Changed some functions to use pointers instead of Ref templates.
Updated to latest XML description.

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.

Added support for sub version 4 headers, object storage, and link method.  Some objects like NiNodes already read correctly.

1. Update NiStencilProperty based on Shon's changes
2. Rewrote large chunks of WriteFileGroup related routines.
3. Added a WriteNifTree which allows for multiple roots (not exposed publically)
4. Added option to BindSkin to scene instead of skeleton root.
5. Fixed bug in RemoveController
6. Added helpers to NiControllerManager for sequence management
7. Propegated user_version in routines which take a version

Fixed the relative include paths and tried to update solution, but havn't got the precompiled header working right.

Minor fixes so that the iterator iterates and doesn't cause an infinate loop when these functions are accessed.

Commented out functions written by Amorilia that I need to figure out how to fix.

Major update to python generation scripts and others.  Currently just namepace and mutable size members with appropriate generated code.

Fix iterator issue with NiNode when clearing children and Clearing issue with NiObjectNET and controllers.

More functions implemented.  NiNode and NiObjectNET are now good examples of how to deal with pointers.
With implementation of NiNode::GetChildren function, I was able to re-enable the building up of the bind position.

Incorporated defines into the h and cpp files I'd already made for NiNode, NiObjectNET, and NiAVObject.

Noticed that I had forgot to include NiObject.cpp in my last commit... unfortunately I've already started splitting off classes into their own files so that's included in this commit as well.
I also noticed that I never implemented the member functions of Ref!  I still haven't, but I was just surprised it's been compiling without complaint.