Stubbing out the site_map.
Initial implementation of mask_reindex.
Comments and tweak.
Only giving a reind_arr when it is needed.

A bit more complicated, but logically more satisfactory, and paves the
way for fewer matrix exponentiations.

@nhoffman-- Could you give this one a spin? I'd be interested in a speed
comparison (though that is of course secondary).
Merge branch 'cat-rate-integrity' into 318-placement-specific-mask

@nhoffman-- here you go. It would be fun if you could keep the old
simulation results around.