Managed to fix the structure generation.

Moved all generated files to gen sub directory.
Renamed some generated files.

gen/ShortString.h

+/* Copyright (c) 2006, NIF File Format Library and Tools
+All rights reserved.  Please see niflib.h for licence. */
+
+#ifndef _SHORTSTRING_H_
+#define _SHORTSTRING_H_
+
+#include "NIF_IO.h"
+
+/*!
+ * Another string format, for short strings.  Specific to Bethesda-
+ * specific header tags.
+ */
+struct ShortString {
+  /*! Default Constructor */
+  ShortString();
+  /*! Default Destructor */
+  ~ShortString();
+  /*!
+   * The string length.
+   */
+  byte length;
+  /*!
+   * The string itself, null terminated (the null terminator is taken into
+   * account in the length byte).
+   */
+  vector<byte > value;
+};
+
+#endif

gen/SkinData.h

+/* Copyright (c) 2006, NIF File Format Library and Tools
+All rights reserved.  Please see niflib.h for licence. */
+
+#ifndef _SKINDATA_H_
+#define _SKINDATA_H_
+
+#include "NIF_IO.h"
+#include "gen/SkinWeight.h"
+
+/*!
+ * Skinning data component.
+ */
+struct SkinData {
+  /*! Default Constructor */
+  SkinData();
+  /*! Default Destructor */
+  ~SkinData();
+  /*!
+   * Rotation offset of the skin from this bone in bind position.
+   */
+  Matrix33 rotation;
+  /*!
+   * Translation offset of the skin from this bone in bind position.
+   */
+  Vector3 translation;
+  /*!
+   * Scale offset of the skin from this bone in bind position. (Assumption
+   * - this is always 1.0 so far)
+   */
+  float scale;
+  /*!
+   * This has been verified not to be a normalized quaternion.  They may or
+   * may not be related to each other so their specification as an array of
+   * 4 floats may be misleading.
+   */
+  vector<float > unknown4Floats;
+  /*!
+   * Number of weighted vertices.
+   */
+  ushort numVertices;
+  /*!
+   * The vertex weights.
+   */
+  vector<SkinWeight > vertexWeights;
+};
+
+#endif

gen/SkinPartition.cpp

+/* Copyright (c) 2006, NIF File Format Library and Tools
+All rights reserved.  Please see niflib.h for licence. */
+
+#include "SkinPartition.h"
+
+//Constructor
+SkinPartition::SkinPartition() : numVertices((ushort)0), numTriangles((ushort)0), numBones((ushort)0), numStrips((ushort)0), numWeightsPerVertex((ushort)0), hasVertexMap(false), hasVertexWeights(false), hasStrips(false), hasBoneIndices(false) {};
+
+//Destructor
+SkinPartition::~SkinPartition() {};

gen/SkinPartition.h

+/* Copyright (c) 2006, NIF File Format Library and Tools
+All rights reserved.  Please see niflib.h for licence. */
+
+#ifndef _SKINPARTITION_H_
+#define _SKINPARTITION_H_
+
+#include "NIF_IO.h"
+
+/*!
+ * Skinning data for a submesh, optimized for hardware skinning. Part of
+ * NiSkinPartition.
+ */
+struct SkinPartition {
+  /*! Default Constructor */
+  SkinPartition();
+  /*! Default Destructor */
+  ~SkinPartition();
+  /*!
+   * Number of vertices in this submesh.
+   */
+  ushort numVertices;
+  /*!
+   * Number of triangles in this submesh.
+   */
+  ushort numTriangles;
+  /*!
+   * Number of bones influencing this submesh.
+   */
+  ushort numBones;
+  /*!
+   * Number of strips in this submesh (zero if not stripped).
+   */
+  ushort numStrips;
+  /*!
+   * Number of weight coefficients per vertex.
+   */
+  ushort numWeightsPerVertex;
+  /*!
+   * List of bones.
+   */
+  vector<ushort > bones;
+  /*!
+   * Do we have a vertex map?
+   */
+  bool hasVertexMap;
+  /*!
+   * Maps the weight/influence lists in this submesh to the vertices in the
+   * shape being skinned.
+   */
+  vector<ushort > vertexMap;
+  /*!
+   * Do we have vertex weights?
+   */
+  bool hasVertexWeights;
+  /*!
+   * The vertex weights.
+   */
+  vector<vector<float > > vertexWeights;
+  /*!
+   * The strip lengths.
+   */
+  vector<ushort > stripLengths;
+  /*!
+   * Do we have strip data?
+   */
+  bool hasStrips;
+  /*!
+   * The strips.
+   */
+  vector<vector<ushort > > strips;
+  /*!
+   * The triangles.
+   */
+  vector<Triangle > triangles;
+  /*!
+   * Do we have bone indices?
+   */
+  bool hasBoneIndices;
+  /*!
+   * Bone indices, they index into 'Bones'.
+   */
+  vector<vector<byte > > boneIndices;
+};
+
+#endif

