diff --git a/cmake/GENIESetup.cmake b/cmake/GENIESetup.cmake
index 09d6572..3d22ddb 100644
--- a/cmake/GENIESetup.cmake
+++ b/cmake/GENIESetup.cmake
@@ -1,227 +1,231 @@
 # Copyright 2016 L. Pickering, P Stowell, R. Terri, C. Wilkinson, C. Wret
 
 ################################################################################
 #    This file is part of NUISANCE.
 #
 #    NUISANCE is free software: you can redistribute it and/or modify
 #    it under the terms of the GNU General Public License as published by
 #    the Free Software Foundation, either version 3 of the License, or
 #    (at your option) any later version.
 #
 #    NUISANCE is distributed in the hope that it will be useful,
 #    but WITHOUT ANY WARRANTY; without even the implied warranty of
 #    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 #    GNU General Public License for more details.
 #
 #    You should have received a copy of the GNU General Public License
 #    along with NUISANCE.  If not, see <http://www.gnu.org/licenses/>.
 ################################################################################
 
 # TODO
 # check system for libxml2
 # check whether we need the includes
 # check if we can use a subset of the GENIE libraries
 
+include(${CMAKE_SOURCE_DIR}/cmake/parseConfigApp.cmake)
 ################################################################################
 #                            Check Dependencies
 ################################################################################
 
 #################################  GENIE  ######################################
 if(GENIE STREQUAL "")
   cmessage(FATAL_ERROR "Variable GENIE is not defined. "
     "The location of a pre-built GENIE install must be defined either as"
-    " $ cmake -DGENIE=/path/to/GENIE or as and environment vairable"
+    " $ cmake -DGENIE=/path/to/GENIE or as an environment variable"
     " $ export GENIE=/path/to/GENIE")
 endif()
 
 if (BUILD_GEVGEN)
   cmessage(STATUS "Building custom gevgen")
   LIST(APPEND EXTRA_CXX_FLAGS -D__GEVGEN_ENABLED__)
 endif()
 
 if(GENIE_EMPMEC_REWEIGHT)
   cmessage(STATUS "Enable EMPMEC dials")
   LIST(APPEND EXTRA_CXX_FLAGS -D__GENIE_EMP_MECRW_ENABLED)
 endif()
 
 # Extract GENIE VERSION
 if (GENIE_VERSION STREQUAL "AUTO")
    execute_process (COMMAND ${CMAKE_SOURCE_DIR}/cmake/getgenieversion.sh ${GENIE}
    OUTPUT_VARIABLE GENIE_VERSION OUTPUT_STRIP_TRAILING_WHITESPACE)
 endif()
 
 execute_process(COMMAND genie-config --version
 OUTPUT_VARIABLE GENIE_VER OUTPUT_STRIP_TRAILING_WHITESPACE)
 cmessage(STATUS "genie_ver: ${GENIE_VER}")
 if(GENIE_VER VERSION_GREATER 3.0.0)
   set(GENIE_POST_R3 1)
   string(REPLACE "." "" GENIE_VERSION ${GENIE_VER})
   cmessage(STATUS "set genie_post_r3")
 endif()
 
 if(NOT GENIE_POST_R3)
 LIST(APPEND EXTRA_CXX_FLAGS -DGENIE_PRE_R3)
 cmessage(STATUS "setting genie_pre_r3 ${EXTRA_CXX_FLAGS}")
 endif()
 
-execute_process (COMMAND genie-config
-  --libs OUTPUT_VARIABLE GENIE_LD_FLAGS_STR OUTPUT_STRIP_TRAILING_WHITESPACE)
+GETLIBDIR(genie-config --libs GENIE_LIB_DIR)
+
 execute_process (COMMAND genie-config
   --topsrcdir OUTPUT_VARIABLE GENIE_INCLUDES_DIR OUTPUT_STRIP_TRAILING_WHITESPACE)
 
