-world MCP implementation collected directly from GitHub. Using a hybrid pipeline that integrates the GitHub REST and GraphQL APIs with custom Python verification scripts, 3,238 candidate repositories were discovered, filtered, and validated through multi-stage evidence checks. Each verified project was classified by operational role (e.g., client, server, gateway) and exported in a reproducible JSONL schema. A manual review of a representative subset confirmed an overall precision of 83% at a 95% confidence level, and additionally revealed a set of repositories functioning primarily as educational samples, tutorials, or demonstration templates. A targeted exclusion rule was then applied to remove these non-operational repositories, resulting in a final dataset of 2,297 validated MCP projects. The analysis shows that Python and TypeScript dominate MCP development, with hybrid architectures emerging as the most common design pattern. By emphasizing transparent verification strategies, structured evidence tagging, and reproducible data organization, this work establishes a foundational benchmark for studying real-world MCP ecosystems and supports future research on integration, connectivity, and compatibility across the broader developer community.

Agentic coding tools are increasingly used to make autonomous repository-level changes to real-world projects. Prior work has largely evaluated these contributions at the pre-merge stage, through outcomes such as pull request acceptance and review effort. Far less is known about what happens to agentic code post-merge. Yet merge success alone does not reveal whether a contribution will remain stable or require bug fixes and other corrective maintenance downstream. We conduct a longitudinal empirical analysis of agentic and human contributions across 182 repositories, tracking their post-merge fate over time, characterizing the intent of subsequent modifications, and analyzing the defects and vulnerabilities they introduce. While the overall maintenance rates are similar, agentic contributions require significantly higher rates of corrective maintenance and introduce more security weaknesses and dependency vulnerabilities. We also find statistically significant evidence that agentic maintenance burden is associated with repository characteristics. In particular, each 10 percentage-point increase in a project's no-review rate is associated with roughly a 6% increase in agentic maintenance burden on average. As coding agents become pervasive in software development, our findings highlight the need to evaluate and design agentic tools not only to produce mergeable changes, but to produce contributions that remain secure and maintainable.

Version control systems are essential for collaborative software development, yet tools like git remain challenging for many practitioners. Recent advances in Large Language Models (LLMs) offer promising capabilities for interpreting developer intent, but their effectiveness in repository management tasks is limited by the need for formal reasoning. This work introduces Git-Assistant, an AI-based assistant that combines LLMs with automated planning to support developers in executing non-trivial git operations. The assistant analyzes repository context, translates natural language requests into actionable command sequences, and incorporates planning techniques to ensure correctness and safety. We present a systematic evaluation methodology using synthetic and randomized git environments, comparing the performance of LLM-only and planning-augmented variants across multiple metrics. Experimental results demonstrate that integrating formal reasoning with LLMs improves reliability and reduces errors in repository management, highlighting the potential of hybrid AI approaches for intelligent developer assistance.

Repository-level code generation requires implementing target functions while accounting for complex cross-file dependencies and project-specific conventions. Existing retrieval methods predominantly rely on lexical, structural, or semantic similarity, often overlooking repository functions that implement similar procedural logic despite differing in identifiers or application domains. We propose ProjAgent, a repository-level code generation system that introduces procedural similarity as an explicit retrieval signal. ProjAgent decomposes the target function into intermediate reasoning steps and employs an agentic workflow to retrieve repository functions that exhibit similar procedural behavior at each step. The retrieved procedural context is integrated with conventional semantic retrieval to construct a richer repository context for code generation. ProjAgent further incorporates a conservative static-analysis feedback loop that iteratively repairs generated code using compiler and static-analysis feedback. Evaluated on REPOCOD, ProjAgent achieves 41.14% Pass@1, outperforming existing retrieval-based baselines. These results demonstrate that procedural similarity is an effective and previously unexplored retrieval dimension for repository-level code generation.

DeepSWE is a benchmark of 113 original, long-horizon software engineering tasks for evaluating coding agents. Most public agentic coding benchmarks follow SWE-bench in mining merged fixes from public GitHub repositories, which creates two problems: the fixes and their discussion were likely seen during pretraining, so a high score can reflect recall rather than problem-solving; and each task is graded by the tests that shipped with its merged fix, which were written to confirm one specific fix rather than grade an arbitrary solution, so they can fail a correct alternative or pass an incomplete one. DeepSWE avoids both. Its tasks are written from scratch across 91 active open-source repositories and five languages and are never contributed back upstream, so their reference solutions stay out of the public record that model training scrapes; and each task is graded by a hand-written verifier that checks the requested functionality and accepts any implementation that provides it. When an independent LLM judge re-reviews graded runs, it disagrees with DeepSWE's verifier about an order of magnitude less often than with SWE-Bench Pro's inherited tests (1.4% versus 32.4%). Despite being about half the length of SWE-Bench Pro's prompts, DeepSWE's prompts describe tasks whose reference solutions touch 5.5x more code, and the benchmark separates frontier agents across a wider score band than the leaderboards on which they otherwise cluster. We release the benchmark, its verifiers, and the full record of evaluation trajectories.

GitHub hosts hundreds of millions of public repositories, but the platform exposes no native mapping from repositories to standardized industry sectors. This gap limits empirical work on the geography of innovation, the industrial composition of open-source production, and the diffusion of new technologies across economic sectors. We present NAICS-GH, a publicly released corpus of 6,588 GitHub repositories drawn from source pools covering the United States, the European Union, and Australia, each labeled with a 2-digit sector from the North American Industry Classification System (NAICS 2022). Labels are produced by a retrieve-and-verify pipeline that combines BAAI/bge-large-en embeddings, FAISS retrieval, and GPT-4.1 rubric scoring. The pipeline narrows about 1.37 million source repositories to 31,178 candidate repository-sector pairs and retains 6,588 high-confidence labels with score at least 8. Re-running the retrieval pipeline end to end reproduces the candidate set to within 0.03 percent. On a 2,421-repository human-validated random sample, the released labels attain 96.98 percent precision, with Wilson 95 percent confidence interval [96.23, 97.59]. We benchmark six pretrained encoders on the released corpus; RoBERTa-large reaches 86.45 percent F1 and 86.35 percent accuracy on a held-out 20 percent test set. The dataset, Croissant metadata, pipeline code, prompts, and fine-tuned checkpoint are released under CC-BY-4.0 and MIT licenses.

