diff --git a/include/Cantera.h b/include/Cantera.h
deleted file mode 100755
index b03a7d51a..000000000
--- a/include/Cantera.h
+++ /dev/null
@@ -1,25 +0,0 @@
-
-#ifndef CANTERA_H_INCL
-#define CANTERA_H_INCL
-
-namespace std{}
-using namespace std;
-
-// definitions
-#include "kernel/ct_defs.h"
-
-// some useful functions
-#include "kernel/global.h"
-
-// the CanteraError exception class
-#include "kernel/ctexceptions.h"
-
-using namespace Cantera;
-
-#endif
-
-
-
-
-
-
diff --git a/include/GRI30.h b/include/GRI30.h
deleted file mode 100644
index 5f32f8dbd..000000000
--- a/include/GRI30.h
+++ /dev/null
@@ -1,43 +0,0 @@
-#ifndef CXX_IDEALGASMIX
-#define CXX_IDEALGASMIX
-
-#include <string>
-
-#include "kernel/IdealGasPhase.h"
-#include "kernel/GRI_30_Kinetics.h"
-#include "kernel/importCTML.h"
-
-namespace Cantera {
-
-    class GRI30 : 
-        public IdealGasPhase, public GRI_30_Kinetics
-    {
-    public:
-        GRI30() : m_ok(false), m_r(0) {
-            m_r = get_XML_File("gri30.xml");
-            m_ok = buildSolutionFromXML(*m_r, "gri30", "phase", this, this);
-            if (!m_ok) throw CanteraError("GRI30",
-                "buildSolutionFromXML returned false");
-        }
-
-
-        virtual ~GRI30() {}
-
-        bool operator!() { return !m_ok;}
-        bool ready() { return m_ok; }
-        friend ostream& operator<<(ostream& s, GRI30& mix) {
-            string r = report(mix, true);
-            s << r;
-            return s;
-        }
-
-    protected:
-        bool m_ok;
-        XML_Node* m_r;
-
-    private:
-    };
-}
-
-
-#endif
diff --git a/include/IdealGasMix.h b/include/IdealGasMix.h
deleted file mode 100644
index 9e4665e7e..000000000
--- a/include/IdealGasMix.h
+++ /dev/null
@@ -1,49 +0,0 @@
-#ifndef CXX_IDEALGASMIX
-#define CXX_IDEALGASMIX
-
-#include <string>
-
-#include "kernel/IdealGasPhase.h"
-#include "kernel/GasKinetics.h"
-#include "kernel/importCTML.h"
-
-namespace Cantera {
-
-    class IdealGasMix : 
-        public IdealGasPhase, public GasKinetics
-    {
-    public:
-        IdealGasMix(string infile, string id="") : m_ok(false), m_r(0) {
-            
-        m_r = get_XML_File(infile); 
-        if (id == "-") id = "";
-        m_ok = buildSolutionFromXML(*m_r, id, "phase", this, this);
-        if (!m_ok) throw CanteraError("IdealGasMix",
-            "buildSolutionFromXML returned false");
-        }
-
-
-        IdealGasMix(XML_Node& root, string id) : m_ok(false), m_r(0) {
-            m_ok = buildSolutionFromXML(root, id, "phase", this, this);
-        }
-        
-        virtual ~IdealGasMix() {}
-
-        bool operator!() { return !m_ok;}
-        bool ready() { return m_ok; }
-        friend ostream& operator<<(ostream& s, IdealGasMix& mix) {
-            string r = report(mix, true);
-            s << r;
-            return s;
-        }
-
-    protected:
-        bool m_ok;
-        XML_Node* m_r;
-
-    private:
-    };
-}
-
-
-#endif
diff --git a/include/Interface.h b/include/Interface.h
deleted file mode 100644
index 2f0414ec7..000000000
--- a/include/Interface.h
+++ /dev/null
@@ -1,47 +0,0 @@
-#ifndef CXX_INTERFACE
-#define CXX_INTERFACE
-
-#include <string>
-
-#include "kernel/SurfPhase.h"
-#include "kernel/InterfaceKinetics.h"
-#include "kernel/importCTML.h"
-
-namespace Cantera {
-
-    class Interface : 
-        public SurfPhase, public InterfaceKinetics
-    {
-    public:
-        Interface(string infile, string id, vector<ThermoPhase*> phases) 
-            : m_ok(false), m_r(0) {
-
-            m_r = get_XML_File(infile); 
-            if (id == "-") id = "";
-
-            XML_Node* x = get_XML_Node("#"+id, m_r);
-            if (!x)                 
-                throw CanteraError("Interface","error in get_XML_Node");
-
-            importPhase(*x, this);
-            phases.push_back(this);
-            importKinetics(*x, phases, this);
-            m_ok = true;
-        }
-
-
-        virtual ~Interface() {}
-
-        bool operator!() { return !m_ok;}
-        bool ready() { return m_ok; }
-
-    protected:
-        bool m_ok;
-        XML_Node* m_r;
-
-    private:
-    };
-}
-
-
-#endif
diff --git a/include/README b/include/README
index aca7e258a..486e5891e 100644
--- a/include/README
+++ b/include/README
@@ -1,4 +1,7 @@
 
+NOTE: The header files that used to be located here are now in
+Cantera/cxx/include.