-string(REGEX MATCH "-L\([^ ]+\) \(.*\)$" PARSE_GENIE_LIBS_MATCH ${GENIE_LD_FLAGS_STR})
-
-cmessage(DEBUG "genie-config --libs: ${GENIE_LD_FLAGS_STR}")
-
-if(NOT PARSE_GENIE_LIBS_MATCH)
-  cmessage(FATAL_ERROR "Expected to be able to parse the result of genie-config --libs to a lib directory and a list of libraries to include, but got: \"${GENIE_LD_FLAGS_STR}\"")
-endif()
-
-if(${CMAKE_MATCH_1})
-  set(GENIE_LIB_DIR ${CMAKE_MATCH_1})
-else()
-  set(GENIE_LIB_DIR $ENV{GENIE_LIB})
-endif()
-
-set(GENIE_LIBS_RAW ${CMAKE_MATCH_2})
-string(REPLACE "-l" "" GENIE_LIBS_STRIPED "${GENIE_LIBS_RAW}")
+GETLIBDIRS(genie-config --libs GENIE_LIB_DIR)
+GETLIBS(genie-config --libs GENIE_LIBS)
 
 cmessage(STATUS "GENIE version : ${GENIE_VERSION}")
 cmessage(STATUS "GENIE libdir  : ${GENIE_LIB_DIR}")
-cmessage(STATUS "GENIE libs    : ${GENIE_LIBS_STRIPED}")
+cmessage(STATUS "GENIE libs    : ${GENIE_LIBS}")
 
-string(REGEX MATCH "ReinSeghal" WASMATCHED ${GENIE_LIBS_STRIPED})
+string(REGEX MATCH "ReinSeghal" WASMATCHED ${GENIE_LIBS})
 if(WASMATCHED AND GENIE_VERSION STREQUAL "210")
-  set(GENIE_SEHGAL ${GENIE_LIBS_STRIPED})
-  STRING(REPLACE "ReinSeghal" "ReinSehgal" GENIE_LIBS_STRIPED ${GENIE_SEHGAL})
-  cmessage(DEBUG "Fixed inconsistency in library naming: ${GENIE_LIBS_STRIPED}")
+  set(GENIE_SEHGAL ${GENIE_LIBS})
+  STRING(REPLACE "ReinSeghal" "ReinSehgal" GENIE_LIBS ${GENIE_SEHGAL})
+  cmessage(DEBUG "Fixed inconsistency in library naming: ${GENIE_LIBS}")
 endif()
 
 if(NOT GENIE_POST_R3)
-  string(REGEX MATCH "ReWeight" WASMATCHED ${GENIE_LIBS_STRIPED})
-  if(NOT WASMATCHED)
-    set(GENIE_LIBS_STRIPED "GReWeight ${GENIE_LIBS_STRIPED}")
-    cmessage(DEBUG "Force added ReWeight library: ${GENIE_LIBS_STRIPED}")
+  LIST(FIND GENIE_LIBS GReWeight WAS_FOUND)
+  if(WAS_FOUND STREQUAL "-1")
+    LIST(APPEND GENIE_LIBS GReWeight)
+    cmessage(DEBUG "Force added ReWeight library: ${GENIE_LIBS}")
   endif()
 else()
-  string(REGEX MATCH "RwFwk" WASMATCHED ${GENIE_LIBS_STRIPED})
-  if(NOT WASMATCHED)
-    set(GENIE_LIBS_STRIPED "GRwClc GRwFwk GRwIO ${GENIE_LIBS_STRIPED}")
-    cmessage(DEBUG "Force added ReWeight library: ${GENIE_LIBS_STRIPED}")
+  LIST(FIND GENIE_LIBS GRwFwk WAS_FOUND)
+  if(WAS_FOUND STREQUAL "-1")
+    LIST(APPEND GENIE_LIBS GRwClc GRwFwk GRwIO)
+    cmessage(DEBUG "Force added ReWeight library: ${GENIE_LIBS}")
   endif()
 endif()
 
