diff --git a/src/base/Makefile.am b/src/base/Makefile.am
index 3778a0064..463ea07c8 100644
--- a/src/base/Makefile.am
+++ b/src/base/Makefile.am
@@ -1,9 +1,10 @@
 h_sources               = LogPrintCtrl.h
 
-cc_sources              = ct2ctml.cpp ctml.cpp plots.cpp     \
-			  stringUtils.cpp xml.cpp clockWC.cpp         \
-	                  PrintCtrl.cpp LogPrintCtrl.cpp mdp_allo.cpp \
-			  checkFinite.cpp	
+cc_sources              = ct2ctml.cpp ctml.cpp plots.cpp                   \
+			  stringUtils.cpp xml.cpp clockWC.cpp              \
+	                  PrintCtrl.cpp LogPrintCtrl.cpp mdp_allo.cpp      \
+			  checkFinite.cpp application.cpp ctexceptions.cpp \
+	                  global.cpp
 
 AM_CPPFLAGS             = -I$(top_builddir) -I$(top_builddir)/include
 AM_CXXFLAGS             = $(AM_CPPFLAGS)
diff --git a/src/kinetics/Makefile.am b/src/kinetics/Makefile.am
index 7f68ab41b..a953becec 100644
--- a/src/kinetics/Makefile.am
+++ b/src/kinetics/Makefile.am
@@ -3,7 +3,7 @@ cc_sources = importKinetics.cpp GRI_30_Kinetics.cpp KineticsFactory.cpp  \
              GasKinetics.cpp AqueousKinetics.cpp FalloffFactory.cpp      \
 	     ReactionStoichMgr.cpp Kinetics.cpp solveSP.cpp              \
 	     ReactionPath.cpp InterfaceKinetics.cpp ImplicitSurfChem.cpp \
-             Group.cpp
+             Group.cpp Kinetics.cpp
 
 AM_CPPFLAGS             = -I$(top_builddir)/include/
 AM_CXXFLAGS             = $(AM_CPPFLAGS)
diff --git a/src/thermo/Makefile.am b/src/thermo/Makefile.am
index d664db5c2..a703953d1 100644
--- a/src/thermo/Makefile.am
+++ b/src/thermo/Makefile.am
@@ -1,5 +1,30 @@
 h_sources  = 
-cc_sources = Elements.cpp Phase.cpp RedlichKisterVPSSTP.cpp                \
+cc_sources = ConstCpPoly.cpp ConstDensityThermo.cpp DebyeHuckel.cpp        \
+             Elements.cpp FixedChemPotSSTP.cpp GeneralSpeciesThermo.cpp    \
+             GibbsExcessVPSSTP.cpp HMWSoln.cpp HMWSoln_input.cpp           \
+             IdealGasPhase.cpp IdealMolalSoln.cpp IdealSolidSolnPhase.cpp  \
+	     IdealSolnGasVPSS.cpp IonsFromNeutralVPSSTP.cpp                \
+             LatticePhase.cpp LatticeSolidPhase.cpp MargulesVPSSTP.cpp     \
+	     MetalSHEelectrons.cpp MineralEQ3.cpp                          \
+	     MixedSolventElectrolyte.cpp MixtureFugacityTP.cpp             \
+	     MolalityVPSSTP.cpp MolarityIonicVPSSTP.cpp Mu0Poly.cpp        \
+	     Nasa9Poly1.cpp Nasa9PolyMultiTempRegion.cpp PDSS.cpp          \
+             PDSS_ConstVol.cpp PDSS_HKFT.cpp PDSS_IdealGas.cpp             \
+	     PDSS_IonsFromNeutral.cpp PDSS_SSVol.cpp PDSS_Water.cpp        \
+	     Phase.cpp PhaseCombo_Interaction.cpp PseudoBinaryVPSSTP.cpp   \
+             PureFluidPhase.cpp RedlichKisterVPSSTP.cpp                    \
+             RedlichKwongMFTP.cpp SemiconductorPhase.cpp SingleSpeciesTP.cpp \
+	     SpeciesThermoFactory.cpp SpeciesThermoInterpType.cpp          \
+	     StoichSubstance.cpp SurfPhase.cpp ThermoPhase.cpp             \
+	     StoichSubstanceSSTP.cpp ThermoFactory.cpp VPSSMgr.cpp         \
+             VPSSMgrFactory.cpp VPSSMgr_ConstVol.cpp VPSSMgr_General.cpp   \
+             VPSSMgr_IdealGas.cpp VPSSMgr_Water_ConstVol.cpp               \
+             VPSSMgr_Water_HKFT.cpp VPStandardStateTP.cpp WaterProps.cpp   \
+             WaterPropsIAPWS.cpp WaterPropsIAPWSphi.cpp WaterSSTP.cpp
+
+
+
+#Elements.cpp Phase.cpp RedlichKisterVPSSTP.cpp                \
              ThermoPhase.cpp IdealGasPhase.cpp ConstDensityThermo.cpp      \
              SpeciesThermoFactory.cpp ConstCpPoly.cpp Nasa9Poly1.cpp       \
 	     Nasa9PolyMultiTempRegion.cpp PDSS_Water.cpp PDSS_HKFT.cpp     \
diff --git a/src/transport/Makefile.am b/src/transport/Makefile.am
index f1d99d021..01bda90c9 100644
--- a/src/transport/Makefile.am
+++ b/src/transport/Makefile.am
@@ -6,7 +6,8 @@ cc_sources = AqueousTransport.cpp LiquidTransport.cpp MMCollisionInt.cpp \
 	     LiquidTranInteraction.cpp LiquidTransportData.cpp           \
              LiquidTransportParams.cpp TortuosityBase.cpp                \
              TortuosityBruggeman.cpp TortuosityMaxwell.cpp               \
-             TortuosityPercolation.cpp TransportParams.cpp
+             TortuosityPercolation.cpp TransportParams.cpp GasTransport.cpp
+
 
 AM_CPPFLAGS             = -I$(top_builddir)/include
 AM_CXXFLAGS             = $(AM_CPPFLAGS)