  We consider minimally supersymmetric Yang-Mills theory with a Chern-Simons
term on a flat spatial two-torus. The Witten index may be computed in the weak
coupling limit, where the ground state wave-functions localize on the moduli
space of flat gauge connections. We perform such computations by considering
this moduli space as an orbifold of a certain flat complex torus. Our results
agree with those obtained previously by instead considering the moduli space as
a complex projective space. An advantage of the present method is that it
allows for a more straightforward determination of the discrete electric 't
Hooft fluxes of the ground states in theories with non-simply connected gauge
groups. A consistency check is provided by the invariance of the results under
the mapping class group of a (Euclidean) three-torus.