-string(REPLACE " " ";" GENIE_LIBS_LIST "-Wl,--no-as-needed -Wl,--start-group ${GENIE_LIBS_STRIPED} -Wl,--end-group")
-cmessage(DEBUG "genie-config --libs -- MATCH1: ${CMAKE_MATCH_1}")
-cmessage(DEBUG "genie-config --libs -- MATCH2: ${CMAKE_MATCH_2}")
-cmessage(DEBUG "genie-config --libs -- libs stripped: ${GENIE_LIBS_STRIPED}")
-cmessage(DEBUG "genie-config --libs -- libs list: ${GENIE_LIBS_LIST}")
+LIST(APPEND GENIE_LIBS -Wl,--end-group )
+LIST(REVERSE GENIE_LIBS)
+LIST(APPEND GENIE_LIBS -Wl,--start-group -Wl,--no-as-needed )
+LIST(REVERSE GENIE_LIBS)
+
+cmessage(DEBUG "GENIE_LIBS: ${GENIE_LIBS}")
 
 ################################  LHAPDF  ######################################
 if(LHAPDF_LIB STREQUAL "")
-  cmessage(FATAL_ERROR "Variable LHAPDF_LIB is not defined. The location of a pre-built lhapdf install must be defined either as $ cmake -DLHAPDF_LIB=/path/to/LHAPDF_libraries or as and environment vairable $ export LHAPDF_LIB=/path/to/LHAPDF_libraries")
+  cmessage(FATAL_ERROR "Variable LHAPDF_LIB is not defined. The location of a pre-built lhapdf install must be defined either as $ cmake -DLHAPDF_LIB=/path/to/LHAPDF_libraries or as an environment variable $ export LHAPDF_LIB=/path/to/LHAPDF_libraries")
 endif()
 
 if(LHAPDF_INC STREQUAL "")
-  cmessage(FATAL_ERROR "Variable LHAPDF_INC is not defined. The location of a pre-built lhapdf install must be defined either as $ cmake -DLHAPDF_INC=/path/to/LHAPDF_includes or as and environment vairable $ export LHAPDF_INC=/path/to/LHAPDF_includes")
+  cmessage(FATAL_ERROR "Variable LHAPDF_INC is not defined. The location of a pre-built lhapdf install must be defined either as $ cmake -DLHAPDF_INC=/path/to/LHAPDF_includes or as an environment variable $ export LHAPDF_INC=/path/to/LHAPDF_includes")
 endif()
 
 if(LHAPATH STREQUAL "")
-  cmessage(FATAL_ERROR "Variable LHAPATH is not defined. The location of a the LHAPATH directory must be defined either as $ cmake -DLHAPATH=/path/to/LHAPATH or as and environment variable $ export LHAPATH=/path/to/LHAPATH")
+  cmessage(FATAL_ERROR "Variable LHAPATH is not defined. The location of a the LHAPATH directory must be defined either as $ cmake -DLHAPATH=/path/to/LHAPATH or as an environment variable $ export LHAPATH=/path/to/LHAPATH")
 endif()
 
 ################################  LIBXML  ######################################
 if(LIBXML2_LIB STREQUAL "")
-  # Check for xml2-config
-  find_program(LIBXMLCFGLIBS xml2-config)
-  if(NOT LIBXMLCFGLIBS STREQUAL "LIBXMLLIBS-NOTFOUND")
-    execute_process (COMMAND ${LIBXMLCFGLIBS} --libs
-      OUTPUT_VARIABLE LIBXML2_LIB OUTPUT_STRIP_TRAILING_WHITESPACE)
-  else()
-    message(FATAL_ERROR "Variable LIBXML2_LIB is not defined and could not find xml2-config. The location of a pre-built libxml2 install must be defined either as $ cmake -DLIBXML2_LIB=/path/to/LIBXML2_libraries or as and environment vairable $ export LIBXML2_LIB=/path/to/LIBXML2_libraries")
+  GETLIBDIR(xml2-config --libs LIBXML2_LIB IGNORE_EMPTY_RESPONSE)
+  if(LIBXML2_LIB STREQUAL "")
+    message(WARNING "Variable LIBXML2_LIB is not defined, as xml2-config was found and didn't report a library include path, it is likely that libxml2.so can be found in the standard system location, lets hope so.")
   endif()
 endif()
 
