More surface molecule renaming.
Removed the reference diffusion constant

The reference diffusion constant served no obvious purpose and was never
documented in the QRG or anywhere else. As such, it is being removed to
minimize the amount of clutter in the code.
Reformated and updated the code notes.

Issues that are known to be fixed have been removed. The remainder of
valid issues should be moved to the github tracker. Actual notes that
explain portions of the code could likely stay (or be moved to the
github wiki).