diff --git a/Cantera/cxx/include/thermo.h b/Cantera/cxx/include/thermo.h
index a27b23336..0f713c4cc 100755
--- a/Cantera/cxx/include/thermo.h
+++ b/Cantera/cxx/include/thermo.h
@@ -9,9 +9,9 @@
 #ifndef CT_THERMO_INCL
 #define CT_THERMO_INCL
 
-#include "kernel/ThermoFactory.h"
+#include "ThermoFactory.h"
 #include "importPhase.h"
-#include "kernel/SurfPhase.h"
-#include "kernel/EdgePhase.h"
+#include "SurfPhase.h"
+#include "EdgePhase.h"
 
 #endif
diff --git a/test_problems/cathermo/DH_graph_NM/Makefile.am b/test_problems/cathermo/DH_graph_NM/Makefile.am
index e0ff0a8ba..1182f8991 100644
--- a/test_problems/cathermo/DH_graph_NM/Makefile.am
+++ b/test_problems/cathermo/DH_graph_NM/Makefile.am
@@ -1,13 +1,13 @@
 cc_sources = DH_graph_1.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                 = -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         = DH_graph_1
diff --git a/test_problems/cathermo/DH_graph_Pitzer/Makefile.am b/test_problems/cathermo/DH_graph_Pitzer/Makefile.am
index e0ff0a8ba..1182f8991 100644
--- a/test_problems/cathermo/DH_graph_Pitzer/Makefile.am
+++ b/test_problems/cathermo/DH_graph_Pitzer/Makefile.am
@@ -1,13 +1,13 @@
 cc_sources = DH_graph_1.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                 = -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         = DH_graph_1
diff --git a/test_problems/cathermo/DH_graph_bdotak/Makefile.am b/test_problems/cathermo/DH_graph_bdotak/Makefile.am
index e0ff0a8ba..1182f8991 100644
--- a/test_problems/cathermo/DH_graph_bdotak/Makefile.am
+++ b/test_problems/cathermo/DH_graph_bdotak/Makefile.am
@@ -1,13 +1,13 @@
 cc_sources = DH_graph_1.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                 = -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         = DH_graph_1
diff --git a/test_problems/cathermo/HMW_dupl_test/HMW_dupl_test.cpp b/test_problems/cathermo/HMW_dupl_test/HMW_dupl_test.cpp
index bd10b9ae1..c51c74caa 100644
--- a/test_problems/cathermo/HMW_dupl_test/HMW_dupl_test.cpp
+++ b/test_problems/cathermo/HMW_dupl_test/HMW_dupl_test.cpp
@@ -18,7 +18,7 @@
 #include "importCTML.h"
 #else
 #include "Cantera.h"
-#include "kernel/logger.h"
+#include "logger.h"
 #include "thermo.h"
 #include "TemperatureTable.h"
 #include "HMWSoln.h"
diff --git a/test_problems/cathermo/HMW_dupl_test/Makefile.am b/test_problems/cathermo/HMW_dupl_test/Makefile.am
index 4e3343760..eed80551d 100644
--- a/test_problems/cathermo/HMW_dupl_test/Makefile.am
+++ b/test_problems/cathermo/HMW_dupl_test/Makefile.am
@@ -1,13 +1,13 @@
 cc_sources = HMW_dupl_test.cpp sortAlgorithms.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         = HMW_dupl_test
diff --git a/test_problems/cathermo/HMW_graph_CpvT/HMW_graph_CpvT.cpp b/test_problems/cathermo/HMW_graph_CpvT/HMW_graph_CpvT.cpp
index e8ecab23d..5112c3ff2 100755
--- a/test_problems/cathermo/HMW_graph_CpvT/HMW_graph_CpvT.cpp
+++ b/test_problems/cathermo/HMW_graph_CpvT/HMW_graph_CpvT.cpp
@@ -18,7 +18,7 @@
 #include "importCTML.h"
 #else
 #include "Cantera.h"
-#include "kernel/logger.h"
+#include "logger.h"
 #include "thermo.h"
 #include "TemperatureTable.h"
 #include "HMWSoln.h"
diff --git a/test_problems/cathermo/HMW_graph_CpvT/Makefile.am b/test_problems/cathermo/HMW_graph_CpvT/Makefile.am
index 753aa999b..84f0e807e 100644
--- a/test_problems/cathermo/HMW_graph_CpvT/Makefile.am
+++ b/test_problems/cathermo/HMW_graph_CpvT/Makefile.am
@@ -1,13 +1,13 @@
 cc_sources = HMW_graph_CpvT.cpp sortAlgorithms.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         = HMW_graph_CpvT
diff --git a/test_problems/cathermo/HMW_graph_GvI/HMW_graph_GvI.cpp b/test_problems/cathermo/HMW_graph_GvI/HMW_graph_GvI.cpp
index 772975c77..088674be7 100644
--- a/test_problems/cathermo/HMW_graph_GvI/HMW_graph_GvI.cpp
+++ b/test_problems/cathermo/HMW_graph_GvI/HMW_graph_GvI.cpp
@@ -11,10 +11,8 @@
 
