We consider the $U(1)$ Chern-Simons gauge theory defined in a general closed oriented 3-manifold $M$; the functional integration is used to compute the normalized partition function and the expectation values of the link holonomies. The nonperturbative path-integral is defined in the space of the gauge orbits of the connections which belong to the various inequivalent $U(1)$ principal bundles over $M$; the different sectors of the configuration space are labelled by the elements of the first homology group of $M$ and are characterized by appropriate background connections. The gauge orbits of flat connections, whose classification is also based on the homology group, control the extent of the nonperturbative contributions to the mean values. The functional integration is achieved in any 3-manifold $M$, and the corresponding path-integral invariants turn out to be strictly related with the abelian Reshetikhin-Turaev surgery invariants.
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