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See [1] M. Bos and V.P. Nair. Coherent State Quantization of Chern-Simons Theory. International Journal of Modern Physics A, A5:959, 1990. and chapter 20 of [2] V.P. Nair. Quantum Field Theory: A modern perspective. Springer, 2005. These references have geometric quantization of abelian Chern-Simons theory for $\Sigma=S^1 \times S^1$ (the first ref. ...