gen/SkinShape.cpp

+/* Copyright (c) 2006, NIF File Format Library and Tools
+All rights reserved.  Please see niflib.h for licence. */
+
+#include "SkinShape.h"
+#include "obj/NiTriShape.h"
+#include "obj/NiSkinInstance.h"
+
+//Constructor
+SkinShape::SkinShape() : shape(NULL), skinInstance(NULL) {};
+
+//Destructor
+SkinShape::~SkinShape() {};

gen/SkinShape.h

+/* Copyright (c) 2006, NIF File Format Library and Tools
+All rights reserved.  Please see niflib.h for licence. */
+
+#ifndef _SKINSHAPE_H_
+#define _SKINSHAPE_H_
+
+#include "NIF_IO.h"
+#include "Ref.h"
+
+//Forward Declarations
+class NiTriShape;
+class NiSkinInstance;
+
+/*!
+ * Reference to shape and skin instance.
+ */
+struct SkinShape {
+  /*! Default Constructor */
+  SkinShape();
+  /*! Default Destructor */
+  ~SkinShape();
+  /*!
+   * The shape.
+   */
+  Ref<NiTriShape > shape;
+  /*!
+   * Skinning instance for the shape?
+   */
+  Ref<NiSkinInstance > skinInstance;
+};
+
+#endif

gen/SkinShapeGroup.cpp

+/* Copyright (c) 2006, NIF File Format Library and Tools
+All rights reserved.  Please see niflib.h for licence. */
+
+#include "SkinShapeGroup.h"
+
+//Constructor
+SkinShapeGroup::SkinShapeGroup() : numLinkPairs((uint)0) {};
+
+//Destructor
+SkinShapeGroup::~SkinShapeGroup() {};

gen/SkinShapeGroup.h

+/* Copyright (c) 2006, NIF File Format Library and Tools
+All rights reserved.  Please see niflib.h for licence. */
+
+#ifndef _SKINSHAPEGROUP_H_
+#define _SKINSHAPEGROUP_H_
+
+#include "NIF_IO.h"
+#include "gen/SkinShape.h"
+
+/*!
+ * Unknown.
+ */
+struct SkinShapeGroup {
+  /*! Default Constructor */
+  SkinShapeGroup();
+  /*! Default Destructor */
+  ~SkinShapeGroup();
+  /*!
+   * Counts unknown.
+   */
+  uint numLinkPairs;
+  /*!
+   * First link is a NiTriShape block. Second link is a NiSkinInstance
+   * block.
+   */
+  vector<SkinShape > linkPairs;
+};
+
+#endif

gen/SkinWeight.cpp

+/* Copyright (c) 2006, NIF File Format Library and Tools
+All rights reserved.  Please see niflib.h for licence. */
+
+#include "SkinWeight.h"
+
+//Constructor
+SkinWeight::SkinWeight() : index((ushort)0), weight(0.0f) {};
+
+//Destructor
+SkinWeight::~SkinWeight() {};