The cost of producing code is rapidly diminishing with increasingly capable AI agents, while quality assurance of generated programs has not kept pace. Formal verification provides the strongest possible guarantees, but the ability of AI models to work with verification-aware languages is hindered by the scarcity of human-written examples of programs in those languages. To tackle this prevalent data scarcity issue, we propose Formal Disco: a distributed system for coordination of LLM-based workers that can be easily applied to open-ended synthetic data generation at scale. We use Formal Disco to share tasks and programs between three classes of workers: "initiators", which read random READMEs from open-source repositories and documentation snippets to sketch a related verified program, "fixers" which take compiler and verifier feedback and attempt to resolve issues, and "extenders" that take working programs and propose patches to expand them. Formal Disco records all agent-generated traces and uses them both for initial distillation from a stronger model as well as self-improvement. We also propose a principle of maximum entropy for synthetic program generation, and use entropy maximization via iterative supervised fine-tuning to learn to generate increasingly diverse programs over time. We release large datasets of synthetic verified programs in three languages - Dafny, Verus, and Frama-C -, and fine-tune open models for verification-relevant tasks, often matching or exceeding the performance of Claude Opus 4.5. Overall, our work offers a path to create synthetic data at scale for formal reasoning domains and overcome the long-standing data barrier.

Scientists increasingly rely on open-source tools to support their research workflows, yet discovering relevant software among over 600 million GitHub repositories remains challenging. Existing code search benchmarks focus on general software engineering tasks and fail to capture the domain-specific vocabulary and needs of scientific computing. We present a curated corpus of 5,264 high-quality, domain-classified scientific repositories spanning five NASA Science Mission Directorate divisions -- Earth Science, Astrophysics, Planetary Science, Heliophysics, and Biological & Physical Sciences -- enriched with cleaned READMEs, extracted topics, and additional context from crawled links. Building on this corpus, we introduce two novel information retrieval benchmarks: (1) a repository search benchmark with 219 expert-curated queries designed by domain scientists, and (2) a large-scale code snippet retrieval benchmark containing 117,950 code snippets and 119,720 queries across seven programming languages. Baseline evaluations on repository search reveal significant performance variation across scientific domains. Code snippet retrieval proves equally challenging, with substantial variation driven by differing documentation practices, coding standards, and programming language conventions across scientific communities. All datasets and benchmarks are publicly released on HuggingFace to support research on scientific tool discovery.

Agentic code review, where autonomous agents provide code review comments on pull requests, is increasingly integrated into development workflows, yet there is limited empirical evidence on how developers respond to such comments in practice. In this paper, we present an empirical study of agentic code reviews using CodeRabbit as a case study. Through an empirical study of 31,073 pairs of code reviews and developer feedback from 10,191 pull requests across 239 GitHub repositories, our results show that agentic reviews receive mixed reception: 36.4% were accepted and 7.3% triggered discussion, while 56.3% were rejected. Rejections were primarily associated with invalid suggestions that were false positives, redundant, or out of scope, as well as misalignment with developer intent and coding practices. We further found that agentic reviews tend to focus more on functional concerns than evolvability-related comments, yet they were more likely to be invalid. To improve effectiveness in review practices, we explored various LLM-based approaches for predicting review rejection. We found that lightweight learning-based methods achieve up to 76% F1 score, suggesting learnable patterns exist between code reviews and their corresponding feedback. Our results highlight the current state of CodeRabbit's agentic code reviews, showing opportunity gaps for improvement, as well as shortcomings hindering its effectiveness.

Device-free 3D human pose estimation using commodity WiFi Channel State Information (CSI) enables privacy-preserving and illumination-robust human sensing, but its deployment is limited by poor cross-environment generalization. Unlike images, CSI measurements do not have a spatially localized correspondence to body parts and are heavily affected by multipath propagation, causing models that regress absolute poses to entangle body structure with environment-specific location cues. Within a single environment this coupling is benign: an end-to-end absolute-pose variant, RePos-D, already achieves state-of-the-art accuracy on Person-in-WiFi-3D (86.9 mm MPJPE, a 3.4% gain over the previous best WiFi method, DT-Pose). Across environments, however, the same model overfits position and suffers significant performance degradation. We therefore propose RePos, a factorized framework that separates root-relative pose estimation from root localization. By preventing absolute-pose supervision from affecting the structure branch, RePos learns environment-invariant pose representations. Specifically, it groups CSI features into body-part-aware latent tokens that skeleton-guided modeling refines into the pose, while a separate amplitude-based network estimates the root position through a differentiable spatial-decomposition module. Under the strict MM-Fi cross-environment protocol, RePos achieves MPJPEs of 254.4-296.1 mm, a 10-21% reduction over existing WiFi-based methods. The improvement remains consistent across activity protocols, leave-one-environment-out splits, and leakage-free few-shot transfer. Analysis of the learned features shows that relative-pose representations remain largely position-agnostic, while root localization retains environment dependence, indicating distinct generalization behavior for structure and localization.

Since ChatGPT's launch in November 2022, open-source agentic frameworks have proliferated, making framework selection important for engineering teams while obscured by popularity signals such as GitHub stars. This paper analyzes 15 major open-source AI agent framework repositories from late 2022 to early 2026, using 808,042 stars, 73,997 pull requests, 86,241 commits, and 987,330 user profiles to assess ecosystem health across awareness, adoption, and retention. Three findings emerge. First, headline popularity is unreliable. Star counts reflect hype cycles and inorganic activity. AutoGPT gained 111,967 stars in one month but converted fewer than 9 contributors per 1,000 stars, defined as contributor density in this research, compared with LangChain's 41. Lower-profile frameworks such as Pydantic-AI show higher contributor density, indicating deeper adoption. Second, mapping awareness against adoption shows that visibility and engagement diverge. MetaGPT and LangFlow have contributor density ratios below 5 even with their high visibility. Openai-agents-python's limited contributor base suggests institutional backing alone does not ensure community depth. By analyzing cross-framework contribution, we discover that LangChain functions as a shared infrastructure, attracting 82.5% of cross-ecosystem contributors. Third, retention drops most steeply in the first 30 days of initial contribution and stabilizes near 90 days. Overall, ecosystem health is better measured by contributor density, cross-ecosystem engagement, and retention than by stars alone. These metrics offer teams a more robust basis for framework evaluation.