+
 The header files in this directory are for use in C++ application
 programs that use Cantera. The Cantera kernel itself does not use these
 header files. The kernel header files are kept in the same directory
diff --git a/include/ctml.h b/include/ctml.h
deleted file mode 100755
index 75d861098..000000000
--- a/include/ctml.h
+++ /dev/null
@@ -1,92 +0,0 @@
-/**
- * @file ctml.h
- *
- * CTML ("Cantera Markup Language") is the variant of XML that Cantera uses
- * to store data. These functions read and write it. 
- * 
- * see also: importCTML, ck2ctml.
- */
-
-
-/* $Author$
- * $Revision$
- * $Date$
- */
-
-// Copyright 2002  California Institute of Technology
-
-
-
-#ifndef CT_CTML_H
-#define CT_CTML_H
-
-#include "ct_defs.h"
-#include "xml.h"
-using namespace Cantera;
-
-namespace ctml {
-
-    bool isBuiltin(string nm);
-
-    void addBool(XML_Node& node, 
-        string title, 
-        bool val);
-
-    void addInteger(XML_Node& node, 
-        string title, 
-        int val, 
-        string units="", 
-        string type="");
-
-    void addFloat(XML_Node& node, 
-        string title, 
-        doublereal val, 
-        string units="", 
-        string type="", 
-        doublereal minval = Undef,
-        doublereal maxval = Undef);
-
-    void addIntegerArray(XML_Node& node, 
-        string title, 
-        int n, 
-        const int* vals, 
-        string units="", 
-        string type="",
-        doublereal minval=Undef, 
-        doublereal maxval=Undef);
-
-    void addFloatArray(XML_Node& node, 
-        string title, 
-        int n, 
-        const double* vals, 
-        string units="", 
-        string type="",
-        doublereal minval = Undef,
-        doublereal maxval = Undef);
-
-    void addString(XML_Node& node, 
-        string title, 
-        string val, 
-        string type="");
-
-    void getFloatArray(XML_Node& node, 
-        vector_fp& v, bool convert=true);
-
-    void getStringArray(XML_Node& node, vector<string>& v);
-    void getMap(XML_Node& node, map<string, string>& m);
-    void getPairs(XML_Node& node, vector<string>& key, vector<string>& val);
-
-    void getIntegers(XML_Node& node, map<string,int>& v);
-    void getFloats(XML_Node& node, map<string,double>& v, bool convert=true);
-    doublereal getFloat(XML_Node& parent, string name, string type="");
-    void getStrings(XML_Node& node, map<string,string>& v);
-    void getFunction(XML_Node& node, string& type, doublereal& xmin,
-        doublereal& xmax, vector_fp& coeffs);
-    XML_Node* getByTitle(XML_Node& node, string title);
-    void getString(XML_Node& node, string title, string& val, 
-        string& type);
-
-    string getString(XML_Node& parent, string name);
-}
-
-#endif
diff --git a/include/equilibrium.h b/include/equilibrium.h
deleted file mode 100755
index efe63d9dd..000000000
--- a/include/equilibrium.h
+++ /dev/null
@@ -1,9 +0,0 @@
-/*
- * header file providing support for chemical equilibrium.