 if(LIBXML2_INC STREQUAL "")
-  # Check for xml2-config
-  find_program(LIBXMLCFGINCS xml2-config)
-  if(NOT LIBXMLCFGINCS STREQUAL "LIBXMLINCS-NOTFOUND")
-    execute_process (COMMAND ${LIBXMLCFGINCS} --cflags
-      OUTPUT_VARIABLE LIBXML2_INC OUTPUT_STRIP_TRAILING_WHITESPACE)
-  else()
-    message(FATAL_ERROR "Variable LIBXML2_INC is not defined and could not find xml2-config. The location of a pre-built libxml2 install must be defined either as $ cmake -DLIBXML2_INC=/path/to/LIBXML2_libraries or as and environment vairable $ export LIBXML2_INC=/path/to/LIBXML2_libraries")
+  GETINCDIR(xml2-config --cflags LIBXML2_INC)
+  if(LIBXML2_INC STREQUAL "")
+    message(FATAL_ERROR "Variable LIBXML2_INC is not defined and could not be found with xml2-config. The location of a pre-built libxml2 install must be defined either as $ cmake -DLIBXML2_INC=/path/to/LIBXML2_includes or as an environment variable $ export LIBXML2_INC=/path/to/LIBXML2_includes")
   endif()
 endif()
 
-string(REPLACE "-llzma" "" LIBXML2_LIB ${LIBXML2_LIB})
-
 ###############################  log4cpp  ######################################
 if(LOG4CPP_LIB STREQUAL "")
-  find_program(LOG4CPPCFG log4cpp-config)
-  if(NOT LOG4CPPCFG STREQUAL "LOG4CPPCFG-NOTFOUND")
-    execute_process (COMMAND ${LOG4CPPCFG}
-      --pkglibdir OUTPUT_VARIABLE LOG4CPP_LIB OUTPUT_STRIP_TRAILING_WHITESPACE)
-  else()
-    message(FATAL_ERROR "Variable LOG4CPP_LIB is not defined. The location of a pre-built log4cpp install must be defined either as $ cmake -DLOG4CPP_LIB=/path/to/LOG4CPP_libraries or as and environment vairable $ export LOG4CPP_LIB=/path/to/LOG4CPP_libraries")
+  GETLIBDIR(log4cpp-config --libs LOG4CPP_LIB)
+  if(LOG4CPP_LIB STREQUAL "")
+    message(FATAL_ERROR "Variable LOG4CPP_LIB is not defined and could not be found with log4cpp-config. The location of a pre-built log4cpp install must be defined either as $ cmake -DLOG4CPP_LIB=/path/to/LOG4CPP_libraries or as an environment variable $ export LOG4CPP_LIB=/path/to/LOG4CPP_libraries")
   endif()
 endif()
 
-if(LOG4CPP_INC  STREQUAL "")
-  find_program(LOG4CPPCFG log4cpp-config)
-  if(NOT LOG4CPPCFG STREQUAL "LOG4CPPCFG-NOTFOUND")
-    execute_process (COMMAND ${LOG4CPPCFG}
-    --pkgincludedir OUTPUT_VARIABLE LOG4CPP_INC OUTPUT_STRIP_TRAILING_WHITESPACE)
-  else()
-    message(FATAL_ERROR "Variable LOG4CPP_INC is not defined. The location of a pre-built log4cpp install must be defined either as $ cmake -DGENIE_LOG4CPP_INC=/path/to/LOG4CPP_includes or as and environment vairable $ export LOG4CPP_INC=/path/to/LOG4CPP_includes")
+if(LOG4CPP_INC STREQUAL "")
+  GETINCDIR(log4cpp-config --cflags LOG4CPP_INC)
+  if(LOG4CPP_INC STREQUAL "")
+    message(FATAL_ERROR "Variable LOG4CPP_INC is not defined and could not be found with log4cpp-config. The location of a pre-built log4cpp install must be defined either as $ cmake -DLOG4CPP_INC=/path/to/LOG4CPP_includes or as an environment variable $ export LOG4CPP_INC=/path/to/LOG4CPP_includes")
   endif()
 endif()
 ################################################################################
 
