diff --git a/Cantera/cxx/include/GRI30.h b/Cantera/cxx/include/GRI30.h
index 6bc28cb26..f48287329 100644
--- a/Cantera/cxx/include/GRI30.h
+++ b/Cantera/cxx/include/GRI30.h
@@ -6,10 +6,10 @@
 
 #include <string>
 
-#include "kernel/IdealGasPhase.h"
-#include "kernel/GRI_30_Kinetics.h"
-#include "kernel/importKinetics.h"
-#include "kernel/stringUtils.h"
+#include "IdealGasPhase.h"
+#include "GRI_30_Kinetics.h"
+#include "importKinetics.h"
+#include "stringUtils.h"
 
 namespace Cantera_CXX {
 
diff --git a/Cantera/cxx/include/reactionpaths.h b/Cantera/cxx/include/reactionpaths.h
index 3450ae2cf..3d4aaaa8d 100644
--- a/Cantera/cxx/include/reactionpaths.h
+++ b/Cantera/cxx/include/reactionpaths.h
@@ -1,6 +1,6 @@
 #ifndef CT_RXNPATHS_H
 #define CT_RXNPATHS_H
 
-#include "kernel/ReactionPath.h"
+#include "ReactionPath.h"
 
 #endif
diff --git a/Cantera/cxx/include/transport.h b/Cantera/cxx/include/transport.h
index be76ab861..0d14763a3 100755
--- a/Cantera/cxx/include/transport.h
+++ b/Cantera/cxx/include/transport.h
@@ -9,8 +9,8 @@
 #ifndef CT_TRANSPORT_INCL
 #define CT_TRANSPORT_INCL
 
-#include "kernel/TransportFactory.h"
-#include "kernel/DustyGasTransport.h"
-#include "kernel/MultiTransport.h"
-#include "kernel/MixTransport.h"
+#include "TransportFactory.h"
+#include "DustyGasTransport.h"
+#include "MultiTransport.h"
+#include "MixTransport.h"
 #endif
diff --git a/Cantera/cxx/include/zerodim.h b/Cantera/cxx/include/zerodim.h
index 168039815..9abe8d17d 100644
--- a/Cantera/cxx/include/zerodim.h
+++ b/Cantera/cxx/include/zerodim.h
@@ -3,13 +3,13 @@
  */
 #ifndef CT_INCL_ZERODIM_H
 #define CT_INCL_ZERODIM_H
-#include "kernel/Reactor.h"
-#include "kernel/ReactorNet.h"
-#include "kernel/Reservoir.h"
-#include "kernel/Wall.h"
-#include "kernel/flowControllers.h"
-#include "kernel/FlowReactor.h"
-#include "kernel/ConstPressureReactor.h"
+#include "Reactor.h"
+#include "ReactorNet.h"
+#include "Reservoir.h"
+#include "Wall.h"
+#include "flowControllers.h"
+#include "FlowReactor.h"
+#include "ConstPressureReactor.h"
 
 using namespace CanteraZeroD;
 
diff --git a/Cantera/src/kinetics/Makefile.am b/Cantera/src/kinetics/Makefile.am
index a3ecc389e..19162e95c 100644
--- a/Cantera/src/kinetics/Makefile.am
+++ b/Cantera/src/kinetics/Makefile.am
@@ -4,7 +4,7 @@ h_sources  = importKinetics.h GRI_30_Kinetics.h KineticsFactory.h      \
              FalloffMgr.h ThirdBodyMgr.h RateCoeffMgr.h ReactionData.h \
              RxnRates.h Enhanced3BConc.h StoichManager.h solveSP.h     \
              AqueousKinetics.h InterfaceKinetics.h ImplicitSurfChem.h  \
-             Group.h
+             Group.h ReactionPath.h
 
 cc_sources = importKinetics.cpp GRI_30_Kinetics.cpp KineticsFactory.cpp  \
              GasKinetics.cpp AqueousKinetics.cpp FalloffFactory.cpp      \
diff --git a/Makefile.am b/Makefile.am
index be53dcb17..52d441ce3 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -2,8 +2,7 @@ include $(top_srcdir)/doxygen/aminclude.am
 
 # Build in these directories:
 SUBDIRS  = Cantera test_problems
-SUBDIRS += doxygen 
-#examples 
+SUBDIRS += doxygen examples 
 
