diff --git a/test_problems/NASA9poly_test/Makefile.am b/test_problems/NASA9poly_test/Makefile.am
index 2861aa81d..39d199d09 100644
--- a/test_problems/NASA9poly_test/Makefile.am
+++ b/test_problems/NASA9poly_test/Makefile.am
@@ -1,12 +1,12 @@
 cc_sources = NASA9poly_test.cpp
 
-INC                  = -I. -I$(top_builddir)/build/include/
+INC                  = -I. -I$(top_builddir)/include/
 AM_CPPFLAGS          = $(INC)
 AM_CXXFLAGS          = $(AM_CPPFLAGS)
 
-LINK                 = -luser -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
+LINK                 = -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
 LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lconverters -lctbase -lcvode 
-LINK                += -lctlapack -lctblas -lctf2c -lctcxx -lm  -lctf2c -lstdc++
+LINK                += -lctlapack -lctblas -lctf2c -lm  -lctf2c -lstdc++
 AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
 LIBS                 =  $(LINK)
 
diff --git a/test_problems/PecosTransport/Makefile.am b/test_problems/PecosTransport/Makefile.am
index 11f79dad4..1ef86da95 100644
--- a/test_problems/PecosTransport/Makefile.am
+++ b/test_problems/PecosTransport/Makefile.am
@@ -1,10 +1,10 @@
 cc_sources = PecosTransport.cpp
 
-INC                  = -I. -I$(top_builddir)/build/include/ -g
+INC                  = -I. -I$(top_builddir)/include/ -g
 AM_CPPFLAGS          = $(INC)
 AM_CXXFLAGS          = $(AM_CPPFLAGS)
 
-LINK                 = -lctcxx -luser -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
+LINK                 = -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
 LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lconverters -lctbase -lcvode 
 LINK                += -lctlapack -lctblas -lctf2c -lm -lstdc++
 AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
diff --git a/test_problems/PecosTransport/PecosTransport.cpp b/test_problems/PecosTransport/PecosTransport.cpp
index e78b2114f..5f61ff545 100644
--- a/test_problems/PecosTransport/PecosTransport.cpp
+++ b/test_problems/PecosTransport/PecosTransport.cpp
@@ -22,10 +22,12 @@ using namespace std;
 /*****************************************************************/
 /*****************************************************************/
 
-#include "Cantera.h"
-#include "transport.h"
-#include "IdealGasMix.h"
-#include "TransportFactory.h"
+
+#include "cantera/transport.h"
+#include "cantera/IdealGasMix.h"
+#include "cantera/transport/TransportFactory.h"
+
+#include "cantera/Cantera.h"
 
 using namespace Cantera;
 using namespace Cantera_CXX;
@@ -144,9 +146,9 @@ int main(int argc, char** argv) {
     grad_T[1] = (T3 - T1) / dist;
 
     int log_level = 0;
-    Transport * tran = newTransportMgr("Pecos", &g, log_level=0);
+    Transport * tran = newTransportMgr("Mix", &g, log_level=0);
 
-    PecosTransport * tranMix = dynamic_cast<PecosTransport *>(tran);
+    MixTransport * tranMix = dynamic_cast<MixTransport *>(tran);
 
     g.setState_TPX(1500.0, pres, DATA_PTR(Xset));
     
diff --git a/test_problems/VPsilane_test/Makefile.am b/test_problems/VPsilane_test/Makefile.am
index efdc073c5..5007dc2a2 100644
--- a/test_problems/VPsilane_test/Makefile.am
+++ b/test_problems/VPsilane_test/Makefile.am
@@ -1,12 +1,12 @@
 cc_sources = silane_equil.cpp
 
-INC                  = -I. -I$(top_builddir)/build/include/
+INC                  = -I. -I$(top_builddir)/include/
 AM_CPPFLAGS          = $(INC)
 AM_CXXFLAGS          = $(AM_CPPFLAGS)
 
-LINK                 = -luser -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
+LINK                 = -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
 LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lconverters -lctbase -lcvode 
-LINK                += -lctlapack -lctblas -lctf2c -lctcxx -lm  -lctf2c -lstdc++
+LINK                += -lctlapack -lctblas -lctf2c -lm  -lctf2c -lstdc++
 AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
 LIBS                 =  $(LINK)
 
diff --git a/test_problems/fracCoeff/Makefile.am b/test_problems/fracCoeff/Makefile.am
index 96c8e3b78..d2c52a075 100644
--- a/test_problems/fracCoeff/Makefile.am
+++ b/test_problems/fracCoeff/Makefile.am
@@ -1,12 +1,12 @@
 cc_sources = fracCoeff.cpp
 
