Managed to fix the structure generation.

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

gen/AVObject.cpp

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

gen/AVObject.h

+/* Copyright (c) 2006, NIF File Format Library and Tools
+All rights reserved.  Please see niflib.h for licence. */
+
+#ifndef _AVOBJECT_H_
+#define _AVOBJECT_H_
+
+#include "NIF_IO.h"
+#include "Ref.h"
+
+//Forward Declarations
+class NiAVObject;
+
+/*!
+ * Used in NiDefaultAVObjectPalette.
+ */
+struct AVObject {
+  /*! Default Constructor */
+  AVObject();
+  /*! Default Destructor */
+  ~AVObject();
+  /*!
+   * Object name.
+   */
+  string name;
+  /*!
+   * Object reference.
+   */
+  NiAVObject * object;
+};
+
+#endif

gen/Bones.cpp

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

gen/Bones.h

+/* Copyright (c) 2006, NIF File Format Library and Tools
+All rights reserved.  Please see niflib.h for licence. */
+
+#ifndef _BONES_H_
+#define _BONES_H_
+
+#include "NIF_IO.h"
+#include "Ref.h"
+
+//Forward Declarations
+class NiNode;
+
+/*!
+ * This is a list of bone influences.  It points to blocks higher in the
+ * hierarchy so ints are used to represent the indices.
+ */
+struct Bones {
+  /*! Default Constructor */
+  Bones();
+  /*! Default Destructor */
+  ~Bones();
+  /*!
+   * The number of node bones referenced as influences.
+   */
+  uint numBones;
+  /*!
+   * Block indicies of the bones.
+   */
+  vector<NiNode * > bones;
+};
+
+#endif

gen/BoundingBox.cpp

+/* Copyright (c) 2006, NIF File Format Library and Tools
+All rights reserved.  Please see niflib.h for licence. */
+
+#include "BoundingBox.h"
+
+//Constructor
+BoundingBox::BoundingBox() : unknownInt((uint)1) {};
+
+//Destructor
+BoundingBox::~BoundingBox() {};

gen/BoundingBox.h

+/* Copyright (c) 2006, NIF File Format Library and Tools
+All rights reserved.  Please see niflib.h for licence. */
+
+#ifndef _BOUNDINGBOX_H_
+#define _BOUNDINGBOX_H_
+
+#include "NIF_IO.h"
+
+/*!
+ * Bounding box.
+ */
+struct BoundingBox {
+  /*! Default Constructor */
+  BoundingBox();
+  /*! Default Destructor */
+  ~BoundingBox();
+  /*!
+   * Usually 1.
+   */
+  uint unknownInt;
+  /*!
+   * Translation vector.
+   */
+  Vector3 translation;
+  /*!
+   * Rotation matrix.
+   */
+  Matrix33 rotation;
+  /*!
+   * Radius, per direction.
+   */
+  Vector3 radius;
+};
+
+#endif

gen/ByteArray.cpp

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

gen/ByteArray.h

+/* Copyright (c) 2006, NIF File Format Library and Tools
+All rights reserved.  Please see niflib.h for licence. */
+
+#ifndef _BYTEARRAY_H_
+#define _BYTEARRAY_H_
+
+#include "NIF_IO.h"
+
+/*!
+ * An array of bytes.
+ */
+struct ByteArray {
+  /*! Default Constructor */
+  ByteArray();
+  /*! Default Destructor */
+  ~ByteArray();
+  /*!
+   * The number of bytes in this array
+   */
+  uint dataSize;
+  /*!
+   * Unknown.
+   */
+  uint unknownInt;
+  /*!
+   * The bytes which make up the array
+   */
+  vector<byte > data;
+};
+
+#endif

gen/ControllerLink.cpp

+/* Copyright (c) 2006, NIF File Format Library and Tools
+All rights reserved.  Please see niflib.h for licence. */
+
+#include "ControllerLink.h"
+#include "obj/NiInterpolator.h"
+#include "obj/NiObject.h"
+#include "obj/NiObject.h"
+#include "obj/NiStringPalette.h"
+
+//Constructor
+ControllerLink::ControllerLink() : interpolator(NULL), unknownLink1(NULL), unknownLink2(NULL), unknownShort0((ushort)0), priority_((byte)0), stringPalette(NULL), nodeNameOffset((uint)0), propertyTypeOffset((uint)0), controllerTypeOffset((uint)0), variableOffset1((uint)0), variableOffset2((uint)0) {};
+
+//Destructor
+ControllerLink::~ControllerLink() {};

