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Reliance on external localization infrastructure and centralized coordination are main limiting factors for formation flying of vehicles in large numbers and in unprepared environments. While solutions using onboard localization address the dependency on external infrastructure, the associated coordination strategies typically lack collision avoidance and scalability. To address these shortcomings, we present a unified pipeline with onboard localization and a distributed, collision-free motion planning strategy that scales to a large number of vehicles. Since distributed collision avoidance strategies are known to result in gridlock, we also present a decentralized task assignment solution to deconflict vehicles. We experimentally validate our pipeline in simulation and hardware. The results show that our approach for solving the optimization problem associated with motion planning gives solutions within seconds in cases where general purpose solvers fail due to high complexity. In addition, our lightweight assignment strategy leads to successful and quicker formation convergence in 96-100% of all trials, whereas indefinite gridlocks occur without it for 33-50% of trials. By enabling large-scale, deconflicted coordination, this pipeline should help pave the way for anytime, anywhere deployment of aerial swarms.