 LIST(APPEND EXTRA_CXX_FLAGS -D__GENIE_ENABLED__ -D__GENIE_VERSION__=${GENIE_VERSION})
 
-LIST(APPEND EXTRA_LIBS ${GENIE_LIBS_LIST})
+LIST(APPEND EXTRA_LIBS ${GENIE_LIBS})
+
+###############################  GSL  ######################################
+if(GENIE_POST_R3)
+  if(GSL_LIB STREQUAL "")
+    GETLIBDIR(gsl-config --libs GSL_LIB)
+    if(GSL_LIB STREQUAL "")
+      message(FATAL_ERROR "Variable GSL_LIB is not defined and could not be found with gsl-config. The location of a pre-built gsl install must be defined either as $ cmake -DGSL_LIB=/path/to/GSL_libraries or as an environment variable $ export GSL_LIB=/path/to/GSL_libraries")
+    endif()
+  endif()
+
+  if(GSL_INC STREQUAL "")
+    GETINCDIR(gsl-config --cflags GSL_INC)
+    if(GSL_INC STREQUAL "")
+      message(FATAL_ERROR "Variable GSL_INC is not defined and could not be found with gsl-config. The location of a pre-built gsl install must be defined either as $ cmake -DGSL_INC=/path/to/GSL_includes or as an environment variable $ export GSL_INC=/path/to/GSL_includes")
+    endif()
+  endif()
+
+  GETLIBS(gsl-config --libs GSL_LIB_LIST)
+
+  if(GENIE_REWEIGHT STREQUAL "")
+    message(FATAL_ERROR "Variable GENIE_REWEIGHT is not defined. When using GENIE v3+, we require the reweight product to be built and accessible via the environment variable GENIE_REWEIGHT")
+  endif()
+endif()
+################################################################################
 
 LIST(APPEND EXTRA_LIBS LHAPDF xml2 log4cpp)
 
 LIST(APPEND EXTRA_LINK_DIRS
   ${GENIE_LIB_DIR}
   ${LHAPDF_LIB}
-  ${LIBXML2_LIB}
   ${LOG4CPP_LIB})
 
 if(NOT GENIE_POST_R3)
   LIST(APPEND RWENGINE_INCLUDE_DIRECTORIES
     ${GENIE_INCLUDES_DIR}
     ${GENIE_INCLUDES_DIR}/GHEP
     ${GENIE_INCLUDES_DIR}/Ntuple
     ${GENIE_INCLUDES_DIR}/ReWeight
     ${GENIE_INCLUDES_DIR}/Apps
     ${GENIE_INCLUDES_DIR}/FluxDrivers
     ${GENIE_INCLUDES_DIR}/EVGDrivers
     ${LHAPDF_INC}
     ${LIBXML2_INC}
     ${LOG4CPP_INC})
 else()
   LIST(APPEND RWENGINE_INCLUDE_DIRECTORIES
     ${GENIE_INCLUDES_DIR}
-    $ENV{GENIE_REWEIGHT}/src
+    ${GENIE_REWEIGHT}/src
     ${GSL_INC}
     ${LHAPDF_INC}
     ${LIBXML2_INC}
     ${LOG4CPP_INC})
-  LIST(APPEND EXTRA_LINK_DIRS $ENV{GSL_LIB})
-  LIST(APPEND EXTRA_LIBS gsl gslcblas)
+
+    LIST(APPEND EXTRA_LINK_DIRS
+      ${GENIE_REWEIGHT}/lib
+      ${GSL_LIB}
+    )
+
+    LIST(APPEND EXTRA_LIBS ${GSL_LIB_LIST})
+
 endif()
 