-INC                  = -I. -I$(top_builddir)/build/include/
+INC                  = -I. -I$(top_builddir)/include/
 AM_CPPFLAGS          = $(INC)
 AM_CXXFLAGS          = $(AM_CPPFLAGS)
 
-LINK                 = -luser -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
+LINK                 = -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
 LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lconverters -lctbase -lcvode 
-LINK                += -lctlapack -lctblas -lctf2c -lctcxx -lm  -lctf2c -lstdc++
+LINK                += -lctlapack -lctblas -lctf2c -lm  -lctf2c -lstdc++
 AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
 LIBS                 =  $(LINK)
 
diff --git a/test_problems/multiGasTransport/Makefile.am b/test_problems/multiGasTransport/Makefile.am
index 280b44c5c..02f3e9e56 100644
--- a/test_problems/multiGasTransport/Makefile.am
+++ b/test_problems/multiGasTransport/Makefile.am
@@ -1,12 +1,12 @@
 cc_sources = multiGasTransport.cpp
 
-INC                  = -I. -I$(top_builddir)/build/include/
+INC                  = -I. -I$(top_builddir)/include/
 AM_CPPFLAGS          = $(INC)
 AM_CXXFLAGS          = $(AM_CPPFLAGS)
 
-LINK                 = -luser -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
+LINK                 = -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
 LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lconverters -lctbase -lcvode 
-LINK                += -lctlapack -lctblas -lctf2c -lctcxx -lm  -lctf2c -lstdc++
+LINK                += -lctlapack -lctblas -lctf2c -lm  -lctf2c -lstdc++
 AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
 LIBS                 =  $(LINK)
 
diff --git a/test_problems/negATest/Makefile.am b/test_problems/negATest/Makefile.am
index 4bb8ff193..07c246d8e 100644
--- a/test_problems/negATest/Makefile.am
+++ b/test_problems/negATest/Makefile.am
@@ -1,10 +1,10 @@
 cc_sources = negATest.cpp
 
-INC                  = -I. -I$(top_builddir)/build/include/ -g
+INC                  = -I. -I$(top_builddir)/include/ -g
 AM_CPPFLAGS          = $(INC)
 AM_CXXFLAGS          = $(AM_CPPFLAGS)
 
-LINK                 = -lctcxx -luser -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
+LINK                 = -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
 LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lconverters -lctbase -lcvode 
 LINK                += -lctlapack -lctblas -lctf2c -lm -lstdc++
 AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
diff --git a/test_problems/printUtilUnitTest/Makefile.am b/test_problems/printUtilUnitTest/Makefile.am
index 7b824815e..e322eaa58 100644
--- a/test_problems/printUtilUnitTest/Makefile.am
+++ b/test_problems/printUtilUnitTest/Makefile.am
@@ -1,12 +1,12 @@
 cc_sources = pUtest.cpp
 
-INC                  = -I. -I$(top_builddir)/build/include/
+INC                  = -I. -I$(top_builddir)/include/ -I$(top_builddir)/src/
 AM_CPPFLAGS          = $(INC)
 AM_CXXFLAGS          = $(AM_CPPFLAGS)
 
-LINK                 = -luser -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
+LINK                 = -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
 LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lconverters -lctbase -lcvode 
-LINK                += -lctlapack -lctblas -lctf2c -lctcxx -lm  -lctf2c -lstdc++
+LINK                += -lctlapack -lctblas -lctf2c -lm  -lctf2c -lstdc++
 AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
 LIBS                 =  $(LINK)
 
diff --git a/test_problems/pureFluidTest/Makefile.am b/test_problems/pureFluidTest/Makefile.am
index 94d5fb54e..4006d3714 100644
--- a/test_problems/pureFluidTest/Makefile.am
+++ b/test_problems/pureFluidTest/Makefile.am
@@ -1,12 +1,12 @@
 cc_sources = testPureWater.cpp
 
-INC                  = -I. -I$(top_builddir)/build/include/
+INC                  = -I. -I$(top_builddir)/include/
 AM_CPPFLAGS          = $(INC)
 AM_CXXFLAGS          = $(AM_CPPFLAGS)
 