- */
-#ifndef CT_EQUIL_INCL
-#define CT_EQUIL_INCL
-#include "kernel/ChemEquil.h"
-#endif
-  
-
diff --git a/include/integrators.h b/include/integrators.h
deleted file mode 100755
index 60f34716c..000000000
--- a/include/integrators.h
+++ /dev/null
@@ -1,6 +0,0 @@
-#ifndef CT_INTEG_H_INCL
-#define CT_INTEG_H_INCL
-
-#include "kernel/CVode.h"
-
-#endif
diff --git a/include/kinetics.h b/include/kinetics.h
deleted file mode 100644
index 99c995213..000000000
--- a/include/kinetics.h
+++ /dev/null
@@ -1,320 +0,0 @@
-/**
- * @file Kinetics.h
- *
- * $Author$
- * $Revision$
- * $Date$
- */
-
-// Copyright 2001  California Institute of Technology
-
-/**
- * @defgroup kineticsGroup Kinetics
- */
-
-#ifndef CT_KINETICS_H
-#define CT_KINETICS_H
-
-#include "ctexceptions.h"
-//#include "Phase.h"
-#include "ThermoPhase.h"
-
-namespace Cantera {
-
-    class ReactionData;
-
-    /**
-     * Public interface for kinetics managers. This class serves as a
-     * base class to derive 'kinetics managers', which are classes
-     * that manage homogeneous chemistry within one phase.
-     */
-    class Kinetics {
-
-    public:
-
-        // typedefs
-        typedef ThermoPhase thermo_t;
-
-        /// Constructor.
-        Kinetics() : m_ii(0), m_thermo(0), m_index(-1) {}
-        Kinetics(thermo_t* thermo) 
-            : m_ii(0), m_index(-1) {
-            if (thermo) {
-                m_start.push_back(0);
-                m_thermo.push_back(thermo);
-            }
-        }
-
-        /// Destructor. Does nothing.
-        virtual ~Kinetics() {} // delete m_xml; }
-
-        int index(){ return m_index; }
-        void setIndex(int index) { m_index = index; }
-
-        //XML_Node& xml() { return *m_xml; }
-
-        /// Identifies subclass.
-        virtual int type() { return 0; }
-
-        int start(int n) { return m_start[n]; }
-
-        /// Number of reactions
-        int nReactions() const {return m_ii;}
-
-        /// Number of species
-        int nTotalSpecies() const {
-            int n=0, np;
-            np = nPhases();
-            for (int p = 0; p < np; p++) n += thermo(p).nSpecies();
-            return n;
-        }
-
-        /**
-         * Stoichiometric coefficient of species k as a reactant in
-         * reaction i.  
-         */
-        virtual doublereal reactantStoichCoeff(int k, int i) const { 
-            err("reactantStoichCoeff");
-            return -1.0;
-        }
-
-        /**
-         * Stoichiometric coefficient of species k as a product in
-         * reaction i.  
-         */
-        virtual doublereal productStoichCoeff(int k, int i) const { 
-            err("productStoichCoeff");
-            return -1.0;
-        }
-
-
-        /**
-         * Returns a read-only reference to the vector of reactant
-         * index numbers for reaction i.
-         */ 
-        virtual const vector_int& reactants(int i) const { 
-            return m_reactants[i]; 
-        }
-        virtual const vector_int& products(int i) const { 
-            return m_products[i]; 
-        }
-
-        /**
-         * Flag specifying the type of reaction. The legal values and
-         * their meaning are specific to the particular kinetics
-         * manager.
-         */
-        virtual int reactionType(int i) const { 
-            err("reactionType"); 
-            return -1; 
-        }
-
-        /**
-         * @name Reaction Rates Of Progress
-         */
-        //@{
-
-        /**
-         * Forward rates of progress.
-         * Return the forward rates of progress in array fwdROP, which
-         * must be dimensioned at least as large as the total number
-         * of reactions.
-         */
-        virtual void getFwdRatesOfProgress(doublereal* fwdROP) {
-            err("getFwdRatesOfProgress");
-        }
- 
-        /**
-         * Reverse rates of progress.
-         * Return the reverse rates of progress in array revROP, which
-         * must be dimensioned at least as large as the total number
-         * of reactions.