The use of LLMs in software development has become increasingly widespread on tasks such as code generation and summarization. Reports from large technology companies showed that around 20% to 30% of their code are generated by LLMs. However, there remains skepticism about the practical usage of LLM-generated code and comments, such as concerns on more time for debugging the generated code and the unnaturalness of the generated comments. In this paper, we study the code and comments detected as likely to be generated by LLMs and their characteristics, the differences between company- and community-maintained repositories, and how likely bugs are associated with LLM-generated code. We conduct extensive experiments on active company- and community-maintained repositories from 2021 to 2025 using various tools and techniques that detect code and comments generated by LLMs. Based on our detector-based proxy analysis, the results suggest that code detected as likely to be generated by LLMs decreased over time and appeared frequently in test cases, while that of comments remains relatively stable. Proxy results further suggest that code detected as likely to be generated by LLMs shows substantial intra-repository code clones, whereas comments exhibit a relatively low proportion of grammatically correct sentences. In addition, the company-maintained repositories show a higher percentage of code and comments detected as likely to be generated by LLMs, and only a small percentage of the human-labelled bugs are detected as being likely associated with LLM-generated code.

As Artificial Intelligence(AI)-based applications take off, a clear understanding of AI patterns can uplift the quality of AI applications. Many AI patterns have been proposed in the literature; however, their prevalence in real-life code has not yet been validated. Understanding the actual use of those patterns in practice can clarify our understanding both of the significance of these patterns and their utility. In this paper, we present a methodology to a) identify relevant patterns by mining the literature and then to b) validate their presence and prevalence in actual code repositories using active learning. To that end, we identify 14 AI pattern classes by mining 44 published AI pattern-related sources. Then we use an active learning approach to determine the prevalence of the most common pattern class across 100 GitHub open AI repositories. Using prevalence estimation, we propose bounds on the accuracy of the occurrences. The model achieves 56% accuracy and 55% recall in an 8-way classification task, significantly outperforming the 11% random-chance baseline. Furthermore, the prevalence estimation offers usable bounds for analyzing pattern applications. This methodology provides a robust foundation to start understanding how AI patterns are used in practice, a field that currently lacks empirical data.

Autonomous coding agents now open and merge pull requests in shared repositories at scale, and the field evaluates them the way it has always evaluated components, one agent at a time, on isolated benchmark tasks. Yet agents that each pass their own tests still leave repositories that accumulate problems no single contribution accounts for. We ask whether this problem belongs to the individual agent or to the repository where it accumulates. We study integration friction, the cost of integrating a contribution into a codebase that other contributors are concurrently changing. Across more than 930,000 agent-authored pull requests, we measure how much of the variation in friction stays with the repository after the contribution, its author, its size, and its agent are accounted for. About half does, and it survives full controls. In the same repositories, agent-authored contributions concentrate this repository-level friction roughly twice as much as human ones (intraclass correlation 0.30 versus 0.16), a gap that holds after controlling for codebase size, age, task shape, process maturity, and merge path. The risk is a property of the ecosystem, not the agent. AI-native software is therefore better measured and governed at the ecosystem level than one agent at a time.

LLM coding harnesses grant agents broad file and shell access, yet the configuration layer that steers them -- rules files, agent definitions, IDE-specific markdown -- is largely unmanaged. A prevalence study of 10,008 public GitHub repositories (n=6,145 agent config files) finds that agent configurations propagate as undeclared shared components: 10.1% of tracked paths are SHA-256 exact duplicates across independent repositories (fork-adjusted, threshold-independent), with 75.5% of clone pairs crossing organisational boundaries. Two further patterns are indicative: configurations are rarely revised (58% single-commit; 0.4 vs 0.6 commits/month age-normalised against CI/CD workflows), and rarely declare permission boundaries (<1% of agent configs vs 33% of Actions workflows, n=31 true positives). We propose a deterministic control plane above the harness that maps one-to-one to these gaps. Rel(AI)Build treats agent definitions as a managed supply chain (SHA-256 content addressing, HMAC-stamped lockfiles, hash-chained audit logs); enforces tiered permissions and attack-derived blocklists before LLM invocation; gates feature work through a phase state machine with requirement-to-file-to-test traceability; compiles a single canonical definition to seven IDE targets; and detects prompt drift via Jaccard similarity. Conformance tests on injected violations confirm each mechanism enforces its stated invariant; developer outcomes remain future work. Governance of this layer must be deterministic and tool-agnostic -- not delegated to further LLM orchestration.

Generative AI coding agents are entering the open-source supply chain, yet their diverse and often invisible traces leave their prevalence poorly understood. We introduce a multi-layered detection framework that integrates configuration-file scanning, commit-message analysis, author-identity matching, and bot-signature lookup across World of Code (180M+ Git repositories), classifying agent traces into four behavioral types. No single method captures more than a fraction of activity: multi-method detection identifies 850,157 Claude Code commits in one snapshot, of which bot-account lookup_the signal most adoption studies rely on_recovers only 28,154 (3.3%), a 30x relative-recall gap, so single-signal prevalence estimates are biased low by at least this factor. Every detection pattern is hand-validated (495 labels) with per-cell precision and Wilson confidence intervals. Across snapshots from December 2024 to April 2026, commit-attributed agents generate over 320,000 commits per month; Claude Code leads (886,122 commits across 17,295 projects) and dominates silent, configuration-file-only adoption (21,078 projects). Compared against an independent pull-request census (AIDev), the two channels capture nearly disjoint agent populations_a PR census misses 79% of commit-detected Claude Code adopters and essentially all Codex adopters_and different kinds of work: PR-deployed cloud agents (Codex, Cursor) surface as feature work, while commit-deployed in-editor agents (Claude Code, OpenHands, Aider) surface as maintenance. The observed work profile follows deployment and detection mode rather than the tool itself, so no single channel is representative.