 # Distribute these directories:
 DIST_SUBDIRS = Cantera examples
diff --git a/configure.ac b/configure.ac
index 50d2f49bc..4bd11998e 100644
--- a/configure.ac
+++ b/configure.ac
@@ -69,8 +69,6 @@ DX_INIT_DOXYGEN(cantera, doxygen/cantera.dox, docs)
 
 # Generate Output Files
 
-#                   examples/Makefile                                       \
-#		   examples/cxx/Makefile                                   \
 
 AC_OUTPUT(Makefile                                                         \
                    test_problems/Makefile                                  \
@@ -119,11 +117,10 @@ AC_OUTPUT(Makefile                                                         \
                    Cantera/src/thermo/Makefile                             \
 		   Cantera/src/transport/Makefile                          \
                    Cantera/src/spectra/Makefile Cantera/src/zeroD/Makefile \
-                   Cantera/src/equil/Makefile)
+                   Cantera/src/equil/Makefile                              \
+                   examples/Makefile                                       \
+		   examples/cxx/Makefile)                                   
 
 # FINAL SUMMARY
 AX_SUMMARIZE_CONFIG 
 
-#  ext/lapack/Makefile                                     \
-
-
diff --git a/examples/cxx/Makefile.am b/examples/cxx/Makefile.am
index c48ee7c38..57263ec09 100644
--- a/examples/cxx/Makefile.am
+++ b/examples/cxx/Makefile.am
@@ -5,18 +5,16 @@ cc_sources = examples.cpp kinetics_example1.cpp kinetics_example2.cpp \
 	     transport_example1.cpp transport_example2.cpp            \
 	     rxnpath_example1.cpp 
 
-LINK                 = -lkinetics -ltransport -lthermo -lctnumerics
-LINK                += -lctbase -ltpx -lctmath -lconverters 
-LINK                += -luser -lcvode -lstdc++ -lctlapack 
-LINK                += -lctblas -lctf2c -lctcxx
+LINK                 = -lctcxx -luser -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
+LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lconverters -lctbase -lcvode 
+LINK                += -lctlapack -lctblas -lctf2c -lm -lstdc++
 
-#LIBS                 = -L$(top_builddir)/build/lib/ $(LINK)
-LIBS                 = -L/workspace/src/cantera/pecos_autotools/build/lib/ $(LINK)
-AM_CPPFLAGS          = -I. -I/workspace/src/cantera/pecos_autotools/build/include/ -I/workspace/src/cantera/pecos_autotools/build/include/cantera -I/workspace/src/cantera/pecos_autotools/build/include/cantera/kernel
+LIBS                 = -L$(top_builddir)/build/lib/ $(LINK)
+AM_CPPFLAGS          = -I. -I$(top_builddir)/build/include/
 AM_CXXFLAGS          = $(AM_CPPFLAGS)
 
 bin_PROGRAMS         = cxx_examples
-library_includedir   = $(includedir) -I/workspace/src/cantera/pecos_autotools/build/include/
+library_includedir   = $(includedir) -I$(top_builddir)/build/include/
 
 #-----------------------
 # Cantera cxx examples
diff --git a/examples/cxx/example_utils.h b/examples/cxx/example_utils.h
index f0bfc667f..a2dd85772 100755
--- a/examples/cxx/example_utils.h
+++ b/examples/cxx/example_utils.h
@@ -1,8 +1,8 @@
 #ifndef CT_EXAMPLE_UTILS_H
 #define CT_EXAMPLE_UTILS_H
 
-#include <kernel/Array.h>
-#include <kernel/plots.h>
+#include <Array.h>
+#include <plots.h>
 
 using namespace Cantera;
 using namespace std;
diff --git a/examples/cxx/examples.cpp b/examples/cxx/examples.cpp
index 70602a928..6c1caa25d 100755
--- a/examples/cxx/examples.cpp
+++ b/examples/cxx/examples.cpp
@@ -1,4 +1,4 @@
-#include <cantera/Cantera.h>
+#include <Cantera.h>
 using namespace Cantera;
 using namespace std;
 
diff --git a/examples/cxx/kinetics_example1.cpp b/examples/cxx/kinetics_example1.cpp
index a56a82754..6a2adcb20 100755
--- a/examples/cxx/kinetics_example1.cpp
+++ b/examples/cxx/kinetics_example1.cpp
@@ -10,9 +10,9 @@
 //
 /////////////////////////////////////////////////////////////
 
