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Achieving long term autonomy of robots operating in dynamic environments such as farms remains a significant challenge. Arguably, the most demanding factors to achieve this are the on-board resource constraints such as energy, planning in the presence of moving individuals such as livestock and people, and handling unknown and undulating terrain. These considerations require a robot to be adaptive in its immediate actions in order to successfully achieve long-term, resource-efficient and robust autonomy. To achieve this, we propose a hierarchical framework that integrates a local dynamic path planner with a longer term objective based planner and advanced motion control methods, whilst taking into consideration the dynamic responses of moving individuals within the environment. The framework is motivated by and synthesizes our recent work on energy aware mission planning, path planning in dynamic environments, and receding horizon motion control. In this paper we detail the proposed framework and outline its integration on a robotic platform. We evaluate the strategy in extensive simulated trials, traversing between objective waypoints to complete tasks such as soil sampling, weeding and recharging across a dynamic environment, demonstrating its capability to robustly adapt long term mission plans in the presence of moving individuals and obstacles for real world applications such as large scale farming.