My understanding of the legislative process is that a bill exists in a stand-alone form while it is being debated. When it is voted upon in its final form, however, lawyers working for the legislative branch convert the "human readable" form of the bill into what is, in effect, a "patch" to the existing law (i.e., "Paragraph B of subsection 2 of title 18 shall be amended to read ..."). My (albeit cursory) understanding is that these literal changes to the code are what are actually voted into law.
http://en.wikipedia.org/wiki/Congressional_Research_Service
Conceivably, changes to the US code could be tracked in the same way that changes to a bill are tracked, and every bill could be introduced as a branch of the US Code (i.e. a patch on the trunk), and every vote on a bill would be a vote to merge that branch.