Cleared up all Doxygen and SWIG warnings.

Replaced _WRITE, _READ, _STRING, AND _FIXLINKS defines with the corresponding internal function call.
Replaced STANDARD_INTERNAL_FUNCTIONS with the internal function signatures.
Made my Doxygen config file use relative paths and added it to SVN so everyone can generate the same documentation for themselves.
Removed includes WZ added to ComplexShape.  These were not missing, they are up to the user to include if they wish.