Recent advances in retrieval-augmented generation (RAG) and large language models (LLMs) enable researchers to integrate AI into scientific workflows. However, using proprietary commercial AI systems raises concerns about transparency, reproducibility and privacy, which are essential for scientific practices. To this end, AquiLLM was developed as an open-source modular RAG-LLM framework using open-weight models, designed to support research groups in capturing tacit knowledge. In this work, we present a series of architectural improvements and feature enhancements to AquiLLM, including local embedding and reranking, multimodal capabilities, OpenAI-compatible inference interfaces, user interface improvements, semantic and episodic memory capabilities, and skills support. These enhancements were informed by discussions with domain experts, including astrophysicists and environmental researchers, and represent a step toward AI systems more closely aligned with scientific research practices.

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