Index: /issm/trunk-jpl/externalpackages/dakota/install-6.2-discover.sh
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/install-6.2-discover.sh	(revision 28179)
+++ /issm/trunk-jpl/externalpackages/dakota/install-6.2-discover.sh	(revision 28180)
@@ -23,13 +23,19 @@
 export DAK_BUILD=$ISSM_DIR/externalpackages/dakota/build
 export MPIHOME=$ISSM_DIR/externalpackages/mpich/install
-cp $DAK_SRC/cmake/BuildDakotaTemplate.cmake $DAK_SRC/cmake/BuildDakotaCustom.cmake
+
+# Copy customized source and configuration files to 'src' directory
+cp configs/${VER}/packages/DDACE/src/Analyzer/MainEffectsExcelOutput.cpp ${DAK_SRC}/packages/DDACE/src/Analyzer
+cp configs/${VER}/packages/queso/src/misc/src/1DQuadrature.C ${DAK_SRC}/packages/queso/src/misc/src
+cp configs/${VER}/packages/surfpack/src/surfaces/nkm/NKM_KrigingModel.cpp ${DAK_SRC}/packages/surfpack/src/surfaces/nkm
+cp configs/${VER}/packages/VPISparseGrid/src/sandia_rules.cpp ${DAK_SRC}/packages/VPISparseGrid/src
+cp configs/${VER}/src/DakotaInterface.cpp ${DAK_SRC}/src
+cp configs/${VER}/src/NonDLocalReliability.cpp ${DAK_SRC}/src
+cp configs/${VER}/src/NonDSampling.cpp ${DAK_SRC}/src
+cp configs/${VER}/cmake/DakotaDev.cmake ${DAK_SRC}/cmake
+
+#Apply patches
 patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/6.2/BuildDakotaCustom.cmake.discover.patch
-patch $DAK_SRC/cmake/DakotaDev.cmake configs/6.2/DakotaDev.cmake.patch
 patch $DAK_SRC/CMakeLists.txt configs/6.2/CMakeLists.txt.discover20.patch
 
-#Apply patches
-patch src/src/NonDSampling.cpp configs/6.2/NonDSampling.cpp.patch
-patch src/src/NonDLocalReliability.cpp configs/6.2/NonDLocalReliability.cpp.patch
-patch src/packages/pecos/src/pecos_global_defs.hpp configs/6.2/pecos_global_defs.hpp.patch
 
 #Configure dakota
Index: /issm/trunk-jpl/externalpackages/dakota/install-6.2-linux-static.sh
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/install-6.2-linux-static.sh	(revision 28179)
+++ /issm/trunk-jpl/externalpackages/dakota/install-6.2-linux-static.sh	(revision 28180)
@@ -51,6 +51,4 @@
 cp configs/${VER}/src/NonDLocalReliability.cpp ${DAK_SRC}/src
 cp configs/${VER}/src/NonDSampling.cpp ${DAK_SRC}/src
-
-# Copy customized source and configuration files specific to Linux to 'src' directory
 cp configs/${VER}/static/cmake/BuildDakotaCustom.cmake ${DAK_SRC}/cmake
 cp configs/${VER}/cmake/DakotaDev.cmake ${DAK_SRC}/cmake
Index: /issm/trunk-jpl/externalpackages/dakota/install-6.2-linux.sh
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/install-6.2-linux.sh	(revision 28179)
+++ /issm/trunk-jpl/externalpackages/dakota/install-6.2-linux.sh	(revision 28180)
@@ -48,6 +48,4 @@
 cp configs/${VER}/src/NonDLocalReliability.cpp ${DAK_SRC}/src
 cp configs/${VER}/src/NonDSampling.cpp ${DAK_SRC}/src
-
-# Copy customized source and configuration files specific to Linux to 'src' directory
 cp configs/${VER}/cmake/BuildDakotaCustom.cmake ${DAK_SRC}/cmake
 cp configs/${VER}/cmake/DakotaDev.cmake ${DAK_SRC}/cmake
Index: /issm/trunk-jpl/externalpackages/dakota/install-6.2-lonestar.sh
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/install-6.2-lonestar.sh	(revision 28179)
+++ /issm/trunk-jpl/externalpackages/dakota/install-6.2-lonestar.sh	(revision 28180)
@@ -24,15 +24,17 @@
 export MPIHOME=/opt/cray/pe/mpt/7.7.3/gni/mpich-intel/16.0/
 
