DeepRepoQA: Code Repository Question Answering with Deep Agent Exploration

Large Language Models (LLMs) have shown impressive capabilities across software engineering tasks, including question answering (QA). However, most studies and benchmarks focus on isolated functions or single-file snippets, overlooking the challenges of real-world program comprehension, which often spans multiple files and system-level dependencies. In this work, we introduce StackRepoQA, the first multi-project, repository-level question answering dataset constructed from 1,318 real developer questions and accepted answers across 134 open-source Java projects. Using this dataset, we systematically evaluate two widely used LLMs (Claude 3.5 Sonnet and GPT-4o) under both direct prompting and agentic configurations. We compare baseline performance with retrieval-augmented generation methods that leverage file-level retrieval and graph-based representations of structural dependencies. Our results show that LLMs achieve moderate accuracy at baseline, with performance improving when structural signals are incorporated. Nonetheless, overall accuracy remains limited for repository-scale comprehension. The analysis reveals that high scores often result from verbatim reproduction of Stack Overflow answers rather than genuine reasoning. To our knowledge, this is the first empirical study to provide such evidence in repository-level QA. We release StackRepoQA to encourage further research into benchmarks, evaluation protocols, and augmentation strategies that disentangle memorization from reasoning, advancing LLMs as reliable tool for repository-scale program comprehension.

Code agents spend much of their effort simply locating the right code inside a repository. Two approaches dominate current practice. In Semantic Search, the agent retrieves code blocks from a vector index built from the repository in advance. In Deep Agentic Search (also known as grep-search by subagent), a planning agent delegates the exploration to a separate subagent that works in an isolated context window and returns only a condensed result. The second design, which is considered good context engineering practice, exists to protect the main agent from context pollution (also known as context rot), the loss of accuracy that occurs as unrelated material accumulates in the context window. Recent code agents (such as Claude Code, Codex, Antigravity, etc) have adopted it quickly, but there is little evidence on whether it produces better answers. We compare the two approaches on SWE-QA, a benchmark for repository-level code question answering. Semantic search answered 65.2% of questions correctly against 46.2% for deep agentic search, and it produced each correct answer at less than half the cost. To explain the gap, we then coded every failed run into a taxonomy of failure modes. The taxonomy shows that deep agentic search did not remove failures but introduced a new class of them: the single largest share of its failures, 41.8%, occurred at the hand-off between the planner and its sub-agent, and these were usually silent, ending in a fluent and confident answer that was wrong. Deep agentic search addresses a real problem and is now the preferred design in many code agents. However, our results show that the protection it offers may not be free, and that for read-only questions over a repository that can be indexed, retrieval was the stronger and cheaper option.

Code agents are currently having skillful performance on repository-level software engineering benchmarks, but it remains unclear whether success on end-to-end tasks such as issue resolution truly reflects repository context reasoning, the ability to identify the task-relevant information across multiple files and reason over the relations among them. To investigate this question, we introduce RepoMirage, a two-stage evaluation suite built on SWE-Bench Verified that adopts perturbation as a diagnostic tool to increase the demand for context reasoning by transforming how the repository is exposed. First, RepoMirage-Perturb applies three types of semantics-preserving repository-level perturbations, revealing a clear performance drop when correct solving requires broader context access. RepoMirage-Extend further turns perturbation-targeted structural bottlenecks into explicit tasks beyond issue resolution, where the average performance declines from 66.8% in the original setting to 25.3%, indicating a significant deficiency in repository context reasoning. Further trajectory analysis reveals an exploration drift, where agents access broader repository context but fail to turn it into effective structure information. Motivated by this observation, we propose RepoAnchor, a structure-first prototype workflow that separates repository exploration from downstream problem solving, and show that explicit structural scaffolding yields notable gains. These results uncover an previously overlooked gap in repository context reasoning for code agents and suggest that stronger structure-aware methods are potential to improve them.