 
 #include "Cantera.h"
-
-#include "kernel/logger.h"
+#include "logger.h"
 #include "HMWSoln.h"
-
 #include <cstdio>
 
 using namespace std;
diff --git a/test_problems/cathermo/HMW_graph_GvI/Makefile.am b/test_problems/cathermo/HMW_graph_GvI/Makefile.am
index c7583d584..7dd653144 100644
--- a/test_problems/cathermo/HMW_graph_GvI/Makefile.am
+++ b/test_problems/cathermo/HMW_graph_GvI/Makefile.am
@@ -1,13 +1,13 @@
 cc_sources = HMW_graph_GvI.cpp sortAlgorithms.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/ -I$(top_builddir)/build/include/cantera -I$(top_builddir)/build/include/cantera/kernel
 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         = HMW_graph_GvI
diff --git a/test_problems/cathermo/HMW_graph_GvT/HMW_graph_GvT.cpp b/test_problems/cathermo/HMW_graph_GvT/HMW_graph_GvT.cpp
index 7e662a540..065330d15 100644
--- a/test_problems/cathermo/HMW_graph_GvT/HMW_graph_GvT.cpp
+++ b/test_problems/cathermo/HMW_graph_GvT/HMW_graph_GvT.cpp
@@ -19,9 +19,9 @@
 #include "ThermoPhase.h"
 
 #include "Cantera.h"
-#include "kernel/logger.h"
+#include "logger.h"
 #include "thermo.h"
-#include "kernel/HMWSoln.h"
+#include "HMWSoln.h"
 #endif
 
 #include "TemperatureTable.h"
diff --git a/test_problems/cathermo/HMW_graph_GvT/Makefile.am b/test_problems/cathermo/HMW_graph_GvT/Makefile.am
index d01b220bd..242b39ef5 100644
--- a/test_problems/cathermo/HMW_graph_GvT/Makefile.am
+++ b/test_problems/cathermo/HMW_graph_GvT/Makefile.am
@@ -1,13 +1,13 @@
 cc_sources = HMW_graph_GvT.cpp sortAlgorithms.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         = HMW_graph_GvT
diff --git a/test_problems/cathermo/HMW_graph_HvT/HMW_graph_HvT.cpp b/test_problems/cathermo/HMW_graph_HvT/HMW_graph_HvT.cpp
index dc017c290..6e64e9c67 100644
--- a/test_problems/cathermo/HMW_graph_HvT/HMW_graph_HvT.cpp
+++ b/test_problems/cathermo/HMW_graph_HvT/HMW_graph_HvT.cpp
@@ -11,7 +11,7 @@
 
 #include "Cantera.h"
 #include "thermo.h"
-#include "kernel/HMWSoln.h"
+#include "HMWSoln.h"
 #include "TemperatureTable.h"
 
 #include <cstdio>
diff --git a/test_problems/cathermo/HMW_graph_HvT/Makefile.am b/test_problems/cathermo/HMW_graph_HvT/Makefile.am
index 6a933469e..1bae5df66 100644
--- a/test_problems/cathermo/HMW_graph_HvT/Makefile.am
+++ b/test_problems/cathermo/HMW_graph_HvT/Makefile.am
@@ -1,13 +1,13 @@
 cc_sources = HMW_graph_HvT.cpp sortAlgorithms.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         = HMW_graph_HvT
diff --git a/test_problems/cathermo/HMW_graph_VvT/HMW_graph_VvT.cpp b/test_problems/cathermo/HMW_graph_VvT/HMW_graph_VvT.cpp
index 8e0a62845..fddc7b504 100755
--- a/test_problems/cathermo/HMW_graph_VvT/HMW_graph_VvT.cpp
+++ b/test_problems/cathermo/HMW_graph_VvT/HMW_graph_VvT.cpp
@@ -19,7 +19,7 @@
 #include "Cantera.h"
 //#include "vcs_Cantera_input.h"
 //#include "vcs_Cantera_convert.h"
-#include "kernel/logger.h"
+#include "logger.h"
 #include "thermo.h"
 #include "TemperatureTable.h"
 #include "HMWSoln.h"
diff --git a/test_problems/cathermo/HMW_graph_VvT/Makefile.am b/test_problems/cathermo/HMW_graph_VvT/Makefile.am
index 28cc1b6d1..7cccd4a33 100644
--- a/test_problems/cathermo/HMW_graph_VvT/Makefile.am
+++ b/test_problems/cathermo/HMW_graph_VvT/Makefile.am
@@ -1,14 +1,14 @@
 cc_sources = HMW_graph_VvT.cpp sortAlgorithms.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/ 
 LIBS                 =  $(LINK)
+AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
 
