  We calculate the topological string partition function to all genus on the
conifold, in the presence of branes. We demonstrate that the partition
functions for different brane backgrounds (smoothly connected along a quantum
corrected moduli space) can be interpreted as the same wave function in
different polarizations. This behavior has a natural interpretation in the
Chern-Simons target space description of the topological theory. Our detailed
analysis however indicates that non-perturbatively, a modification of real
Chern-Simons theory is required to capture the correct target space theory of
the topological string.
  We perform our calculations in the framework of a free fermion representation
of the open topological string, demonstrating that this framework extends
beyond the simple C^3 geometry. The notion of a fermionic brane creation
operator arises in this setting, and we study to what extent the wave function
properties of the partition function can be extended to this operator.