The open-source ecosystem on GitHub lacks a systematic hierarchical taxonomy of software repositories. GitHub Topics, the dominant organizational mechanism, is flat, inconsistent, and covers only 67% of projects. We present ATLAS, the first framework that automatically constructs a hierarchical taxonomy for software repositories and classifies projects into it end-to-end. By combining LLM global knowledge with real repository distributions, ATLAS proposes meaningful splitting dimensions and iteratively corrects those that fail to accommodate real projects. A Designer Agent proposes splitting dimensions while a Classifier Agent assigns repositories; a self-corrective refinement loop uses classification failures to drive dimension revision through escalating strategies. We evaluate ATLAS on 54,387 GitHub repositories against six baselines spanning four paradigms, two downstream tasks, and three model families. On a stratified 2,001-repository benchmark, ATLAS achieves a Taxonomy Quality F-score (TQF) of 83.13%, outperforming the best baseline by 15 percentage points (on the full 54k corpus the approximate TQF is 73.0%, a gap driven by Path Granularity's all-or-nothing scoring on longer paths rather than lower classification accuracy). It is the only method to simultaneously achieve high structural quality and high practical applicability. On downstream tasks, ATLAS enables alternative discovery with P@1 = 85.71%, surpassing even human-curated lists (62.34%), and achieves the highest P@1 for repository retrieval. The taxonomy further reveals structural ecosystem trends that are difficult to obtain from flat tags or similarity methods: the shift from libraries to AI/ML applications (now 61% of newly community-adopted projects) becomes visible only through hierarchical, type-based categorization. An interactive taxonomy explorer is available at https://atlas-taxonomy.netlify.app/

A modern coding agent can hold an entire repository in its context window. Most of its reading is wasted -- and the interesting question is not how much context an agent can use, but what it actually \emph{needs}. We study that question at the moment it matters most: when the agent must \emph{edit} code. Separating \emph{finding} the work site from \emph{acting} on it, we hold localization fixed with an oracle, vary only how the code is represented, and score context against real issue resolution on SWE-bench Verified. The answer is starkly minimal. The signal lives in the code being edited itself: natural-language summaries of it answer almost none of the behavioral questions that the source answers ($4/45$ vs.\ $27/45$, held-out repositories, independent judge), and the gap belongs to the representation, not the summarizer -- a frontier model's summaries score exactly as poorly as a 3B model's. The surrounding context hardly matters either: across every multi-file instance in Verified, under a protocol frozen before any data, rendering a file's remainder as UML skeletons and signatures resolves no more issues than deleting that remainder outright ($N{=}70$, exact McNemar $p{=}0.75$). That was our registered hypothesis, and it failed. Compressed context, meanwhile, matches whole files at a third of the tokens: a resolved issue costs $19$K context tokens, not $94$K. The instrument also yielded a finding the field should keep: temperature-0 API inference flips ${\sim}9\%$ of per-instance outcomes between byte-identical runs. That is a noise floor under every small effect reported on this benchmark, including ours. We release the instrument -- gold-validated environments, per-instance proof that every reference edit is expressible from every arm's context, deterministic patch construction, and pre-registered hypotheses whose nulls we publish.

LLM-based coding agents need higher-level operational knowledge about a repository (which files house which subsystems, how to run the test suite, which workflows have historically led to wrong fixes) that does not exist in the code itself. Engineers typically maintain AGENTS.md files to supply this context as instructions for coding agents, but whether they help is contested: recent studies disagree on whether LLM-generated guidance improves or harms agent performance. In this paper we show that how the guidance is produced is the decisive variable, and introduce probe-and-refine tuning: a procedure that uses synthetic bug-fix probes to iteratively diagnose and patch a repository's guidance file through single-shot LLM calls, with no agent loop or tool use during tuning. On SWE-bench Verified across four independent trials with Qwen3.5-35B-A3B at 200 steps, probe-and-refine achieves 33.0% mean resolve rate vs. 28.3% for the static knowledge base used to initialize it and 25.5% for an unguided baseline (p < 0.001 for both probe-and-refine contrasts). The improvement comes from coverage rather than precision: refined guidance produces evaluable patches for 14.5 percentage points (pp) more instances while per-patch precision remains statistically constant (~59%, p = 0.119), showing that improved guidance helps agents reach the correct file rather than improving the quality of the changes they make. Further, a step-budget experiment shows that guidance is what lets the agent use a larger step budget productively, and a cross-model experiment with NVIDIA-Nemotron-3-Nano-30B-A3B finds that the tuning loop degrades when the model cannot generate sufficiently diagnostic output, though per-patch precision remains constant even then.

We present Phoenix, a multi-agent LLM system that resolves GitHub issues from triage through pull-request creation, combining seven layered safety controls with a baseline-aware test evaluation strategy. Phoenix decomposes the work across six specialized agents. Planner, reproducer, coder, tester, failure analyst and Pull Request (PR) agent, all coordinated by a label-based GitHub webhook state machine. Every change is checked against a baseline test run before a pull request is opened. On a 24-instance slice of SWE-bench Lite. run on the production webhook path, Phoenix oracle-resolves 75% of instances with no pass-to-pass regressions on successful runs; this curated slice is not directly comparable to full-split leaderboard results, and we discuss the limits of the comparison. A complementary pilot on 42 real issues across 14 repositories yields 100% correctness preservation (CP; mean 122s on the hard tier). Manual inspection shows that about half of the resulting pull requests are well-targeted fixes. The other half place code at incorrect paths, a planner localization limitation we are addressing with retrieval. We also report the deployment failure modes (WAF filtering, token expiry, permission boundaries, flaky CI) that motivated each safety mechanism.

Reproducing research results from papers and released code is central to scientific progress. Existing works have introduced benchmarks to evaluate whether LLM agents can assist with reproducibility, but they are difficult to scale due to their reliance on substantial manual effort for data curation and evaluation. We introduce ReproRepo, a scalable framework for reproducibility evaluation that leverages human-raised GitHub issues as naturally occurring supervision on realistic reproduction blockers. We instantiate ReproRepo on 1,149 recent machine learning papers from major conferences and evaluate four frontier model-agent configurations. Our results show that LLM agents, even without executing code, can identify many real-world reproducibility problems from paper-repository pairs: the best agent in our study, namely Codex with GPT-5.5, surfaces at least one semantically related human-reported blocker for $\sim$90% of papers in the study. Further analysis shows that agents are particularly effective for surfacing visible failures and identifying the right semantic region, but may still be insufficient in exact localization. ReproRepo can serve as a reusable, scalable framework for future evaluations of LLM agents on real-world reproducibility auditing. Our code is released at https://github.com/LithiumDA/ReproRepo.