gen/ControllerLink.h

+/* Copyright (c) 2006, NIF File Format Library and Tools
+All rights reserved.  Please see niflib.h for licence. */
+
+#ifndef _CONTROLLERLINK_H_
+#define _CONTROLLERLINK_H_
+
+#include "NIF_IO.h"
+#include "Ref.h"
+
+//Forward Declarations
+class NiInterpolator;
+class NiObject;
+class NiObject;
+class NiStringPalette;
+
+/*!
+ * In a .kf file, this links to a controllable block, via its name (or
+ * for version 10.2.0.0 and up, a link and offset to a NiStringPalette
+ * that contains the name), and a sequence of interpolators that apply to
+ * this controllable block, via links.
+ */
+struct ControllerLink {
+  /*! Default Constructor */
+  ControllerLink();
+  /*! Default Destructor */
+  ~ControllerLink();
+  /*!
+   * Name of a controllable block in another NIF file.
+   */
+  string name;
+  /*!
+   * Link to an interpolator.
+   */
+  Ref<NiInterpolator > interpolator;
+  /*!
+   * Unknown link. Usually -1.
+   */
+  Ref<NiObject > unknownLink1;
+  /*!
+   * Unknown.
+   */
+  Ref<NiObject > unknownLink2;
+  /*!
+   * Unknown.
+   */
+  ushort unknownShort0;
+  /*!
+   * Idle animations tend to have low values for this, and blocks that have
+   * high values tend to correspond with the important parts of the
+   * animation. WARNING: BREAKS CIV4 NIF FILES! Only observed in Oblivion
+   * NIF files so far.
+   */
+  byte priority_;
+  /*!
+   * Refers to the NiStringPalette which contains the name of the
+   * controlled block.
+   */
+  Ref<NiStringPalette > stringPalette;
+  /*!
+   * The name of the animated node.
+   */
+  string nodeName;
+  /*!
+   * Offset in the string palette where the name of the controlled node
+   * (NiNode, NiTriShape, ...) starts.
+   */
+  uint nodeNameOffset;
+  /*!
+   * Name of the property (NiMaterialProperty, ...), if this controller
+   * controls a property.
+   */
+  string propertyType;
+  /*!
+   * Offset in the string palette where the property (NiMaterialProperty,
+   * ...) starts, if this controller controls a property. Otherwise, -1.
+   */
+  uint propertyTypeOffset;
+  /*!
+   * Probably the block type name of the controller in the NIF file that is
+   * child of the controlled block.
+   */
+  string controllerType;
+  /*!
+   * Apparently the offset in the string palette of some type of controller
+   * related to Interpolator (for example, a 'NiTransformInterpolator' will
+   * have here a 'NiTransformController', etc.). Sometimes the type of
+   * controller that links to the interpolator. Probably it refers to the
+   * controller in the NIF file that is child of the controlled block, via
+   * its type name.
+   */
+  uint controllerTypeOffset;
+  /*!
+   * Some variable string (such as 'SELF_ILLUM', '0-0-TT_TRANSLATE_U',
+   * 'tongue_out', etc.).
+   */
+  string variable1;
+  /*!
+   * Offset in the string palette where some variable string starts (such
+   * as 'SELF_ILLUM', '0-0-TT_TRANSLATE_U', 'tongue_out', etc.). Usually,
+   * -1.
+   */
+  uint variableOffset1;
+  /*!
+   * Another variable string, apparently used for particle system
+   * controllers.
+   */
+  string variable2;
+  /*!
+   * Offset in the string palette where some variable string starts (so far
+   * only 'EmitterActive' and 'BirthRate' have been observed in official
+   * files, used for particle system controllers). Usually, -1.
+   */
+  uint variableOffset2;
+};
+
+#endif

gen/Footer.cpp

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

gen/Footer.h

+/* Copyright (c) 2006, NIF File Format Library and Tools
+All rights reserved.  Please see niflib.h for licence. */
+
+#ifndef _FOOTER_H_
+#define _FOOTER_H_
+
+#include "NIF_IO.h"
+#include "Ref.h"
+
+//Forward Declarations
+class NiAVObject;
+
+/*!
+ * The NIF file footer.
+ */
+struct Footer {
+  /*! Default Constructor */
+  Footer();
+  /*! Default Destructor */
+  ~Footer();
+  /*!
+   * The number of root references.
+   */
+  uint numRoots;
+  /*!
+   * List of root blocks. If there is a camera, for 1st person view, then
+   * this block is referred to as well in this list, even if it is not a
+   * root block (usually we want the camera to be attached to the Bip Head
+   * node).
+   */
+  vector<Ref<NiAVObject > > roots;
+};
+
+#endif

gen/FurniturePosition.cpp

+/* Copyright (c) 2006, NIF File Format Library and Tools
+All rights reserved.  Please see niflib.h for licence. */
+
+#include "FurniturePosition.h"
+
+//Constructor
+FurniturePosition::FurniturePosition() : unknownShort((ushort)0), positionRef1_((byte)0), positionRef2_((byte)0) {};
+
+//Destructor
+FurniturePosition::~FurniturePosition() {};