-         */
-        virtual void getRevRatesOfProgress(doublereal* revROP) {
-            err("getRevRatesOfProgress");
-        } 
-
-        /**
-         * Net rates of progress.  Return the net (forward - reverse)
-         * rates of progress in array netROP, which must be
-         * dimensioned at least as large as the total number of
-         * reactions.
-         */
-        virtual void getNetRatesOfProgress(doublereal* netROP) {
-            err("getNetRatesOfProgress");
-        }
-
-        /**
-         * True if reaction i has been declared to be reversible. If
-         * isReversible(i) is false, then the reverse rate of progress
-         * for reaction i is always zero.
-         */
-        virtual bool isReversible(int i){return false;}
-
-        /**
-         * Species creation rates [kmol/m^3]. Return the species 
-         * creation rates in array cdot, which must be
-         * dimensioned at least as large as the total number of
-         * species.
-         *  
-         */ 
-        virtual void getCreationRates(doublereal* cdot) {
-            err("getCreationRates");
-        }
-
-        /**
-         * Species destruction rates [kmol/m^3]. Return the species 
-         * destruction rates in array ddot, which must be
-         * dimensioned at least as large as the total number of
-         * species.
-         *  
-         */ 
-        virtual void getDestructionRates(doublereal* ddot) {
-            err("getDestructionRates");
-        }
-
-        /**
-         * Species net production rates [kmol/m^3]. Return the species
-         * net production rates (creation - destruction) in array
-         * wdot, which must be dimensioned at least as large as the
-         * total number of species.
-         */ 
-        virtual void getNetProductionRates(doublereal* wdot) {
-            err("getNetProductionRates");
-        }
-
-        /**
-         * Equilibrium constants. Return the equilibrium constants of
-         * the reactions in concentration units in array kc, which
-         * must be dimensioned at least as large as the total number
-         * of reactions.
-         */  
-         virtual void getEquilibriumConstants(doublereal* kc) {
-             err("getEquilibriumConstants");
-         }
-        //@}
-
-
-        /**
-         * @name Reaction Mechanism Construction
-         */
-        //@{
-
-
-        /**
-         * Get the nth Phase object.
-         */
-        //phase_t& phase(int n=0) { return *m_phase[n]; }
-        //const phase_t& phase(int n=0) const { return *m_phase[n]; }
-        int nPhases() const { return m_thermo.size(); }
-        int phaseIndex(string ph) { return m_phaseindex[ph] - 1; }
-
-        /**
-         * Add a phase.
-         */
-        void addPhase(thermo_t& thermo) { 
-            if (m_thermo.size() > 0) {
-                m_start.push_back(m_start.back() 
-                    + m_thermo.back()->nSpecies());
-            }
-            else {
-                m_start.push_back(0);
-            }
-            m_thermo.push_back(&thermo);
-            m_phaseindex[m_thermo.back()->id()] = nPhases();
-        }
-        thermo_t& thermo(int n=0) { return *m_thermo[n]; }
-        const thermo_t& thermo(int n=0) const { return *m_thermo[n]; }
-        thermo_t& phase(int n=0) { return *m_thermo[n]; }
-        const thermo_t& phase(int n=0) const { return *m_thermo[n]; }
-
-        int speciesIndex(int k, int n) {
-            return m_start[n] + k;
-        }
-
-        int speciesIndex(string nm, string ph = "<any>") {
-            int np = m_thermo.size();
-            int k;
-            string id;
-            for (int n = 0; n < np; n++) {
-                id = thermo(n).id();
-                if (ph == id) {
-                    k = thermo(n).speciesIndex(nm);
-                    if (k < 0) return -1;
-                    return k + m_start[n];
-                }
-                else if (ph == "<any>") {
-                    k = thermo(n).speciesIndex(nm);
-                    if (k >= 0) return k + m_start[n];
-                }                    
-            }
-            return -2;
-        }
-
-        /**
-         * Prepare to add reactions.
-         */
-        virtual void init() {err("init");}
-
-        /// Finished adding reactions. Prepare for use.
