Push the new CheckerGenerator through the whole codebase.

CVC3Generator is now tied to the CheckerGenerator interface, allowing for
PVS and SMTLIB to move in.  This caused a huge set of changes in other files,
to push the generator through various places.  Also, the matlab code needed
updating to work with the new functions and CheckerGenerator.  In theory it
should all be fine now.

git-svn-id: https://groke.mcmaster.ca/svn/grad/colin/branches/TableTool_javization@10466 57e6efec-57d4-0310-aeb1-a6c144bb1a8b