-#include <cantera/Cantera.h>
-#include <cantera/zerodim.h>
-#include <cantera/IdealGasMix.h>
+#include <Cantera.h>
+#include <zerodim.h>
+#include <IdealGasMix.h>
 #include <time.h>
 #include "example_utils.h"
 using namespace Cantera;
diff --git a/examples/cxx/kinetics_example2.cpp b/examples/cxx/kinetics_example2.cpp
index 391a7b7ea..d6f1f391b 100755
--- a/examples/cxx/kinetics_example2.cpp
+++ b/examples/cxx/kinetics_example2.cpp
@@ -16,9 +16,9 @@
 #pragma warning(disable:4503)
 #endif
 
-#include <cantera/Cantera.h>
-#include <cantera/GRI30.h>
-#include <cantera/zerodim.h>
+#include <Cantera.h>
+#include <GRI30.h>
+#include <zerodim.h>
 #include <time.h>
 #include "example_utils.h"
 
diff --git a/examples/cxx/kinetics_example3.cpp b/examples/cxx/kinetics_example3.cpp
index e2be7ff7b..834f3b4d3 100644
--- a/examples/cxx/kinetics_example3.cpp
+++ b/examples/cxx/kinetics_example3.cpp
@@ -16,9 +16,9 @@
 #pragma warning(disable:4503)
 #endif
 
-#include <cantera/Cantera.h>
-#include <cantera/zerodim.h>
-#include <cantera/IdealGasMix.h>
+#include <Cantera.h>
+#include <zerodim.h>
+#include <IdealGasMix.h>
 #include <time.h>
 #include "example_utils.h"
 
diff --git a/examples/cxx/rxnpath_example1.cpp b/examples/cxx/rxnpath_example1.cpp
index 9a7756aad..566705d76 100755
--- a/examples/cxx/rxnpath_example1.cpp
+++ b/examples/cxx/rxnpath_example1.cpp
@@ -1,6 +1,6 @@
 /////////////////////////////////////////////////////////////
 //
-//  reaction path diagrams
+//  reactiona diagrams
 //
 //  $Author: hkmoffa $
 //  $Revision: 1.9 $
@@ -16,12 +16,12 @@
 #pragma warning(disable:4503)
 #endif
 
-#include <cantera/Cantera.h>
-#include <cantera/zerodim.h>
+#include <Cantera.h>
+#include <zerodim.h>
 #include <time.h>
 #include "example_utils.h"
-#include <cantera/reactionpaths.h>
-#include <cantera/IdealGasMix.h>
+#include <reactionpaths.h>
+#include <IdealGasMix.h>
 
 // #include <iostream>
 // using namespace std;
diff --git a/examples/cxx/transport_example1.cpp b/examples/cxx/transport_example1.cpp
index 65fd37499..4de4e514e 100755
--- a/examples/cxx/transport_example1.cpp
+++ b/examples/cxx/transport_example1.cpp
@@ -16,11 +16,11 @@
 #pragma warning(disable:4503)
 #endif
 
-#include <cantera/Cantera.h>
-#include <cantera/transport.h>
+#include <Cantera.h>
+#include <transport.h>
 #include <time.h>
 #include "example_utils.h"
-#include <cantera/IdealGasMix.h>
+#include <IdealGasMix.h>
 
 using namespace Cantera;
 using namespace Cantera_CXX;
diff --git a/examples/cxx/transport_example2.cpp b/examples/cxx/transport_example2.cpp
index 83086651b..d5753bb1b 100755
--- a/examples/cxx/transport_example2.cpp
+++ b/examples/cxx/transport_example2.cpp
@@ -16,12 +16,12 @@
 #pragma warning(disable:4503)
 #endif
 
-#include <cantera/Cantera.h>
-#include <cantera/transport.h>
+#include <Cantera.h>
+#include <transport.h>
 #include <time.h>
 #include "example_utils.h"
-#include <cantera/equilibrium.h>
-#include <cantera/IdealGasMix.h>
+#include <equilibrium.h>
+#include <IdealGasMix.h>
 
 using namespace Cantera;
 using namespace Cantera_CXX;