Retrieval-Augmented Generation (RAG) is increasingly used to ground large language model (LLM) outputs in scientific literature. However, in open-ended literature exploration, the evidence context used for generation is often produced through hidden retrieval, reranking, assessment, and filtering steps. Users may receive retrieval summaries without knowing how the system constructed the evidence context, which evidence units were retained or discarded, or whether potentially useful evidence was excluded before synthesis. We present FootprintRAG, an LLM-agent-powered visual analytics system for evidence context refinement in RAG-based scientific literature exploration. The core idea is to treat the RAG evidence context as an explicit, inspectable, and revisable analytical object before generation. FootprintRAG parses scientific literature into text and figure evidence units, expands an initial query into parallel query variants, retrieves and assesses evidence across iterative rounds, and surfaces ERS-ranked supplementary candidates from the corpus-level evidence space. Through coordinated views, the system connects retrieval trajectories, evidence-state revision, and provenance-aware summary generation into a user-steerable workflow. We evaluate FootprintRAG through two case studies, a user study, and a workflow-level comparison with representative RAG systems. The results show that FootprintRAG helps users compare retrieval directions, revise candidate evidence, recover potentially overlooked evidence, and trace generated summaries back to supporting evidence units. FootprintRAG is available at https://github.com/meteorshowering/FootprintRAGVA.git.

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