-        virtual void finalize() {err("finalize");}
-
-        virtual void addReaction(const ReactionData& r) {err("addReaction");}
-
-        virtual string reactionString(int i) const {
-            err("reactionString"); return "<null>";
-        }
-
-
-        virtual const vector<grouplist_t>& reactantGroups(int i)  
-            { err("reactantGroups"); return m_dummygroups; }
-
-        virtual const vector<grouplist_t>& productGroups(int i) 
-            { err("productGroups"); return m_dummygroups; }
-
-        /**
-         * @name Altering Reaction Rates
-         *
-         * These methods alter reaction rates. They are designed
-         * primarily for carrying out sensitivity analysis.
-         */
-        //@{
-
-        /// The current value of the multiplier for reaction i.
-        doublereal multiplier(int i) const {return m_perturb[i];}
-
-        /// Set the multiplier for reaction i to f.
-        void setMultiplier(int i, doublereal f) {m_perturb[i] = f;}
-        
-        //@}
-
-        void incrementRxnCount() { m_ii++; m_perturb.push_back(1.0); }
-
-        virtual bool ready() const {return false;}
-
-    protected:
-
-        int m_ii;
-        vector_fp m_perturb;
-        vector<vector_int> m_reactants;
-        vector<vector_int> m_products;
-        vector<thermo_t*> m_thermo;
-        vector_int  m_start;
-        //        XML_Node* m_xml;
-        map<string, int> m_phaseindex;
-        int m_index;
-
-    private:
-
-        vector<grouplist_t> m_dummygroups;
-        void err(string m) const {
-            throw CanteraError("Kinetics::"+m,"Base class method called.");
-        }
-    };
-
-    typedef Kinetics kinetics_t;
-}
-
-
-
-#endif
diff --git a/include/numerics.h b/include/numerics.h
deleted file mode 100755
index 79422ec7c..000000000
--- a/include/numerics.h
+++ /dev/null
@@ -1,7 +0,0 @@
-#ifndef CT_NUM_H_INCL
-#define CT_NUM_H_INCL
-
-#include "kernel/DenseMatrix.h"
-#include "kernel/BandMatrix.h"
-
-#endif
diff --git a/include/onedim.h b/include/onedim.h
deleted file mode 100755
index 9dc433542..000000000
--- a/include/onedim.h
+++ /dev/null
@@ -1,11 +0,0 @@
-#ifndef CT_INCL_ONEDIM_H
-#define CT_INCL_ONEDIM_H
-
-#include "kernel/oneD/Sim1D.h"
-#include "kernel/oneD/OneDim.h"
-#include "kernel/oneD/Domain1D.h"
-#include "kernel/oneD/Inlet1D.h"
-#include "kernel/oneD/MultiNewton.h"
-#include "kernel/oneD/MultiJac.h"
-#endif
-
diff --git a/include/reactionpaths.h b/include/reactionpaths.h
deleted file mode 100644
index 3450ae2cf..000000000
--- a/include/reactionpaths.h
+++ /dev/null
@@ -1,6 +0,0 @@
-#ifndef CT_RXNPATHS_H
-#define CT_RXNPATHS_H
-
-#include "kernel/ReactionPath.h"
-
-#endif
diff --git a/include/surface.h b/include/surface.h
deleted file mode 100755
index c530b61ab..000000000
--- a/include/surface.h
+++ /dev/null
@@ -1,7 +0,0 @@
-#ifndef CT_SURFACE_INCL
-#define CT_SURFACE_INCL
-
-#include "SurfPhase.h"
-#include "InterfaceKinetics.h"
-
-#endif
diff --git a/include/transport.h b/include/transport.h
deleted file mode 100755
index 793634846..000000000
--- a/include/transport.h
+++ /dev/null
@@ -1,6 +0,0 @@
-#ifndef CT_TRANSPORT_INCL
-#define CT_TRANSPORT_INCL
-
-#include "kernel/transport/TransportFactory.h"
-#include "kernel/transport/DustyGasTransport.h"
-#endif
diff --git a/include/zerodim.h b/include/zerodim.h
deleted file mode 100644
index 6d9c0a339..000000000
--- a/include/zerodim.h
+++ /dev/null
@@ -1,9 +0,0 @@
-#ifndef CT_INCL_ZERODIM_H
-#define CT_INCL_ZERODIM_H
-
-#include "kernel/zeroD/Reactor.h"
-#include "kernel/zeroD/Reservoir.h"
-#include "kernel/zeroD/Wall.h"
-#include "kernel/zeroD/flowControllers.h"
-#endif
-