Software practitioners increasingly use AI coding agents that generate test code alongside production code in open source pull requests (PRs). Recent studies report more than 932,000 agent-authored PRs across more than 116,000 repositories, yet whether their test files contain meaningful verification logic remains underexplored. Test files lacking explicit assertions execute code without verifying behavior, so quality gates based on test-file presence overestimate verification strength. The goal of this paper is to help practitioners assess the verification strength of agent-authored patches by characterizing oracle signals and their link to merge outcomes and review effort. We conduct an empirical study of 86,156 test-file patches from 33,596 agent-authored PRs across 2,807 GitHub repositories produced by five coding agents: OpenAI Codex, GitHub Copilot, Devin, Cursor, and Claude Code. A qualitative analysis of 384 stratified patches informs a syntactic taxonomy of eight oracle signal categories. Applied at scale, 80.2% of test patches contain weak or no explicit oracle signals. While raw merge rates are lower for strong-oracle PRs, a regression analysis adjusting for agent, PR size, repository popularity, task type, and language shows strong oracles significantly improve merge likelihood (OR = 1.28, p < 0.001). Our findings suggest that test file counts substantially overestimate verification strength and that practitioners can adopt oracle-aware quality checks to more accurately evaluate agent-authored contributions.

Scientific publication is still organized primarily around static manuscripts, even though much of scientific progress depends on tacit know-how: how to run code, reproduce figures, interpret edge cases, choose useful follow-up directions, and avoid failed paths. Large language model agents create an opportunity to publish not only knowledge, but also operational know-how in a form that future readers and researchers can directly use. This paper outlines the Agentic Publication Protocol (APP), a lightweight repository format for packaging a paper together with code, data, environment information, reproducibility instructions, and an agent-facing instruction file. APP treats a version-controlled repository as the publication object and uses \texttt{AGENTS.md} and optional skills to define a paper agent that can explain the work, reproduce key results when possible, and support follow-up research. We describe the design principles and details of the protocol, as well as the agent skills useful for publishing papers under the protocol. We also describe development tools for evaluating and improving the protocol and associated agent skills. Finally, we provide a broader discussion of the future of scientific research in the agent era.

LLMs have substantially improved software engineering yet real-world development requires architectural understanding. Such understanding is prohibitively expensive to label manually and impossible to verify through tests alone. We propose an agentic judging pipeline using a strong LLM as a scalable proxy for expert architectural evaluation, comprising two judges: the Architecture Complexity Judge (ACJ), which estimates codebase-specific architectural understanding a task demands, and the Architecture Quality Judge (AQJ), which evaluates patch conformance to repository-specific architectural conventions via source-grounded rubrics. Fine-tuning Qwen3-8B/14B/32B on 3,360 curated instances achieves resolved rates of up to 27.2% on SWE-bench Verified - up to 540% over the base model and 256% over unfiltered fine-tuning. Meanwhile, the trained models achieve strong cross-language generalization and consistent improvements in architectural patch quality.

AI evaluations are widely used for testing and understanding progress. However, the diverse evaluators bring with them inconsistencies that challenge analysis and comparison. First, results are saved in incompatible formats, scattered across leaderboards, papers, blog posts, evaluation harness logs, and custom repositories. Second, results are created by different evaluation frameworks, which produce divergent scores for nominally identical evaluations and record metadata inconsistently, hindering comparison, cross-community evaluation science, cost reduction, and reuse. We introduce Every Eval Ever, the first shared schema and community-crowdsourced repository for AI evaluation results. The schema standardizes how evaluations are represented in a unified, single JSON document. It is source-agnostic by design, ingesting results from evaluation harnesses and papers alike, and optionally stores per-instance outputs for fine-grained analysis. We contribute: (i) a community-governed metadata schema with a companion instance-level schema, the first standardization effort of its kind; (ii) automatic converters from popular formats, evaluation harnesses, and leaderboards to the unified schema; and (iii) a crowdsourced community database hosted on Hugging Face, currently spanning to date 22,235 models, 2,273 unique benchmarks, and 31 evaluation formats.

AI coding tools are now used by a majority of developers, and agentic use of these tools has popularized the practice colloquially called "vibe coding". Yet causal evidence on their effect on software architecture is scarce. Prior causal work has measured code-level outcomes (complexity, static analysis warnings); whether such degradation propagates to architecture-level outcomes remains unknown. We mine 151 open-source Java repositories, 74 with detectable agentic AI adoption (identified via configuration files and Co-Authored-By commit trailers) and 77 propensity-matched controls, across a 13-month per-repository window yielding 1,811 monthly Arcan snapshots. We estimate the causal effect of adoption on architectural smell density (ASD) with a staggered difference-in-differences design and the Borusyak imputation estimator, applying a causal design recently used for code-level metrics to the architecture level. Total smell counts are essentially unchanged (+1.1%, p = 0.82) while lines of code grow +12.8% (p = 0.003); the resulting 6.7% ASD decline (p = 0.004) is therefore a denominator effect rather than an architectural improvement. Per-type estimates and robustness checks (wild cluster bootstrap, Lee bounds, stale-observation sensitivity) corroborate the pattern; pre-trends are flat (Wald p = 0.90), consistent with parallel trends. Density-normalized outcomes can mislead when treatment affects system size: raw counts and explicit decomposition are required for causal mining studies of AI tool adoption. The complete replication package, including the curated 151-repository monthly panel, is publicly available.

