Correctly allocate neq elements for E->U and E->u1 (previously neq+1
elements were being allocated, though only 0:neq-1 were being used)
Petsc related cleanup following the 1-based to 0-based fixes for E->P etc
cleaned up PETSc related initialization in general_stokes_solver_setup following the 1-based to 0-based fixes for E->P etc
further cleanup of PETSc related code