-cp $DAK_SRC/cmake/BuildDakotaTemplate.cmake $DAK_SRC/cmake/BuildDakotaCustom.cmake
-patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/6.2/BuildDakotaCustom.cmake.patch
-patch $DAK_SRC/cmake/DakotaDev.cmake configs/6.2/DakotaDev.cmake.patch
-patch $DAK_SRC/CMakeLists.txt configs/6.2/CMakeLists.txt.lonestar.patch
+# Copy customized source and configuration files to 'src' directory
+cp configs/${VER}/packages/DDACE/src/Analyzer/MainEffectsExcelOutput.cpp ${DAK_SRC}/packages/DDACE/src/Analyzer
+cp configs/${VER}/packages/queso/src/misc/src/1DQuadrature.C ${DAK_SRC}/packages/queso/src/misc/src
+cp configs/${VER}/packages/surfpack/src/surfaces/nkm/NKM_KrigingModel.cpp ${DAK_SRC}/packages/surfpack/src/surfaces/nkm
+cp configs/${VER}/packages/VPISparseGrid/src/sandia_rules.cpp ${DAK_SRC}/packages/VPISparseGrid/src
+cp configs/${VER}/src/DakotaInterface.cpp ${DAK_SRC}/src
+cp configs/${VER}/src/NonDLocalReliability.cpp ${DAK_SRC}/src
+cp configs/${VER}/src/NonDSampling.cpp ${DAK_SRC}/src
+cp configs/${VER}/cmake/BuildDakotaCustom.cmake ${DAK_SRC}/cmake
+cp configs/${VER}/cmake/DakotaDev.cmake ${DAK_SRC}/cmake
 
 #Apply patches
-patch src/src/NonDSampling.cpp configs/6.2/NonDSampling.cpp.patch
-patch src/src/NonDLocalReliability.cpp configs/6.2/NonDLocalReliability.cpp.patch
-patch src/packages/pecos/src/pecos_global_defs.hpp configs/6.2/pecos_global_defs.hpp.patch
-patch src/packages/surfpack/src/surfaces/nkm/NKM_KrigingModel.cpp configs/6.2/NKM_KrigingModel.patch
-patch src/packages/DDACE/src/Analyzer/MainEffectsExcelOutput.cpp configs/6.2/MainEffectsExcelOutput.patch
+patch $DAK_SRC/CMakeLists.txt configs/6.2/CMakeLists.txt.lonestar.patch
 patch src/src/DakotaInterface.cpp configs/6.2/DakotaInterface.patch
 
Index: /issm/trunk-jpl/externalpackages/dakota/install-6.2-mac-static.sh
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/install-6.2-mac-static.sh	(revision 28179)
+++ /issm/trunk-jpl/externalpackages/dakota/install-6.2-mac-static.sh	(revision 28180)
@@ -52,8 +52,8 @@
 cp configs/${VER}/src/NonDLocalReliability.cpp ${DAK_SRC}/src
 cp configs/${VER}/src/NonDSampling.cpp ${DAK_SRC}/src
+cp configs/${VER}/static/cmake/BuildDakotaCustom.cmake ${DAK_SRC}/cmake
+cp configs/${VER}/cmake/DakotaDev.cmake ${DAK_SRC}/cmake
 
 # Copy customized source and configuration files specific to Mac to 'src' directory
-cp configs/${VER}/static/cmake/BuildDakotaCustom.cmake ${DAK_SRC}/cmake
-cp configs/${VER}/cmake/DakotaDev.cmake ${DAK_SRC}/cmake
 cp configs/${VER}/mac/cmake/InstallDarwinDylibs.cmake ${DAK_SRC}/cmake
 
Index: /issm/trunk-jpl/externalpackages/dakota/install-6.2-mac.sh
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/install-6.2-mac.sh	(revision 28179)
+++ /issm/trunk-jpl/externalpackages/dakota/install-6.2-mac.sh	(revision 28180)
@@ -49,8 +49,8 @@
 cp configs/${VER}/src/NonDLocalReliability.cpp ${DAK_SRC}/src
 cp configs/${VER}/src/NonDSampling.cpp ${DAK_SRC}/src
+cp configs/${VER}/cmake/BuildDakotaCustom.cmake ${DAK_SRC}/cmake
+cp configs/${VER}/cmake/DakotaDev.cmake ${DAK_SRC}/cmake
 
 # Copy customized source and configuration files specific to Mac to 'src' directory
-cp configs/${VER}/cmake/BuildDakotaCustom.cmake ${DAK_SRC}/cmake
-cp configs/${VER}/cmake/DakotaDev.cmake ${DAK_SRC}/cmake
 cp configs/${VER}/mac/cmake/InstallDarwinDylibs.cmake ${DAK_SRC}/cmake