@gidden, I am fine with this.  In fact, most of boost was actually included in bright until very recently.  The only thing that you really need to consider is the licensing terms for redistribution.  This is a non-issue for boost if the license is included (and it is).  

> file naming; should it be named the same or should we differentiate?

The file name should be the same for provenance reasons more than anything.

> documenting adjustments; right now it's really difficult to see what changes were made. where/how do you suggest we document these changes? it looks like spirit (and perhaps boost in general) doesn't really do much documentation.

Just put a couple of comment lines after the license section that say "WARNING, this file was modified by X for cyclus from the original file in Boost vX.X.X (link: http//...)"  If someone *really* wants they can always diff.