Beyond Correctness: Enhancing Architectural Reasoning in Code LLMs via Scalable Labeling with Agentic Judgment

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.

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.

Architectural code smells erode software maintainability and are costly to repair manually, yet unlike localized bugs, they require cross-module reasoning about design intent that challenges both developers and automated tools. While large language model agents excel at bug fixing and code-level refactoring, their ability to repair architectural code smells remains unexplored. We present the first empirical evaluation of LLM agents on architectural code smell repair. We contribute SmellBench, a task orchestration framework that incorporates smell-type-specific optimized prompts and supports iterative multi-step execution, together with a scoring methodology that separately evaluates repair effectiveness, false positive identification, and net codebase impact. We evaluate 11 agent configurations from four model families (GPT, Claude, Gemini, Mistral) on 65 hard-severity architectural smells detected by PyExamine in the Python project scikit-learn, validated against expert judgments. Expert validation reveals that 63.1% of detected smells are false positives, while the best agent achieves a 47.7% resolution rate. Agents identify false positives with up to $κ= 0.94$ expert agreement, but repair aggressiveness and net codebase quality are inversely related: the most aggressive agent introduces 140 new smells. These findings expose a gap between current LLM capabilities in localized code transformations and the architectural understanding needed for cross-module refactoring. SmellBench provides reusable infrastructure for tracking progress on this underexplored dimension of automated software engineering. We release our code and data at https://doi.org/10.5281/zenodo.19247588.