The integration of Large Language Models (LLMs) into software engineering has shifted the focus from function-level generation to repository-scale assistance. However, existing benchmarks largely rely on bug reports from GitHub Issues, which often allow models to bypass genuine understanding via pattern matching on error logs. This misalignment under-measures Edit Bias, which refers to premature generation, where models prematurely propose code modifications instead of understanding the existing repository architecture. Furthermore, current LLM-as-a-Judge scalar scoring suffers from high variance and low interpretability. This work introduces RepoProbe, a novel benchmark for evaluating repository-level code understanding through open-ended Q&A using GitHub Discussions, which focuses on open-ended architectural inquiries rather than defect reporting. To ensure rigorous evaluation, we propose a Checklist-Based Verification Protocol that decomposes answers into atomic, verifiable facts, thereby replacing subjective ratings with objective verification. Our evaluation of state-of-the-art (SOTA) LLMs reveals a persistent gap between high clarity and evidencegrounded technical correctness. It also quantitatively confirms the prevalence of edit bias, in which models prioritize code generation instead of architectural analysis. Finally, we demonstrate that our verification protocol significantly improves evaluation reliability compared to traditional evaluations with scalar scoring.
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.
Kirill Vasilevski, Ximing Dong, Benjamin Rombaut +8
Large Language Models (LLMs) are increasingly used as assistants across the software development lifecycle, yet their ability to reason about software architecture remains largely unmeasured. Architectural decision-making depends on quality attribute trade-offs, design patterns, and system-level constraints, none of which are exercised by benchmarks that target syntactic or algorithmic tasks. We introduce SAKE (Software Architectural Knowledge Evaluation), a standardized and reproducible benchmark for assessing software architectural knowledge in LLMs. SAKE comprises 2154 expert-curated multiple-choice questions, each with four options, stratified across eight architectural categories and four context-length levels. We evaluate 11 proprietary and open-weight models in zero-shot and five-shot settings. Overall accuracy is high, but performance varies markedly across categories, revealing competency gaps in areas central to professional practice. SAKE, its evaluation scripts, and all results are released as open source to give the community a baseline for tracking architectural reasoning in LLMs.
Tiziano Santilli, Francesco Daghero, Mayhar Tourchi Moghaddam
Large language models (LLMs) are increasingly used in coding tasks, but their ability to reason about code execution remains unclear. Existing repository-level QA benchmarks mainly evaluate static code understanding and often rely on LLM-based evaluation, while execution-reasoning benchmarks are mostly limited to snippets or functions. We introduce SWE-Flux, a repository-level benchmark for dynamic execution reasoning containing 480 execution-grounded instances across 12 real Python repositories, with gold answers automatically harvested from instrumented test executions rather than written manually or judged by LLMs. The benchmark covers singletest and multi-test questions over control flow, loops, program state, dataflow, exceptions, and program invariants. Evaluating five LLMs shows that this task remains challenging. The best model achieves only 37% accuracy. Models perform better on localized behavior such as invariants, intra-procedural control flow, exceptions, and simple loops, but struggle with dataflow, inter-procedural execution, precise state reasoning, and suite-level aggregation. Finally, we show that the oracle-harvesting pipeline can generate fresh benchmark variants using input perturbation. It successfully harvests valid variants for almost 90% of the selected instances, and the resulting variants are substantially more challenging for the evaluated models.
Hamed Taherkhani, Mohammad Abdollahi, Melika Sepidband +3