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Reconfigurability is set to be an important facet in the evolving world of mobile and wireless communications, through which technologies such as cognitive radio are greatly facilitated. Given advances in the scope and applicability of software functionalities, reconfigurability is increasingly becoming possible at many layers of the protocol stack which would until recently have been maintained only by intransigent fixed hardware components. Moreover, given the complexity and range of emerging reconfiguration possibilities, it would be useful for devices and networks to be able to efficiently partake in reconfiguration procedures with reduced-or even zero-human input. This would maximise the realisation of potential performance improvements through reconfiguration-associated technologies. This paper therefore discusses the development of an end-to-end system architecture that incorporates cognition and autonomics aspects into reconfiguration procedures. The architecture, its overall context, and its mapping to the emerging 3GPP System Architecture Evolution (SAE), are discussed.