-LINK                 = -luser -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
+LINK                 = -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
 LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lconverters -lctbase -lcvode 
-LINK                += -lctlapack -lctblas -lctf2c -lctcxx -lm  -lctf2c -lstdc++
+LINK                += -lctlapack -lctblas -lctf2c -lm  -lctf2c -lstdc++
 AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
 LIBS                 =  $(LINK)
 
diff --git a/test_problems/silane_equil/Makefile.am b/test_problems/silane_equil/Makefile.am
index 4b8e65eef..5df0d9717 100644
--- a/test_problems/silane_equil/Makefile.am
+++ b/test_problems/silane_equil/Makefile.am
@@ -1,12 +1,12 @@
 cc_sources = silane_equil.cpp
 
-INC                  = -I. -I$(top_builddir)/build/include/
+INC                  = -I. -I$(top_builddir)/include/
 AM_CPPFLAGS          = $(INC)
 AM_CXXFLAGS          = $(AM_CPPFLAGS)
 
-LINK                 = -luser -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
+LINK                 = -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
 LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lconverters -lctbase -lcvode 
-LINK                += -lctlapack -lctblas -lctf2c -lctcxx -lm  -lctf2c -lstdc++
+LINK                += -lctlapack -lctblas -lctf2c -lm  -lctf2c -lstdc++
 AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
 LIBS                 =  $(LINK)
 
diff --git a/test_problems/spectroscopy/Makefile.am b/test_problems/spectroscopy/Makefile.am
index e6e24fc42..2aa5482b1 100644
--- a/test_problems/spectroscopy/Makefile.am
+++ b/test_problems/spectroscopy/Makefile.am
@@ -1,12 +1,12 @@
 cc_sources = spectratest.cpp
 
-INC                  = -I. -I$(top_builddir)/build/include/
+INC                  = -I. -I$(top_builddir)/include/ -I$(top_builddir)/src/
 AM_CPPFLAGS          = $(INC)
 AM_CXXFLAGS          = $(AM_CPPFLAGS)
 
-LINK                 = -luser -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
+LINK                 = -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
 LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lconverters -lctbase -lcvode 
-LINK                += -lctlapack -lctblas -lctf2c -lctcxx -lm  -lctf2c -lstdc++
+LINK                += -lctlapack -lctblas -lctf2c -lm  -lctf2c -lstdc++
 AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
 LIBS                 =  $(LINK)
 
diff --git a/test_problems/surfSolverTest/Makefile.am b/test_problems/surfSolverTest/Makefile.am
index c7cf5b769..8ae321594 100644
--- a/test_problems/surfSolverTest/Makefile.am
+++ b/test_problems/surfSolverTest/Makefile.am
@@ -1,13 +1,13 @@
 cc_sources = surfaceSolver.cpp
 cc2_sources = surfaceSolver2.cpp
 
-INC                  = -I. -I$(top_builddir)/build/include/
+INC                  = -I. -I$(top_builddir)/include/ -I$(top_builddir)/src/
 AM_CPPFLAGS          = $(INC)
 AM_CXXFLAGS          = $(AM_CPPFLAGS)
 
-LINK                 = -luser -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
+LINK                 = -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
 LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lconverters -lctbase -lcvode 
-LINK                += -lctlapack -lctblas -lctf2c -lctcxx -lm  -lctf2c -lstdc++
+LINK                += -lctlapack -lctblas -lctf2c -lm  -lctf2c -lstdc++
 AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
 LIBS                 =  $(LINK)
 
diff --git a/test_problems/surfkin/Makefile.am b/test_problems/surfkin/Makefile.am
index 18d793ea6..68a1d9ff8 100644
--- a/test_problems/surfkin/Makefile.am
+++ b/test_problems/surfkin/Makefile.am
@@ -1,12 +1,12 @@
 cc_sources = surfdemo.cpp
 
-INC                  = -I. -I$(top_builddir)/build/include/
+INC                  = -I. -I$(top_builddir)/include/
 AM_CPPFLAGS          = $(INC)
 AM_CXXFLAGS          = $(AM_CPPFLAGS)
 
-LINK                 = -luser -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
+LINK                 = -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
 LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lconverters -lctbase -lcvode 
-LINK                += -lctlapack -lctblas -lctf2c -lctcxx -lm  -lctf2c -lstdc++
+LINK                += -lctlapack -lctblas -lctf2c -lm  -lctf2c -lstdc++
 AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
 LIBS                 =  $(LINK)