Large Language Models (LLMs) equipped with external tools have demonstrated enhanced performance on complex reasoning tasks. The widespread adoption of this tool-augmented reasoning is hindered by the scarcity of domain-specific tools. For instance, in domains such as physics question answering, suitable and specialized tools are often missing. Recent work has explored automating tool creation by extracting reusable functions from Chain-of-Thought (CoT) reasoning traces; however, these approaches face a critical scalability bottleneck. As the number of generated tools grows, storing them in an unstructured collection leads to significant retrieval challenges, including an expanding search space and ambiguity between function-related tools. To address this, we propose a systematic approach to automatically refactor an unstructured collection of tools into a structured tool library. Our system first generates discrete, task-specific tools and clusters them into semantically coherent topics. Within each cluster, we introduce a multi-agent framework to consolidate scattered functionalities: a code agent refactors code to extract shared logic and creates versatile, aggregated tools, while a reviewing agent ensures that these aggregated tools maintain the complete functional capabilities of the original set. This process transforms numerous question-specific tools into a smaller set of powerful, aggregated tools without loss of functionality. Experimental results demonstrate that our approach significantly improves tool retrieval accuracy and overall reasoning performance across multiple reasoning tasks. Furthermore, our method shows enhanced scalability compared with baselines as the number of question-specific increases.