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janky fix to smoothing prior -- other housekeeping

Bruce Edelman requested to merge smoothing_bound_fix into main
  • janky fix to the smoothing prior at the boundary issue
  • Added some docstrings pointing towards code where we re-implemented things in jax.numpy
  • Change all naming references to a "penalty" to "prior"
  • Add some more info in the README.md. We may want to move the TODO's somewhere else now that it is semi-public even thought the progress is slim

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