Code Comprehensor: Hierarchical Documentation and Cross-Modal Retrieval for Large Repositories

Large Language Model (LLM) coding agents typically explore codebases through repeated file-reading and grep-searching, consuming thousands of tokens per query without structural understanding. We present Codebase-Memory, an open-source system that constructs a persistent, Tree-Sitter-based knowledge graph via the Model Context Protocol (MCP), parsing 66 languages through a multi-phase pipeline with parallel worker pools, call-graph traversal, impact analysis, and community discovery. Evaluated across 31 real-world repositories, Codebase-Memory achieves 83% answer quality versus 92% for a file-exploration agent, at ten times fewer tokens and 2.1 times fewer tool calls. For graph-native queries such as hub detection and caller ranking, it matches or exceeds the explorer on 19 of 31 languages.

Code search, framed as information retrieval (IR), underpins modern software engineering and increasingly powers retrieval-augmented generation (RAG), improving code discovery, reuse, and the reliability of LLM-based coding. Yet existing code IR models remain largely text-centric and often overlook the visual and structural aspects inherent in programming artifacts such as web interfaces, data visualizations, SVGs, schematic diagrams, and UML. To bridge this gap, we introduce MMCoIR, the first comprehensive benchmark for evaluating multimodal code IR across five visual domains, eight programming languages, eleven libraries, and show the challenge of the task through extensive evaluation. Therefore, we then propose CodeMMR, a unified retrieval model that jointly embeds natural language, code, and images into a shared semantic space through instruction-based multimodal alignment. CodeMMR achieves strong generalization across modalities and languages, outperforming competitive baselines (e.g., UniIR, GME, VLM2Vec) by an average of 10 points on nDCG@10. Moreover, integrating CodeMMR into RAG enhances code generation fidelity and visual grounding on unseen code generation tasks, underscoring the potential of multimodal retrieval as a core enabler for next-generation intelligent programming systems. Datasets are available at HuggingFace.

Large Language Models (LLMs) have recently emerged as capable coding assistants that operate over large codebases through either agentic exploration or full-context generation. Existing benchmarks capture a broad range of coding capabilities, such as resolving GitHub issues, but none of them directly isolate and measure how effectively LLMs leverage repository-level context during code generation. To address this, we introduce ReCUBE, a benchmark in which LLMs reconstruct a masked file within a real-world repository, using all remaining source files, dependency specifications, and documentation as their only source of context. ReCUBE evaluates reconstructed code with usage-aware test cases that simulate both internal module logic and external cross-file integration, reflecting real-world software usage patterns. We further propose the Caller-Centric Exploration (CCE) toolkit, a set of dependency graph-based tools that can be integrated into agentic frameworks to guide agents toward the most relevant caller files during repository exploration. Experiments across eight models in four settings show that repository-level context utilization remains highly challenging even for state-of-the-art models, with GPT-5 achieving only 37.57% strict pass rate in the full-context setting. Agents augmented with our CCE toolkit consistently outperform all baselines across all evaluated models, with improvements of up to 7.56% in strict pass rate. We release our benchmark, code, and evaluation framework as open source for the NLP research community.