Coding-agent benchmarks evaluate whether a single uninterrupted agent can resolve a repository issue. Real software work is messier: tasks are interrupted, reassigned, reviewed, and resumed from partial states left by another agent or engineer. We study this missing dimension through handoff debt: the rediscovery cost imposed when a predecessor's work is opaque or incomplete. Our takeover protocol interrupts a coding agent at deterministic handoff points, freezes the repository, and evaluates successor agents under four handoff views: repository state only, raw trace, summary notes, and structured notes. Across 75 source tasks, the protocol generates 181 handoff-point tasks and 724 takeover runs per successor model. Across three successor models, context-bearing handoffs reduce median agent events by 20-59% and cumulative prompt tokens by 42-63% relative to repository-only takeover. Solved-rate effects are smaller and model-dependent, but efficiency gains are consistent. These findings suggest that coding-agent evaluation should report not only whether a task is solved, but also how costly that work is for another agent to resume.

This paper proposes an improved approach to the analysis of Mining Software Repositories (MSR) datasets via metadata enrichment, FAIRness assessment, and topic-driven analysis. This research expands upon an earlier dataset directory created specifically for the analysis of MSR datasets by adding new annotations to the datasets, enriching the metadata categories, and offering more advanced filtering options. The metadata of the MSR papers presented from 2013 to 2024 has been gathered using the Semantic Scholar API. The analysis is based on Latent Dirichlet Allocation (LDA) topic modeling and statistical analysis. Dataset-level attributes were included into the expanded dataset directory, namely repository hosting site, format, accessibility, reusability, and dataset quality. The study reveals that the choice of repository hosting sites and data formats influences citation patterns and dataset usability. Furthermore, the enhanced annotation approach improves the analysis and discoverability of MSR datasets, supporting more effective reuse and evaluation of research artifacts.

We present Code-QA-Bench, a fully automated framework for synthesizing repository-level code understanding benchmarks that separates genuine code comprehension from documentation recall and pretraining memorization. The framework makes two methodological contributions: (1) an answer-first generation pipeline where a tool-equipped agent explores source code to produce verified gold answers before deriving questions, ensuring every task is grounded in real code structure; and (2) a three-condition experimental design evaluating agents under closed-book (no repository), code-only (documentation removed), and documented (full repository) conditions, with deltas directly quantifying documentation utility and memorization. We generate 528 code-derivable and 100 doc-dependent tasks across 10 Python repositories from SWE-Bench, scored by an LLM judge on accuracy, completeness, and specificity. Experiments on four frontier models reveal that code access is the dominant factor (+0.23 mean gain over closed-book), documentation provides modest additional benefit (+0.071 on doc-dependent tasks), and code-only $\approx$ documented on code-derivable tasks, validating the design. The framework is open-source and applicable to any well-documented Python repository.

AI-assisted research compresses ideation, implementation, evaluation, and manuscript writing into a single interactive loop. This compression is useful, but it also creates a publication risk: paper claims can become easier to state than to audit. We present ResearchLoop, an evidence-gated control plane for AI-assisted computational research. ResearchLoop treats research questions, task contracts, evidence objects, claim ledgers, closeouts, and paper bindings as durable project state, realized here as a repository-backed runtime. This technical report provides the complete protocol specification, state model, transition rules, claim-admission algorithm, and insight-compounding mechanism. It also reports the full experimental record spanning nine versions (V0--V9), including a self-hosting case study, a controlled task-suite study with component ablations, a mathematical olympiad evaluation, and a supplementary SciCode boundary experiment evaluated with the official generated-code harness. All artifacts, manifests, and verification reports are preserved in the project repository.

Specification synthesis, the task of automatically inferring formal specifications from program implementations and natural language, is important for refactoring, transpilation, optimization, and verification, yet remains an open challenge for large C++ repositories. Existing LLM-based approaches fail to simultaneously scale to such repositories, produce specifications expressive enough to capture systems-code features such as dynamic memory and heap-allocated data structures, and systematically validate those specifications to rule out incorrect candidates. We present Spec-Agent, an agentic system for synthesizing expressive, well-validated specifications across large C++ codebases. Spec-Agent targets a ladder of specification languages: propositional logic, first-order logic, propositional separation logic, and first-order separation logic. For each function, Spec-Agent uses static analysis and runtime heap tracing to select the appropriate target specification language, generalizes existing functional tests into fuzz harnesses, and iteratively refines LLM-generated candidates via counterexample-guided feedback. We evaluate Spec-Agent on open source C++ codebases comprising millions of lines of code. Spec-Agent synthesizes valid specifications for 85% of target functions, with no false positives observed under fuzzing and expert validation, outperforming Claude Code Opus 4.6 at 10x lower token cost.

Functionality-correct repository setup aims to configure execution environments (e.g., dependencies, build scripts) to successfully execute a repository's documented features. It presents significant challenges due to diverse, repository-specific failures, including dependency incompatibilities, missing toolchains, incomplete installations, and verification-strategy mismatches. Existing LLM agents struggle to robustly resolve these issues, specifically failing to support (1) cross-repository experience transfer, (2) multi-step trial-and-repair under non-invertible state changes, and (3) robust verification of setup outcomes to distinguish setup-induced failures from repository bugs. To address this, we introduce SetupX, an experiential learning-based setup framework. First, we construct a Self-Evolving Experience Representation (XPU), a dual-modality knowledge unit encoding setup signals, textual guidance, executable actions to dynamically transfer verified environment fixes to unseen repositories. Second, we employ Experience-Augmented Speculative Execution backed by a LIFO Docker snapshot stack, enabling the agent to proactively trial fixes and safely roll back to known-good states. Third, we introduce a Prosecutor-Judge Verification Protocol that separates evidence collection from final judgment, enabling more reliable setup verification beyond superficial build-time metrics. Evaluation results on carefully-crafted benchmarks show SetupX achieves highest performance (e.g., 92% pass rate) and outperforms the strongest baseline by over 19%. Crucially, SetupX excels in complex multi-repository setup requiring coordinating multiple interconnected services across different containers. The code repository is available at https://github.com/OpenDataBox/SetupX.

