BUG: Removed output of dual rules for source files that are processed by both the compiler and by a custom command.  Also removed generation of duplicate CMakeLists.txt in the project files.

ENH: Changed WriteConfiguration to non-const so it can do error checking.  Added parsing and output of a name for each WrapperSet generated from a CABLE_WRAP command.

BUG: Fixed output of dependencies.  It needs to loop over the makefile's targets, not the source lists.

ERR: We can't assume a vector iterator is a pointer.  It must be dereferenced to get a reference to the element, and then we can take the address of that to get a pointer.  "i" becomes "&*i"