+cmessage(WARNING ${EXTRA_LINK_DIRS})
+cmessage(WARNING ${EXTRA_LIBS})
+
 SAYVARS()
 
 if(USE_PYTHIA8)
   set(NEED_PYTHIA8 TRUE)
   set(NEED_ROOTPYTHIA8 TRUE)
 else()
   set(NEED_PYTHIA6 TRUE)
   set(NEED_ROOTPYTHIA6 TRUE)
 endif()
 set(NEED_ROOTEVEGEN TRUE)
 
 SET(USE_GENIE TRUE CACHE BOOL "Whether to enable GENIE (reweight) support. Requires external libraries. <FALSE>" FORCE)
diff --git a/cmake/ReweightEnginesSetup.cmake b/cmake/ReweightEnginesSetup.cmake
index 16b9e85..753c11a 100644
--- a/cmake/ReweightEnginesSetup.cmake
+++ b/cmake/ReweightEnginesSetup.cmake
@@ -1,87 +1,86 @@
 # Copyright 2016 L. Pickering, P Stowell, R. Terri, C. Wilkinson, C. Wret
 
 ################################################################################
 #    This file is part of NUISANCE.
 #
 #    NUISANCE is free software: you can redistribute it and/or modify
 #    it under the terms of the GNU General Public License as published by
 #    the Free Software Foundation, either version 3 of the License, or
 #    (at your option) any later version.
 #
 #    NUISANCE is distributed in the hope that it will be useful,
 #    but WITHOUT ANY WARRANTY; without even the implied warranty of
 #    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 #    GNU General Public License for more details.
 #
 #    You should have received a copy of the GNU General Public License
 #    along with NUISANCE.  If not, see <http://www.gnu.org/licenses/>.
 ################################################################################
 
 ##################################  T2K   ######################################
 if(USE_T2K)
   include(${CMAKE_SOURCE_DIR}/cmake/T2KSetup.cmake)
   cmessage(STATUS "Using T2K Reweight engine.")
   set(USE_T2K TRUE CACHE BOOL "Whether to enable T2KReWeight support. Requires external libraries. <FALSE>" FORCE)
 endif()
 ##################################  NIWG  ######################################
 if(USE_NIWG)
   include(${CMAKE_SOURCE_DIR}/cmake/NIWGSetup.cmake)
   cmessage(STATUS "Using NIWG Reweight engine.")
   set(USE_NIWG TRUE CACHE BOOL "Whether to enable (T2K) NIWG ReWeight support. Requires external libraries. <FALSE>" FORCE)
 endif()
 ##################################  MINERvA   ######################################
 if(USE_MINERvA_RW)
   include(${CMAKE_SOURCE_DIR}/cmake/MINERvASetup.cmake)
   cmessage(STATUS "Using MINERvA Reweight engine.")
   set(USE_MINERvA_RW TRUE CACHE BOOL "Whether to enable MINERvA ReWeight support. <FALSE>" FORCE)
 endif()
 ##################################  NEUT  ######################################
 if(USE_NEUT)
   include(${CMAKE_SOURCE_DIR}/cmake/NEUTSetup.cmake)
   cmessage(STATUS "Using NEUT Reweight engine.")
   set(USE_NEUT TRUE CACHE BOOL "Whether to enable NEUT (reweight) support. Requires external libraries. <FALSE>" FORCE)
 endif()
 #################################  NuWro  ######################################
 if(USE_NuWro)
   include(${CMAKE_SOURCE_DIR}/cmake/NuWroSetup.cmake)
   cmessage(STATUS "Using NuWro Reweight engine.")
   set(USE_NuWro TRUE CACHE BOOL "Whether to enable NuWro support. <FALSE>" FORCE)
 endif()
 ##################################  GENIE  #####################################
 if(USE_GENIE)
   include(${CMAKE_SOURCE_DIR}/cmake/GENIESetup.cmake)
   cmessage(STATUS "Using GENIE Reweight engine.")
   set(USE_GENIE TRUE CACHE BOOL "Whether to enable GENIE (reweight) support. Requires external libraries. <FALSE>" FORCE)
 endif()
 
