Cohomology of line bundles on compactified Jacobians

Let C be an integral projective curve with surficial singularities. We prove that topologically trivial line bundles on the compactified Jacobian of C are in one-to-one correspondence with line bundles on C (the autoduality conjecture), and compute the cohomology of the line bundles. We also show that the natural Fourier-Mukai functor between the derived categories of quasi-coherent sheaves on the Jacobian and on the compactified Jacobian is fully faithful.