gen/FurniturePosition.h

+/* Copyright (c) 2006, NIF File Format Library and Tools
+All rights reserved.  Please see niflib.h for licence. */
+
+#ifndef _FURNITUREPOSITION_H_
+#define _FURNITUREPOSITION_H_
+
+#include "NIF_IO.h"
+
+/*!
+ * Describes a furniture position?
+ */
+struct FurniturePosition {
+  /*! Default Constructor */
+  FurniturePosition();
+  /*! Default Destructor */
+  ~FurniturePosition();
+  /*!
+   * Unknown. Position?
+   */
+  Vector3 unknownVector;
+  /*!
+   * Unknown.
+   */
+  ushort unknownShort;
+  /*!
+   * This might refer to a furnituremarkerxx.nif file.
+   */
+  byte positionRef1_;
+  /*!
+   * This might also refer to a furnituremarkerxx.nif file.
+   */
+  byte positionRef2_;
+};
+
+#endif

gen/Header.cpp

+/* Copyright (c) 2006, NIF File Format Library and Tools
+All rights reserved.  Please see niflib.h for licence. */
+
+#include "Header.h"
+
+//Constructor
+Header::Header() : version((uint)0x04000002), endianType((byte)1), userVersion((uint)0), numBlocks((uint)0), unknownInt1((uint)0), unknownInt3((uint)0), numBlockTypes((ushort)0), unknownInt2((uint)0) {};
+
+//Destructor
+Header::~Header() {};

gen/Header.h

+/* Copyright (c) 2006, NIF File Format Library and Tools
+All rights reserved.  Please see niflib.h for licence. */
+
+#ifndef _HEADER_H_
+#define _HEADER_H_
+
+#include "NIF_IO.h"
+#include "gen/ShortString.h"
+#include "gen/ShortString.h"
+#include "gen/ShortString.h"
+
+/*!
+ * The NIF file header.
+ */
+struct Header {
+  /*! Default Constructor */
+  Header();
+  /*! Default Destructor */
+  ~Header();
+  /*!
+   * 'NetImmerse File Format x.x.x.x' (versions <= 10.0.1.2) or 'Gamebryo
+   * File Format x.x.x.x' (versions >= 10.1.0.0), with x.x.x.x the version
+   * written out. Ends with a newline character (0x0A).
+   */
+  HeaderString headerString;
+  /*!
+   * The NIF version, in hexadecimal notation: 0x04000002, 0x0401000C,
+   * 0x04020002, 0x04020100, 0x04020200, 0x0A000100, 0x0A010000,
+   * 0x0A020000, 0x14000004, ...
+   */
+  uint version;
+  /*!
+   * Determines the endian-ness of the data.  1 = little endian (default) 0
+   * = big endian
+   */
+  byte endianType;
+  /*!
+   * An extra version number, for companies that decide to modify the file
+   * format.
+   */
+  uint userVersion;
+  /*!
+   * Number of file blocks.
+   */
+  uint numBlocks;
+  /*!
+   * Unknown.
+   */
+  uint unknownInt1;
+  /*!
+   * Unknown.
+   */
+  uint unknownInt3;
+  /*!
+   * Could be the name of the creator of the NIF file?
+   */
+  ShortString creator_;
+  /*!
+   * Unknown. Can be something like 'TriStrip Process Script'.
+   */
+  ShortString exportType_;
+  /*!
+   * Unknown. Possibly the selected option of the export script. Can be
+   * something like 'Default Export Script'.
+   */
+  ShortString exportScript_;
+  /*!
+   * Number of block types in this NIF file.
+   */
+  ushort numBlockTypes;
+  /*!
+   * List of all block types used in this NIF file.
+   */
+  vector<string > blockTypes;
+  /*!
+   * Maps file blocks on their corresponding type: first file block is of
+   * type block_types[block_type_index[0]], the second of
+   * block_types[block_type_index[1]], etc.
+   */
+  vector<ushort > blockTypeIndex;
+  /*!
+   * Unknown.
+   */
+  uint unknownInt2;
+};
+
+#endif

gen/KeyGroup.cpp

+/* Copyright (c) 2006, NIF File Format Library and Tools
+All rights reserved.  Please see niflib.h for licence. */
+
+#include "KeyGroup.h"
+
+//Constructor
+template <class T >
+KeyGroup<T>::KeyGroup() : numKeys((uint)0), interpolation((KeyType)0) {};
+
+//Destructor
+template <class T >
+KeyGroup<T>::~KeyGroup() {};