 ################################################################################
 
 ################################  Prob3++   ####################################
 include(${CMAKE_SOURCE_DIR}/cmake/Prob3++Setup.cmake)
 ################################################################################
 
 
 cmessage(STATUS "Reweight engine include directories: ${RWENGINE_INCLUDE_DIRECTORIES}")
 
 if(NEED_ROOTEVEGEN)
   cmessage(STATUS "Require ROOT eve generation libraries")
   LIST(REVERSE ROOT_LIBS)
   LIST(APPEND ROOT_LIBS
     Gui
     Ged
     Geom
     TreePlayer
     EG
     Eve)
   LIST(REVERSE ROOT_LIBS)
 endif()
 
 if(NEED_ROOTPYTHIA6)
   cmessage(STATUS "Require ROOT Pythia6 libraries")
   LIST(APPEND ROOT_LIBS
-    EGPythia6
-    Pythia6)
+    EGPythia6)
 endif()
 
 
 LIST(APPEND EXTRA_LIBS ${ROOT_LIBS})
diff --git a/cmake/c++CompilerSetup.cmake b/cmake/c++CompilerSetup.cmake
index 9b95a37..34e0adc 100644
--- a/cmake/c++CompilerSetup.cmake
+++ b/cmake/c++CompilerSetup.cmake
@@ -1,117 +1,119 @@
 # Copyright 2016 L. Pickering, P Stowell, R. Terri, C. Wilkinson, C. Wret
 
 ################################################################################
 #    This file is part of NUISANCE.
 #
 #    NUISANCE is free software: you can redistribute it and/or modify
 #    it under the terms of the GNU General Public License as published by
 #    the Free Software Foundation, either version 3 of the License, or
 #    (at your option) any later version.
 #
 #    NUISANCE is distributed in the hope that it will be useful,
 #    but WITHOUT ANY WARRANTY; without even the implied warranty of
 #    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 #    GNU General Public License for more details.
 #
 #    You should have received a copy of the GNU General Public License
 #    along with NUISANCE.  If not, see <http://www.gnu.org/licenses/>.
 ################################################################################
 
 if(USE_OMP)
   LIST(APPEND EXTRA_CXX_FLAGS -fopenmp)
 endif()
 
 if(USE_DYNSAMPLES)
   LIST(APPEND EXTRA_LIBS dl)
   LIST(APPEND EXTRA_CXX_FLAGS -D__USE_DYNSAMPLES__)
 endif()
 
 set(CXX_WARNINGS -Wall )
 
 cmessage(DEBUG "EXTRA_CXX_FLAGS: ${EXTRA_CXX_FLAGS}")
 string(REPLACE ";" " " STR_EXTRA_CXX_FLAGS "${EXTRA_CXX_FLAGS}")
 set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${STR_EXTRA_CXX_FLAGS} ${CXX_WARNINGS}")
   set(CMAKE_Fortran_FLAGS_RELEASE "-fPIC")
 
 set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -O0")
 
 if(USE_DYNSAMPLES)
   set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fPIC")
   set(CMAKE_Fortran_FLAGS_DEBUG "-fPIC")
 endif()
 
 set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -fPIC -O3")
 
 if(CMAKE_BUILD_TYPE MATCHES DEBUG)
   set(CURRENT_CMAKE_CXX_FLAGS ${CMAKE_CXX_FLAGS_DEBUG})
 elseif(CMAKE_BUILD_TYPE MATCHES RELEASE)
   set(CURRENT_CMAKE_CXX_FLAGS ${CMAKE_CXX_FLAGS_RELEASE})
 else()
   cmessage(FATAL_ERROR "[ERROR]: Unknown CMAKE_BUILD_TYPE (\"${CMAKE_BUILD_TYPE}\"): Should be \"DEBUG\" or \"RELEASE\".")
 endif()
 
