diff --git a/Cantera/cxx/include/IdealGasMix.h b/Cantera/cxx/include/IdealGasMix.h
index 590c18568..2ca2232d0 100644
--- a/Cantera/cxx/include/IdealGasMix.h
+++ b/Cantera/cxx/include/IdealGasMix.h
@@ -3,10 +3,10 @@
 
 #include <string>
 
-#include "kernel/IdealGasPhase.h"
-#include "kernel/GasKinetics.h"
-#include "kernel/importKinetics.h"
-#include "kernel/stringUtils.h"
+#include "IdealGasPhase.h"
+#include "GasKinetics.h"
+#include "importKinetics.h"
+#include "stringUtils.h"
 
 namespace Cantera_CXX {
 
diff --git a/Cantera/cxx/include/equilibrium.h b/Cantera/cxx/include/equilibrium.h
index 1de354127..af1d0ddbb 100755
--- a/Cantera/cxx/include/equilibrium.h
+++ b/Cantera/cxx/include/equilibrium.h
@@ -8,11 +8,11 @@
  */
 #ifndef CT_EQUIL_INCL
 #define CT_EQUIL_INCL
-#include "kernel/equil.h"
-#include "kernel/ChemEquil.h"
-#include "kernel/MultiPhaseEquil.h"
+#include "equil.h"
+#include "ChemEquil.h"
+#include "MultiPhaseEquil.h"
 #ifdef WITH_VCSNONIDEAL
-#include "kernel/vcs_MultiPhaseEquil.h"
+#include "vcs_MultiPhaseEquil.h"
 #endif
 #endif
   
diff --git a/test_problems/ChemEquil_gri_matrix/Makefile.am b/test_problems/ChemEquil_gri_matrix/Makefile.am
index b1125ee3b..a721a0195 100644
--- a/test_problems/ChemEquil_gri_matrix/Makefile.am
+++ b/test_problems/ChemEquil_gri_matrix/Makefile.am
@@ -1,13 +1,13 @@
 cc_sources = gri_matrix.cpp
 
-INC                  = -I. -I$(top_builddir)/build/include/ -I$(top_builddir)/build/include/cantera -I$(top_builddir)/build/include/cantera/kernel
+INC                  = -I. -I$(top_builddir)/build/include/
 AM_CPPFLAGS          = $(INC)
 AM_CXXFLAGS          = $(AM_CPPFLAGS)
 
 LINK                 = -luser -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
 LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lconverters -lctbase -lcvode 
 LINK                += -lctlapack -lctblas -lctf2c -lctcxx -lm  -lctf2c -lstdc++
-AM_LDFLAGS           = -L/workspace/src/cantera/pecos_autotools/build/lib/ 
+AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
 LIBS                 =  $(LINK)
 
 bin_PROGRAMS         = gri_matrix
diff --git a/test_problems/cathermo/VPissp/ISSPTester.cpp b/test_problems/cathermo/VPissp/ISSPTester.cpp
index a6686a90f..da465f1f4 100644
--- a/test_problems/cathermo/VPissp/ISSPTester.cpp
+++ b/test_problems/cathermo/VPissp/ISSPTester.cpp
@@ -25,8 +25,8 @@
 
 
 #include "Cantera.h"
-#include "kernel/IdealSolidSolnPhase.h"
-#include "kernel/IdealSolnGasVPSS.h"
+#include "IdealSolidSolnPhase.h"
+#include "IdealSolnGasVPSS.h"
 
 #include <cstdio>
 
diff --git a/test_problems/cathermo/ims/IMSTester.cpp b/test_problems/cathermo/ims/IMSTester.cpp
index 57fb56c11..563808f88 100644
--- a/test_problems/cathermo/ims/IMSTester.cpp
+++ b/test_problems/cathermo/ims/IMSTester.cpp
@@ -28,7 +28,7 @@
 #include "IdealMolalSoln.h"
 #else
 #include "Cantera.h"
-#include "kernel/IdealMolalSoln.h"
+#include "IdealMolalSoln.h"
 #endif
 
