This research explores the challenges and opportunities of using long-context Large Language Models (LLMs) in Retrieval-Augmented Generation (RAG) systems. The authors find that while increasing the number of retrieved passages initially improves performance, it can lead to a decline due to the detrimental impact of irrelevant passages, known as "hard negatives." To overcome this challenge, the paper proposes three solutions: training-free retrieval reordering, RAG-specific implicit LLM fine-tuning, and RAG-oriented LLM fine-tuning with intermediate reasoning. The paper concludes with a systematic analysis of the training-based methods, examining the effects of data distribution, retriever for training, and training context length.