 bin_PROGRAMS         = HMW_graph_VvT
 library_includedir   = $(INC)
diff --git a/test_problems/cathermo/HMW_test_1/HMW_test_1.cpp b/test_problems/cathermo/HMW_test_1/HMW_test_1.cpp
index 7f6646d14..32f898213 100644
--- a/test_problems/cathermo/HMW_test_1/HMW_test_1.cpp
+++ b/test_problems/cathermo/HMW_test_1/HMW_test_1.cpp
@@ -7,7 +7,7 @@
 
 
 #include "Cantera.h"
-#include "kernel/HMWSoln.h"
+#include "HMWSoln.h"
 
 #include <cstdio>
 
diff --git a/test_problems/cathermo/HMW_test_1/Makefile.am b/test_problems/cathermo/HMW_test_1/Makefile.am
index 3a5cc66c4..c02a37977 100644
--- a/test_problems/cathermo/HMW_test_1/Makefile.am
+++ b/test_problems/cathermo/HMW_test_1/Makefile.am
@@ -1,13 +1,13 @@
 cc_sources = HMW_test_1.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         = HMW_test_1
diff --git a/test_problems/cathermo/HMW_test_3/Makefile.am b/test_problems/cathermo/HMW_test_3/Makefile.am
index 8836282e9..d610dc6b5 100644
--- a/test_problems/cathermo/HMW_test_3/Makefile.am
+++ b/test_problems/cathermo/HMW_test_3/Makefile.am
@@ -1,13 +1,13 @@
 cc_sources = HMW_test_3.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         = HMW_test_3
diff --git a/test_problems/cathermo/VPissp/Makefile.am b/test_problems/cathermo/VPissp/Makefile.am
index b9418f493..0a5e76384 100644
--- a/test_problems/cathermo/VPissp/Makefile.am
+++ b/test_problems/cathermo/VPissp/Makefile.am
@@ -1,13 +1,13 @@
 cc_sources = ISSPTester.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         = ISSPTester
diff --git a/test_problems/cathermo/issp/ISSPTester.cpp b/test_problems/cathermo/issp/ISSPTester.cpp
index bfa2ecaf6..f45b2d817 100644
--- a/test_problems/cathermo/issp/ISSPTester.cpp
+++ b/test_problems/cathermo/issp/ISSPTester.cpp
@@ -28,7 +28,7 @@
 #include "IdealSolidSolnPhase.h"
 #else
 #include "Cantera.h"
-#include "kernel/IdealSolidSolnPhase.h"
+#include "IdealSolidSolnPhase.h"
 #endif
 
 #include <cstdio>
diff --git a/test_problems/cathermo/issp/Makefile.am b/test_problems/cathermo/issp/Makefile.am
index b9418f493..0a5e76384 100644
--- a/test_problems/cathermo/issp/Makefile.am
+++ b/test_problems/cathermo/issp/Makefile.am
@@ -1,13 +1,13 @@
 cc_sources = ISSPTester.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         = ISSPTester
diff --git a/test_problems/cathermo/stoichSubSSTP/Makefile.am b/test_problems/cathermo/stoichSubSSTP/Makefile.am
index 72c13e30f..a556f78fd 100644
--- a/test_problems/cathermo/stoichSubSSTP/Makefile.am
+++ b/test_problems/cathermo/stoichSubSSTP/Makefile.am
@@ -1,13 +1,13 @@
 cc_sources = stoichSubSSTP.cpp sortAlgorithms.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         = stoichSubSSTP
diff --git a/test_problems/cathermo/stoichSubSSTP/stoichSubSSTP.cpp b/test_problems/cathermo/stoichSubSSTP/stoichSubSSTP.cpp
index 609f26dd4..bd4bc6103 100644
--- a/test_problems/cathermo/stoichSubSSTP/stoichSubSSTP.cpp
+++ b/test_problems/cathermo/stoichSubSSTP/stoichSubSSTP.cpp
@@ -18,7 +18,7 @@
 #else
 #include "Cantera.h"
 #include "thermo.h"
-#include "kernel/StoichSubstanceSSTP.h"
+#include "StoichSubstanceSSTP.h"
 #endif
 
 #include "TemperatureTable.h"