Code-QA-Bench: Separating Code Reasoning from Documentation Memorization in Repository-Level QA

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.

In this paper, we introduce SWE-QA, a text and code corpus aimed at benchmarking multi-hop code comprehension, addressing the gap between simplified evaluation tasks and the complex reasoning required in real-world software development. While existing code understanding benchmarks focus on isolated snippets, developers must routinely connect information across multiple dispersed code segments. The dataset comprises 9,072 multiple-choice questions systematically generated from 12 Python repositories of SWE-bench, evaluating several recurrent reasoning patterns like Declaration-and-Call questions that link entity definitions to their usage, and Interacting-Entity questions that examine the dynamic relationships among multiple collaborating components. Generated through parsing-based entity extraction and Large Language Model assisted question construction with carefully validated distractors, the benchmark distinguishes genuine comprehension from superficial pattern matching. Evaluation of 15 language models (360M to 671B parameters) reveals significant challenges in multi-hop reasoning, with best performance reaching 74.41% accuracy. Dense architectures consistently outperform mixture-of-experts models by 10-14 percentage points, while reasoning-enhanced variants show inconsistent benefits.

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.