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We extract the macroscopic characteristics of the groundstate sectors of two dimensional Bose-condensed BCS models with a fixed number of magnetic flux quanta, on length scales much larger than the characteristic size of the Cooper-pair bound states. We show that this reduces to the problem of computing the moduli space of gauge-inequivalent solutions to the Gross-Pitaevskii equations on a nontrivial fibre bundle. Inspired in part by the physical arguments of Oshikawa and Senthil in Fractionalization, Topological Order, and Quasiparticle Statistics, we extract a large class of groundstates from this moduli space.

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