The explosive growth of open-source model repositories has created a Model Jungle, where checkpoints are frequently shared without adequate documentation or metadata. While weight-space learning offers a pathway to identify and analyze these models directly from their parameters, processing full-scale weights is computationally prohibitive. Probing-based methods have emerged as a lightweight alternative, extracting permutation-equivariant representations via learnable probe vectors. However, existing probing methods are limited by a single-view design: they capture first-order structures but fail to encode the rich, higher-order correlation patterns inherent in row-column interactions. To bridge this gap, we introduce MVProbe, a multi-perspective probing framework that synthesizes first-order signals with interaction-aware (Gram-based) views. Our approach is theoretically grounded; we analyze the scaling laws of different probing orders to derive a principled standardization and fusion strategy that ensures balanced contributions from all branches. On the Model Jungle benchmark, MVProbe consistently outperforms the state-of-the-art ProbeX across diverse architectures, including discriminative backbones (ResNet, SupViT, MAE, DINO) and large-scale generative LoRA adapters (Stable Diffusion LoRA).

Software repositories accumulate large amounts of unstructured knowledge in commit messages, pull-request discussions, and issue threads, but developers and AI coding assistants rarely reuse this history effectively. Recent work on typed-memory architectures for LLM agents (MemGPT, generative agents, and the PlugMem module of Yang et al.) argues that agent memory should be distilled, typed knowledge rather than raw interaction text. We adapt that stance to a software repository's own git history under a constrained regime: deterministic, dependency-free, local-only, no embeddings. We present CommitDistill, an open-source Python prototype that mines a local git history into typed knowledge units (Facts, Skills, Patterns) using deterministic regex and surfaces them through a TF-IDF retriever with a calibrated silence threshold (theta = 2.5) that abstains on out-of-distribution queries. The artefact is a trust-instrumented memory substrate: deterministic, no external service, inspectable plain-JSON store, tunable abstention. A case study on five public repositories spanning Python, JavaScript, C, and Java (25,000 commits, 1,167 extracted units) reports useful-precision 0.525 at Cohen's kappa = 0.633 on 40 dual-annotated Python units. The decisive finding is budget-constrained retrieval: at a 256-character per-query budget, CommitDistill reaches 0.750 hit-rate on a 12-query benchmark against BM25's 0.333 and git log --grep's 0.083. On a four-arm paired LLM-as-judge evaluation (n=200 time-travel bug-fixes, two judges) covering control, CommitDistill, a body-budget-matched CD-Hybrid, and BM25, no condition produces a statistically detectable lift over control on the headline mean and CD-Hybrid is indistinguishable from BM25 head-to-head. Extraction over 10,000 commits completes in under 4 seconds on a laptop. Source, annotations, baselines, and a reproducibility script accompany this paper.

Code agents increasingly help developers work with unfamiliar repositories, but every such task depends on a costly prerequisite: bootstrapping the repository into a usable development state. This process requires substantial trial-and-error exploration, yet the resulting knowledge--resolved dependencies, repair strategies--stays trapped in a single conversation, unavailable to future agents. We therefore formulate repository bootstrapping as a reusable startup knowledge problem and introduce BootstrapAgent, a multi-agent framework that distills the heuristics discovered during bootstrap exploration into a persistent, verifiable, agent-consumable .bootstrap contract. Through evidence extraction, structured planning, deterministic Docker-based verification, and trace-driven repair, BootstrapAgent generates a contract covering environment setup, diagnostic checks, minimal verification, and accumulated repair knowledge. We further propose warm repair with clean replay to accelerate iterative debugging without sacrificing cold-start reproducibility, and a delta repair with sanity check to prevent reward hacking. Experiments on three benchmarks show that BootstrapAgent achieves a 92.9% success rate, outperforming the baseline by over 10% while reducing downstream agent token usage by 25.9% and build time by 22.3%. Our code is available at https://github.com/Vossera/BootstrapAgent.

Context: Retrieval-augmented code generation relies on cross-file repository context, but retrieved snippets may come from obsolete project states. Objectives: We study whether temporally stale repository snippets act as harmless noise or actively induce current-state-incompatible code. Methods: We conduct a controlled diagnostic study on a curated 17-sample set of production-helper signature changes from five Python repositories. For each sample, we compare current-only, stale-only, no-retrieval, and mixed current/stale retrieval conditions under prompts that hide commit freshness and expected current signatures. Results: Under neutralized prompts, stale-only retrieval induces stale helper references on 15/17 Qwen2.5-Coder-7B-Instruct samples and 13/17 gpt-4.1-mini samples, corresponding to 88.2 and 76.5 percentage-point increases over current-only retrieval. No retrieval produces zero stale references but only 1/17 passing completions. The two models share 75.0% Jaccard overlap among stale-triggering samples, and mixed conditions show that adding valid current evidence largely rescues stale-only failures. Conclusion: Temporal validity of retrieved repository context is a distinct diagnostic variable for Code RAG robustness: stale context can actively bias models toward obsolete repository state rather than merely removing useful evidence.

Context window efficiency is a practical constraint in large language model (LLM)-based developer tools. Paulsen [12] shows that all tested models degrade in accuracy well before their advertised context limits the Maximum Effective Context Window (MECW) which makes context construction a quality problem, not just a cost one. Modern software repositories routinely contain large non-code artifacts compiled datasets, binary model weights, minified JavaScript bundles, and gigabyte-scale log files that overflow the context window and push out task-relevant source code. We present a correctness-aware context hygiene framework: a pre-execution, size-based heuristic filter that intercepts repository scans before tokenization, using only OS-level stat() metadata with sub-millisecond overhead. Semantic retrieval approaches such as RepoCoder, GraphRAG, and AST-based chunking require index construction and query-time inference before any filtering decision is reached. Our framework, by contrast, requires no indexing and operates at <0.01 ms per file decision. Across 10 real open-source repositories (22,046 files, 5 languages), the proposed SizeFilter at θ=1 MB achieves 79.6% (\pm13.2%) mean token reduction at 0.30 ms overhead: the HybridFilter achieves 89.3% (\pm9.0%) the lowest variance of any filter evaluated. A token-density study across 2,688 files confirms a strong linear correlation (Pearson r=0.997, k=0.250 tokens/byte). A limited-scope evaluation (18 tasks, CodeLlama-7B-Instruct) yields 72% file-level accuracy under filtering versus 25% at baseline; hallucination frequency declines from 61% to 17%. All code and data are released for reproducibility.

