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So, you first construct the F matrix by knowledge of the Green's function G(x,x'). Then you solve the equation for $\phi_{\vec{k}}$, from which you find $\phi(\vec{x})$. Are these the eigenfunctions you are looking for?
Thanks for sharing the information. I also learned this when reading Jackiw's Dirac prize lecture. However, he did not in that work propose the principle and there was no topological argument therein.