gen/SkinWeight.h

+/* Copyright (c) 2006, NIF File Format Library and Tools
+All rights reserved.  Please see niflib.h for licence. */
+
+#ifndef _SKINWEIGHT_H_
+#define _SKINWEIGHT_H_
+
+#include "NIF_IO.h"
+
+/*!
+ * A weighted vertex.
+ */
+struct SkinWeight {
+  /*! Default Constructor */
+  SkinWeight();
+  /*! Default Destructor */
+  ~SkinWeight();
+  /*!
+   * The vertex index, in the mesh.
+   */
+  ushort index;
+  /*!
+   * The vertex weight - between 0.0 and 1.0
+   */
+  float weight;
+};
+
+#endif

gen/StringPalette.cpp

+/* Copyright (c) 2006, NIF File Format Library and Tools
+All rights reserved.  Please see niflib.h for licence. */
+
+#include "StringPalette.h"
+
+//Constructor
+StringPalette::StringPalette() : length((uint)0) {};
+
+//Destructor
+StringPalette::~StringPalette() {};

gen/StringPalette.h

+/* Copyright (c) 2006, NIF File Format Library and Tools
+All rights reserved.  Please see niflib.h for licence. */
+
+#ifndef _STRINGPALETTE_H_
+#define _STRINGPALETTE_H_
+
+#include "NIF_IO.h"
+
+/*!
+ * A list of \\0 terminated strings.
+ */
+struct StringPalette {
+  /*! Default Constructor */
+  StringPalette();
+  /*! Default Destructor */
+  ~StringPalette();
+  /*!
+   * A bunch of 0x00 seperated strings.
+   */
+  string palette;
+  /*!
+   * Length of the palette string is repeated here.
+   */
+  uint length;
+};
+
+#endif

gen/TBC.cpp

+/* Copyright (c) 2006, NIF File Format Library and Tools
+All rights reserved.  Please see niflib.h for licence. */
+
+#include "TBC.h"
+
+//Constructor
+TBC::TBC() : t(0.0f), b(0.0f), c(0.0f) {};
+
+//Destructor
+TBC::~TBC() {};

gen/TBC.h

+/* Copyright (c) 2006, NIF File Format Library and Tools
+All rights reserved.  Please see niflib.h for licence. */
+
+#ifndef _TBC_H_
+#define _TBC_H_
+
+#include "NIF_IO.h"
+
+/*!
+ * Tension, bias, continuity.
+ */
+struct TBC {
+  /*! Default Constructor */
+  TBC();
+  /*! Default Destructor */
+  ~TBC();
+  /*!
+   * Tension.
+   */
+  float t;
+  /*!
+   * Bias.
+   */
+  float b;
+  /*!
+   * Continuity.
+   */
+  float c;
+};
+
+#endif

gen/TexDesc.cpp

+/* Copyright (c) 2006, NIF File Format Library and Tools
+All rights reserved.  Please see niflib.h for licence. */
+
+#include "TexDesc.h"
+#include "obj/NiSourceTexture.h"
+
+//Constructor
+TexDesc::TexDesc() : source(NULL), clampMode((TexClampMode)WRAP_S_WRAP_T), filterMode((TexFilterMode)FILTER_TRILERP), textureSet((uint)0), ps2L((ushort)0), ps2K((ushort)0xFFB5), unknown1((ushort)0), hasTextureTransform(false), wRotation(0.0f), transformType_((uint)0) {};
+
+//Destructor
+TexDesc::~TexDesc() {};