 #include <cstdio>
diff --git a/test_problems/cathermo/ims/Makefile.am b/test_problems/cathermo/ims/Makefile.am
index b50f28b0b..5df20349f 100644
--- a/test_problems/cathermo/ims/Makefile.am
+++ b/test_problems/cathermo/ims/Makefile.am
@@ -1,13 +1,13 @@
 cc_sources = IMSTester.cpp
 
-INC                  = -I. -I$(top_builddir)/build/include/ -I$(top_builddir)/build/include/cantera -I$(top_builddir)/build/include/cantera/kernel
+INC                  = -I$(top_builddir)/build/include/
 AM_CPPFLAGS          = $(INC)
 AM_CXXFLAGS          = $(AM_CPPFLAGS)
 
 LINK                 = -lctcxx -luser -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
 LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lconverters -lctbase -lcvode 
 LINK                += -lctlapack -lctblas -lctf2c -lm -lstdc++
-AM_LDFLAGS           = -L/workspace/src/cantera/pecos_autotools/build/lib/ 
+AM_LDFLAGS           = -L$(top_builddir)/build/lib/
 LIBS                 =  $(LINK)
 
 bin_PROGRAMS         = IMSTester
diff --git a/test_problems/cathermo/testIAPWS/Makefile.am b/test_problems/cathermo/testIAPWS/Makefile.am
index f054b2286..7f8c58791 100644
--- a/test_problems/cathermo/testIAPWS/Makefile.am
+++ b/test_problems/cathermo/testIAPWS/Makefile.am
@@ -1,13 +1,13 @@
 cc_sources = testIAPWSphi.cpp
 
-INC                  = -I. -I$(top_builddir)/build/include/ -I$(top_builddir)/build/include/cantera -I$(top_builddir)/build/include/cantera/kernel
+INC                  = -I$(top_builddir)/build/include/
 AM_CPPFLAGS          = $(INC)
 AM_CXXFLAGS          = $(AM_CPPFLAGS)
 
 LINK                 = -lctcxx -luser -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
 LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lconverters -lctbase -lcvode 
 LINK                += -lctlapack -lctblas -lctf2c -lm -lstdc++
-AM_LDFLAGS           = -L/workspace/src/cantera/pecos_autotools/build/lib/ 
+AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
 LIBS                 =  $(LINK)
 
 bin_PROGRAMS         = testIAPWSphi
diff --git a/test_problems/cathermo/testIAPWSPres/Makefile.am b/test_problems/cathermo/testIAPWSPres/Makefile.am
index d7b1f6e73..cb896d37a 100644
--- a/test_problems/cathermo/testIAPWSPres/Makefile.am
+++ b/test_problems/cathermo/testIAPWSPres/Makefile.am
@@ -1,13 +1,13 @@
 cc_sources = testPress.cpp
 
-INC                  = -I. -I$(top_builddir)/build/include/ -I$(top_builddir)/build/include/cantera -I$(top_builddir)/build/include/cantera/kernel
+INC                  = -I$(top_builddir)/build/include/
 AM_CPPFLAGS          = $(INC)
 AM_CXXFLAGS          = $(AM_CPPFLAGS)
 
 LINK                 = -lctcxx -luser -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
 LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lconverters -lctbase -lcvode 
 LINK                += -lctlapack -lctblas -lctf2c -lm -lstdc++
-AM_LDFLAGS           = -L/workspace/src/cantera/pecos_autotools/build/lib/ 
+AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
 LIBS                 =  $(LINK)
 
 bin_PROGRAMS         = testPress
diff --git a/test_problems/cathermo/testIAPWSTripP/Makefile.am b/test_problems/cathermo/testIAPWSTripP/Makefile.am
index ffe7f63a4..f99546fc9 100644
--- a/test_problems/cathermo/testIAPWSTripP/Makefile.am
+++ b/test_problems/cathermo/testIAPWSTripP/Makefile.am
@@ -1,13 +1,13 @@
 cc_sources = testTripleP.cpp
 
