Large-scale scientific research on historical documents — particularly medieval Arabic manuscripts — remains challenging due to the need for advanced paleographic and linguistic training, the large volume of hand-written materials, and the absence of assisting software. In this paper, we propose InkSight, the first end-to-end Arabic manuscript analysis tool for manuscript-based analytics and research hypothesis testing. InkSight integrates three key components: (i) an Optical Character Recognition (OCR) module utilizing a Large Visual Language Model (LVLM); (ii) a lightweight document indexing and information retrieval module that enables query-based evidence retrieval from book-length manuscripts; and (iii) a flexible Large Language Model (LLM) prompting interface factually grounded to the given manuscript via Retrieval-Augmented Generation (RAG). Empirical evaluation on the existing KITAB OCR benchmark and our in-house dataset of ancient Arabic manuscripts has revealed that historical research can be effectively supported using smaller fine-tuned LVLMs without relying on larger proprietary models. The live web demo for InkSight is available freely at: https://inksight.ru and the source code for InkSight is publicly available at Github: https://github.com/ds-hub-sochi/InkSight-tool.