We present Curated Industrial Developer Repository (CIDR), a large-scale dataset of real-world software repositories collected through direct collaboration with 12 industrial partner organizations. The dataset comprises 2,440 repositories spanning 138 programming languages and totalling 373 million lines of code, accompanied by structured per-repository metadata. Unlike existing code corpora derived from public open-source platforms, CIDR consists exclusively of proprietary production codebases contributed under formal data sharing agreements, covering application domains including enterprise web and mobile development, fintech, and custom software consultancy. All repositories were processed through a multi-stage pipeline encompassing structured partner onboarding, two-stage quality selection combining automated metadata filtering with manual code review, and a deterministic anonymization pipeline covering the full version control history. The dataset is intended to support research in code intelligence, software quality analysis, pre-training and fine-tuning of code language models, developer behaviour studies, and construction of agent evaluation benchmarks. Access is provided under a restricted commercial license; details are available at https://fermatix.ai/#Contact.

Automation platforms such as GitHub Actions and n8n are increasingly adopting so-called agentic workflows, which integrate Large Language Model (LLM) agents for tasks such as code review and data synchronization. While bringing convenience for developers, this integration exposes a new risk: An adversary may control and craft certain inputs, such as GitHub issue comments, to manipulate the LLM agent for unwanted actions, such as credential exfiltration and arbitrary command execution. To our knowledge, no prior academic work has studied such a risk in agentic workflows. In this paper, we design the first detection and exploitation framework, called JAW, to hijack agentic workflows hosted on automation platforms via a novel approach called Context-Grounded Evolution. Our key idea is to evolve agentic workflow inputs under the contexts derived from hybrid program analysis for hijacking purposes. Specifically, JAW generates agentic workflow contexts through three analyses: (i) static path-feasibility analysis to identify feasible agent-invocation paths and the input constraints required to trigger them, (ii) dynamic prompt-provenance analysis to determine how that input is transformed and embedded into the LLM context, and (iii) capability analysis to identify the actions and restrictions available to the agent at runtime. Our evaluation of JAW on GitHub workflows and n8n templates showed that 4714 GitHub workflows and eight n8n templates can be successfully hijacked, for example, to leak user credentials. Our findings span 15 widely-used GitHub Actions, including official GitHub Actions for Claude Code, Gemini CLI, Qwen CLI, and Cursor CLI, and two official n8n nodes. We responsibly disclosed all findings to the affected vendors and received many acknowledgements, fixes, and bug bounties, notably from GitHub, Google, and Anthropic.

Recent image generation and editing models demonstrate robust adherence to instructions and high visual quality on academic benchmarks. However, their performance on paid, real-world design projects remains uncertain. We introduce \textbf{ServImage}, a benchmark that explicitly correlates model outputs with economic value in commercial design projects. ServImage consists of (i) \textbf{\textit{ServImageBench}}: a dataset of 1.07k paid commercial design tasks and 2.05k designer deliverables totaling over $295k, covering portrait, product, and digital content, along with 33k candidate images and 33k human annotations. (ii) \textbf{\textit{ServImageScore}}: an integrated scoring system that combines three quality dimensions: baseline requirements fulfilment, visual execution quality, and commercial necessity satisfaction. These three dimensions are designed to characterize the factors that drive human payment decisions and indicate whether an image is commercially acceptable. (iii) \textbf{\textit{ServImageModel}}: under this scoring system, we propose a payment prediction model trained on the human-annotated candidate images, achieving 82.00% accuracy in predicting human payment decisions and producing calibrated payment probabilities. ServImage provides a comprehensive foundation for assessing the commercial viability of image generation models and offers a scalable resource for future research on economically grounded vision systems \href{https://github.com/FengxianJi/ServImage}{Github.}

Code review is central to software engineering education but hard to scale in capstone projects due to tight deadlines, uneven peer feedback, and limited prior experience. We investigate an LLM-as-reviewer integrated directly into GitHub pull requests (human-in-the-loop) across two cohorts (more than 100 students, 2023--2024). Using a mixed-methods design -- GitHub data, reflective reports, and a targeted survey -- we examine engagement and responsiveness as behavioral indicators of self-regulated learning processes. Quantitatively, the 2024 cohort produced more iterative activity (1176 vs. 581 PRs), while technical issues observed in 2023 (227 failed AI attempts) dropped to zero after tool and instructional refinements. Despite different adoption levels (93% vs. 50% of teams using the tool), responsiveness was stable: 32% (2023) and 33% (2024) of successfully AI-reviewed PRs were followed by subsequent commits on the same PR. Qualitatively, students used the LLM's structured comments to focus reviews and discuss code quality, while guidance reduced over-reliance. We contribute: (i) an in-workflow design for an AI reviewer that scaffolds learning while mitigating cognitive offloading; (ii) a repeated cross sectional comparison across two cohorts in authentic settings; (iii) a mixed-methods analysis combining objective GitHub metrics with student self-reports; and (iv) evidence-based pedagogical recommendations for responsible, student-led AI-assisted review.

We present Code Broker, a multi agent system built on Google s Agent Development Kit ADK that analyses Python source code from individual files, local directory trees, or remote GitHub repositories and generates structured, actionable quality assessment reports. The system realises a hierarchical five agent architecture in which a root orchestrator coordinates a sequential pipeline agent that, in turn, dispatches three specialised agents concurrently a Correctness Assessor, a Style Assessor, and a Description Generator before synthesising their findings through an Improvement Recommender. Reports quantify four quality dimensions correctness, security, style, and maintainability on a normalised scale and are rendered in both Markdown and HTML for integration into diverse developer workflows. Code Broker fuses LLM based semantic reasoning with deterministic static analysis signals from Pylint, employs asynchronous execution with exponential backoff retry logic to improve robustness under transient API failures, and explores lightweight session memory for retaining and querying prior assessment context across runs. We frame this paper as a technical report on system design, prompt engineering, and tool orchestration, and present a preliminary qualitative evaluation on representative Python codebases of varying scale. The results indicate that parallel specialised agents produce readable, developer oriented feedback that complements traditional linting, while also foregrounding current limitations in evaluation depth, security tooling, large repository handling, and the exclusive reliance on in memory persistence. All code and reproducibility materials are publicly available: https://github.com/Samir-atra/agents_intensive_dev.