-INC                  = -I. -I$(top_builddir)/build/include/ -I$(top_builddir)/build/include/cantera -I$(top_builddir)/build/include/cantera/kernel
+INC                  = -I$(top_builddir)/build/include/
 AM_CPPFLAGS          = $(INC)
 AM_CXXFLAGS          = $(AM_CPPFLAGS)
 
 LINK                 = -lctcxx -luser -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
 LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lconverters -lctbase -lcvode 
 LINK                += -lctlapack -lctblas -lctf2c -lm -lstdc++
-AM_LDFLAGS           = -L/workspace/src/cantera/pecos_autotools/build/lib/ 
+AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
 LIBS                 =  $(LINK)
 
 bin_PROGRAMS         = testTripleP
diff --git a/test_problems/cathermo/testWaterPDSS/Makefile.am b/test_problems/cathermo/testWaterPDSS/Makefile.am
index 9171bbb67..afd2b04a8 100644
--- a/test_problems/cathermo/testWaterPDSS/Makefile.am
+++ b/test_problems/cathermo/testWaterPDSS/Makefile.am
@@ -1,13 +1,13 @@
 cc_sources = testWaterPDSS.cpp
 
-INC                  = -I. -I$(top_builddir)/build/include/ -I$(top_builddir)/build/include/cantera -I$(top_builddir)/build/include/cantera/kernel
+INC                  = -I$(top_builddir)/build/include/
 AM_CPPFLAGS          = $(INC)
 AM_CXXFLAGS          = $(AM_CPPFLAGS)
 
 LINK                 = -lctcxx -luser -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
 LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lconverters -lctbase -lcvode 
 LINK                += -lctlapack -lctblas -lctf2c -lm -lstdc++
-AM_LDFLAGS           = -L/workspace/src/cantera/pecos_autotools/build/lib/ 
+AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
 LIBS                 =  $(LINK)
 
 bin_PROGRAMS         = testWaterPDSS
diff --git a/test_problems/cathermo/testWaterTP/Makefile.am b/test_problems/cathermo/testWaterTP/Makefile.am
index 660f5fdd5..60f65d466 100644
--- a/test_problems/cathermo/testWaterTP/Makefile.am
+++ b/test_problems/cathermo/testWaterTP/Makefile.am
@@ -1,13 +1,13 @@
 cc_sources = testWaterSSTP.cpp
 
-INC                  = -I. -I$(top_builddir)/build/include/ -I$(top_builddir)/build/include/cantera -I$(top_builddir)/build/include/cantera/kernel
+INC                  = -I$(top_builddir)/build/include/
 AM_CPPFLAGS          = $(INC)
 AM_CXXFLAGS          = $(AM_CPPFLAGS)
 
 LINK                 = -lctcxx -luser -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
 LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lconverters -lctbase -lcvode 
 LINK                += -lctlapack -lctblas -lctf2c -lm -lstdc++
-AM_LDFLAGS           = -L/workspace/src/cantera/pecos_autotools/build/lib/ 
+AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
 LIBS                 =  $(LINK)
 
 bin_PROGRAMS         = testWaterSSTP
diff --git a/test_problems/cathermo/wtWater/Makefile.am b/test_problems/cathermo/wtWater/Makefile.am
index 2f080ba54..5fc8f2821 100644
--- a/test_problems/cathermo/wtWater/Makefile.am
+++ b/test_problems/cathermo/wtWater/Makefile.am
@@ -1,13 +1,13 @@
 cc_sources = wtWater.cpp
 
-INC                  = -I. -I$(top_builddir)/build/include/ -I$(top_builddir)/build/include/cantera -I$(top_builddir)/build/include/cantera/kernel
+INC                  = -I$(top_builddir)/build/include/
 AM_CPPFLAGS          = $(INC)
 AM_CXXFLAGS          = $(AM_CPPFLAGS)
 
 LINK                 = -lctcxx -luser -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
 LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lconverters -lctbase -lcvode 
 LINK                += -lctlapack -lctblas -lctf2c -lm -lstdc++
-AM_LDFLAGS           = -L/workspace/src/cantera/pecos_autotools/build/lib/ 
+AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
 LIBS                 =  $(LINK)
 
 bin_PROGRAMS         = wtWater