--- a/include/dionysus.h	Tue Feb 19 06:56:49 2008 -0500
+++ b/include/dionysus.h	Tue Feb 19 07:26:01 2008 -0500
@@ -1,6 +1,6 @@
 /*
  * Author: Dmitriy Morozov
- * Department of Computer Science, Duke University, 2006
+ * Department of Computer Science, Duke University, 2006--2008
  *
  * For now file exists only to store the main page of the documentation
  */
@@ -9,3 +9,16 @@
  * Detailed description of Dionysus with references to all the classes, 
  * and code samples goes here.
  */
+
+/**
+ * \defgroup topology Topology Classes
+ */
+
+/**
+ * \defgroup geometry Geometry Classes
+ */
+
+/**
+ * \defgroup kinetic Kinetic Data Structures Classes
+ * \ingroup  geometry
+ */

--- a/include/geometry/euclidean.h	Tue Feb 19 06:56:49 2008 -0500
+++ b/include/geometry/euclidean.h	Tue Feb 19 07:26:01 2008 -0500
@@ -14,6 +14,10 @@
 #include "number-traits.h"
 
 
+/**
+ * Geometric Kernel. Defines operations on geometric primitives.
+ * \ingroup geometry
+ */
 template<class NumberType_ = double>
 class Kernel
 {
@@ -56,7 +60,10 @@
 };
 
 
-/* Point */
+/** 
+ * Point class.
+ * \ingroup geometry 
+ */
 template<class NumberType_>
 class Kernel<NumberType_>::Point: public VectorType
 {
@@ -77,7 +84,10 @@
 };
 
 
-/* Sphere */
+/** 
+ * Sphere class.
+ * \ingroup geometry
+ */
 template<class NumberType_>
 class Kernel<NumberType_>::Sphere
 {

--- a/include/geometry/kinetic-sort.h	Tue Feb 19 06:56:49 2008 -0500
+++ b/include/geometry/kinetic-sort.h	Tue Feb 19 07:26:01 2008 -0500
@@ -16,6 +16,8 @@
  *  \arg Simulator_           the Simulator type, e.g. Simulator. Note that KineticSort does not store 
  *                            a pointer to the Simulator (so a pointer is passed in each relevant operation)
  *  \arg Swap_                is called with an ElementIterator_ when a swap needs to be performed
+ *
+ *  \ingroup kinetic
  */
 template<class ElementIterator_, class TrajectoryExtractor_, 
 		 class Simulator_, class Swap_ = boost::function<void(ElementIterator_ pos, Simulator_* simulator)> >

--- a/include/geometry/simulator.h	Tue Feb 19 06:56:49 2008 -0500
+++ b/include/geometry/simulator.h	Tue Feb 19 07:26:01 2008 -0500
@@ -12,6 +12,8 @@
  * Event addition, and processes events one by one. Degeneracies are handled by 
  * assuming that the RationalFunction responsible for the event must be positive
  * before the Event occurs.
+ *
+ * \ingroup kinetic
  */
 template<class PolyKernel_, template<class Event> class EventComparison_ = std::less>
 class Simulator

--- a/include/topology/cycle.h	Tue Feb 19 06:56:49 2008 -0500
+++ b/include/topology/cycle.h	Tue Feb 19 07:26:01 2008 -0500
@@ -16,6 +16,8 @@
  * The actual order of the elements is defined by OrderCmp. Instances of those 
  * classes are not stored in Cycle for efficiency, and are passed as arguments to those methods 
  * that require them.
+ *
+ * \ingroup topology
  */
 template <class Itm, class OrderCmp, class ConsistencyCmp = OrderCmp>
 class Cycle: public List<Itm>

--- a/include/topology/filtration.h	Tue Feb 19 06:56:49 2008 -0500
+++ b/include/topology/filtration.h	Tue Feb 19 07:26:01 2008 -0500
@@ -22,6 +22,8 @@
  * and provides pair_simplices() method that computes the RU-decomposition
  * for the simplex order stored in the filtration. Iterators remain valid 
  * through all the operations.
+ *
+ * \ingroup topology
  */
 template<class Smplx, class FltrSmplx = FiltrationSimplex<Smplx>, class Vnrd = Vineyard<FltrSmplx> >
 class Filtration: public FltrSmplx::Container

--- a/include/topology/filtrationcontainer.h	Tue Feb 19 06:56:49 2008 -0500
+++ b/include/topology/filtrationcontainer.h	Tue Feb 19 07:26:01 2008 -0500
@@ -13,6 +13,8 @@
  * FiltrationContainer class. Serves as a parent of Filtration that 
  * describes the container functionality. Used by FiltrationSimplex 
  * to get Cycle representation.
+ *
+ * \ingroup topology
  */
 template<class FltrSmplx>
 class FiltrationContainer: public ConsistencyList<FltrSmplx>

--- a/include/topology/filtrationsimplex.h	Tue Feb 19 06:56:49 2008 -0500
+++ b/include/topology/filtrationsimplex.h	Tue Feb 19 07:26:01 2008 -0500
@@ -21,6 +21,8 @@
 /**
  * Evaluator is a base class for the structures that are able to return a value
  * given a simplex.
+ *
+ * \ingroup topology
  */
 template<class Smplx>
 class Evaluator
@@ -37,6 +39,8 @@
 /**
  * FiltrationSimplex stores information needed for the RU-decomposition: 
  * cycle (column of R), trail (row of U), and pair.
+ *
+ * \ingroup topology
  */
 template<class Smplx>
 class FiltrationSimplex: public Smplx

--- a/include/topology/simplex.h	Tue Feb 19 06:56:49 2008 -0500
+++ b/include/topology/simplex.h	Tue Feb 19 07:26:01 2008 -0500
@@ -20,6 +20,8 @@
  * SimplexWithVertices is a basic simplex class. It stores vertices of a given type, 
  * and knows how to compute its own boundary. It should probably be used as a base 
  * class for any explicit simplex representation.
+ *
+ * \ingroup topology
  */
 template<class V>
 class SimplexWithVertices
@@ -83,6 +85,8 @@
 
 /**
  * SimplexWithValue explicitly adds a RealType value to the SimplexWithVertices.
+ *
+ * \ingroup topology
  */
 template<class Vert>
 class SimplexWithValue: public SimplexWithVertices<Vert>
@@ -130,6 +134,8 @@
 
 /**
  * SimplexWithAttachment stores the vertex to which the simplex is attached (meant for lower-star filtrations)
+ *
+ * \ingroup topology
  */
 template<typename V>
 class SimplexWithAttachment: public SimplexWithVertices<V>

--- a/include/topology/vineyard.h	Tue Feb 19 06:56:49 2008 -0500
+++ b/include/topology/vineyard.h	Tue Feb 19 07:26:01 2008 -0500
@@ -23,6 +23,8 @@
 /**
  * Vineyard class. Keeps track of vines and knees. switched() is the key function called
  * by filtration when pairing switches after a Filtration::transpose().
+ *
+ * \ingroup topology
  */
 template<class FltrSmplx>
 class Vineyard
@@ -65,6 +67,8 @@
 
 /**
  * Knee class stores the knee in R^3 as well as the cycle that is associated with the Simplex starting from the Knee.
+ *
+ * \ingroup topology
  */
 template<class S>
 class Knee