Retrieval-Augmented Generation (RAG) equips large language models with external knowledge and is central to knowledge-intensive tasks. As RAG systems enter real-world use, generators must reliably leverage retrieved evidence. Recent fine-tuning methods improve adaptation to RAG scenarios, but optimization remains challenging because retrieval may return incomplete, fragmented, noisy, or conflicting contexts. Complex tasks further require fine-grained evidence dependencies. These challenges make high-quality supervision costly and limit generalization. We present KARE-RAG (Knowledge-Aware Refinement and Enhancement for RAG), a training-time scaffolded alignment framework. It uses structured knowledge representations as temporary scaffolds to expose evidence organization, support localized factual refinement, and construct fine-grained preference pairs. In our main implementation, an expert LLM refines a lightweight graph-structured evidence sketch. The generator is optimized with token-weighted Dense Direct Preference Optimization (DDPO), which focuses learning on edited scaffold regions. Scaffolds are used only for data construction and training supervision. At inference time, the model runs as standard Vanilla RAG without graph construction, extra retrieval, or latency overhead. Experiments show that KARE improves transfer across the evaluated QA and relation extraction datasets with limited training data, while leaving general capabilities largely unchanged. KARE can also complement existing RAG training objectives as an additional alignment stage.

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