I modified the log states to have a function to force writing of a file whether or not you are skipping files. Seems useful to have (and used in the next patch)

and I wrote an example. Perhaps should have more documentation, but it is a start.

finally, the BondDecoratorList now checks to make sure that both particles are contained in the list of particles.

And really finally the SConscript files for the headers weren't all updated after the last move (the restraints one, for example).