gen/TexDesc.h

+/* Copyright (c) 2006, NIF File Format Library and Tools
+All rights reserved.  Please see niflib.h for licence. */
+
+#ifndef _TEXDESC_H_
+#define _TEXDESC_H_
+
+#include "NIF_IO.h"
+#include "Ref.h"
+
+//Forward Declarations
+class NiSourceTexture;
+
+/*!
+ * Texture description.
+ */
+struct TexDesc {
+  /*! Default Constructor */
+  TexDesc();
+  /*! Default Destructor */
+  ~TexDesc();
+  /*!
+   * NiSourceTexture block index.
+   */
+  Ref<NiSourceTexture > source;
+  /*!
+   * 0=clamp S clamp T, 1=clamp S wrap T, 2=wrap S clamp T, 3=wrap S wrap T
+   */
+  TexClampMode clampMode;
+  /*!
+   * 0=nearest, 1=bilinear, 2=trilinear, 3=..., 4=..., 5=...
+   */
+  TexFilterMode filterMode;
+  /*!
+   * Texture set? Usually 0.
+   */
+  uint textureSet;
+  /*!
+   * 0?
+   */
+  ushort ps2L;
+  /*!
+   * 0xFFB5?
+   */
+  ushort ps2K;
+  /*!
+   * Unknown, 0 or 0x0101?
+   */
+  ushort unknown1;
+  /*!
+   * Determines whether or not the texture's coordinates are transformed.
+   */
+  bool hasTextureTransform;
+  /*!
+   * The amount to translate the texture coordinates in each direction?
+   */
+  TexCoord translation;
+  /*!
+   * The number of times the texture is tiled in each direction?
+   */
+  TexCoord tiling;
+  /*!
+   * 2D Rotation of texture image around third W axis after U and V.
+   */
+  float wRotation;
+  /*!
+   * The texture transform type?  Doesn't seem to do anything.
+   */
+  uint transformType_;
+  /*!
+   * The offset from the origin?
+   */
+  TexCoord centerOffset;
+};
+
+#endif

gen/TexSource.cpp

+/* Copyright (c) 2006, NIF File Format Library and Tools
+All rights reserved.  Please see niflib.h for licence. */
+
+#include "TexSource.h"
+#include "obj/NiObject.h"
+#include "obj/NiPixelData.h"
+
+//Constructor
+TexSource::TexSource() : useExternal((byte)0), unknownLink(NULL), unknownByte((byte)0), pixelData(NULL) {};
+
+//Destructor
+TexSource::~TexSource() {};

gen/TexSource.h

+/* Copyright (c) 2006, NIF File Format Library and Tools
+All rights reserved.  Please see niflib.h for licence. */
+
+#ifndef _TEXSOURCE_H_
+#define _TEXSOURCE_H_
+
+#include "NIF_IO.h"
+#include "Ref.h"
+
+//Forward Declarations
+class NiObject;
+class NiPixelData;
+
+/*!
+ * A texture source.
+ */
+struct TexSource {
+  /*! Default Constructor */
+  TexSource();
+  /*! Default Destructor */
+  ~TexSource();
+  /*!
+   * Is the texture external?
+   */
+  byte useExternal;
+  /*!
+   * The external texture file name.  Note: all original morrowind nifs use
+   * name.ext only for addressing the textures, but most mods use something
+   * like textures/[subdir/]name.ext. This is due to a feature in Morrowind
+   * resource manager: it loads name.ext, textures/name.ext and
+   * textures/subdir/name.ext but NOT subdir/name.ext.
+   */
+  string fileName;
+  /*!
+   * Unknown.
+   */
+  Ref<NiObject > unknownLink;
+  /*!
+   * Unknown.
+   */
+  byte unknownByte;
+  /*!
+   * The original source filename of the image embedded by the referred
+   * NiPixelData block.
+   */
+  string originalFileName_;
+  /*!
+   * Pixel data block index.
+   */
+  Ref<NiPixelData > pixelData;
+};
+
+#endif

gen/hkTriangle.cpp

+/* Copyright (c) 2006, NIF File Format Library and Tools
+All rights reserved.  Please see niflib.h for licence. */
+
+#include "hkTriangle.h"
+
+//Constructor
+hkTriangle::hkTriangle() : unknownShort((ushort)0) {};
+
+//Destructor
+hkTriangle::~hkTriangle() {};