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This article discusses the scientifically and industrially important problem of automating the process of unloading goods from standard shipping containers. We outline some of the challenges barring further adoption of robotic solutions to this problem, ranging from handling a vast variety of shapes, sizes, weights, appearances, and packing arrangements of the goods, through hard demands on unloading speed and reliability, to ensuring that fragile goods are not damaged. We propose a modular and reconfigurable software framework in an attempt to efficiently address some of these challenges. We also outline the general framework design and the basic functionality of the core modules developed. We present two instantiations of the software system on two different fully integrated demonstrators: 1) coping with an industrial scenario, i.e., the automated unloading of coffee sacks with an already economically interesting performance; and 2) a scenario used to demonstrate the capabilities of our scientific and technological developments in the context of medium- to long-term prospects of automation in logistics. We performed evaluations that allowed us to summarize several important lessons learned and to identify future directions of research on autonomous robots for the handling of goods in logistics applications.