 
 SET(STR_EXTRA_LINK_DIRS)
 if(NOT EXTRA_LINK_DIRS STREQUAL "")
   string(REPLACE ";" " -L" STR_EXTRA_LINK_DIRS "-L${EXTRA_LINK_DIRS}")
 endif()
 
 SET(STR_EXTRA_LIBS)
 if(NOT EXTRA_LIBS STREQUAL "")
   SET(STR_EXTRA_LIBS_NO_SCRUB_LINKOPTS)
   string(REPLACE ";" " -l" STR_EXTRA_LIBS_NO_SCRUB_LINKOPTS "-l${EXTRA_LIBS}")
   string(REPLACE "-l-" "-" STR_EXTRA_LIBS ${STR_EXTRA_LIBS_NO_SCRUB_LINKOPTS})
 endif()
 
 SET(STR_EXTRA_SHAREDOBJS)
 if(NOT EXTRA_SHAREDOBJS STREQUAL "")
   string(REPLACE ";" " " STR_EXTRA_SHAREDOBJS "${EXTRA_SHAREDOBJS}")
 endif()
 
 SET(STR_EXTRA_LINK_FLAGS)
 if(NOT EXTRA_LINK_FLAGS STREQUAL "")
   string(REPLACE ";" " " STR_EXTRA_LINK_FLAGS "${EXTRA_LINK_FLAGS}")
 endif()
 
 cmessage(DEBUG "EXTRA_LINK_DIRS: ${STR_EXTRA_LINK_DIRS}")
 cmessage(DEBUG "EXTRA_LIBS: ${STR_EXTRA_LIBS}")
 cmessage(DEBUG "EXTRA_SHAREDOBJS: ${STR_EXTRA_SHAREDOBJS}")
 cmessage(DEBUG "EXTRA_LINK_FLAGS: ${STR_EXTRA_LINK_FLAGS}")
 
 if(NOT STR_EXTRA_LINK_DIRS STREQUAL "" AND NOT STR_EXTRA_LIBS STREQUAL "")
   SET(CMAKE_DEPENDLIB_FLAGS "${STR_EXTRA_LINK_DIRS} ${STR_EXTRA_LIBS}")
 endif()
 
 if(NOT EXTRA_SHAREDOBJS STREQUAL "")
   SET(CMAKE_DEPENDLIB_FLAGS "${CMAKE_DEPENDLIB_FLAGS} ${EXTRA_SHAREDOBJS}")
 endif()
 
 if(NOT EXTRA_SHAREDOBJS STREQUAL "")
   if(NOT STR_EXTRA_LINK_FLAGS STREQUAL "")
     SET(STR_EXTRA_LINK_FLAGS "${STR_EXTRA_SHAREDOBJS} ${STR_EXTRA_LINK_FLAGS}")
   else()
     SET(STR_EXTRA_LINK_FLAGS "${STR_EXTRA_SHAREDOBJS}")
   endif()
 endif()
 
 if(NOT EXTRA_LINK_FLAGS STREQUAL "")
   if(NOT CMAKE_LINK_FLAGS STREQUAL "")
     SET(CMAKE_LINK_FLAGS "${CMAKE_LINK_FLAGS} ${STR_EXTRA_LINK_FLAGS}")
   else()
     SET(CMAKE_LINK_FLAGS "${STR_EXTRA_LINK_FLAGS}")
   endif()
 endif()
 
 if(USE_OMP)
   cmessage(FATAL_ERROR "No OMP features currently enabled so this is a FATAL_ERROR to let you know that you don't gain anything with this declaration.")
 endif()
 
 
+STRING(REGEX REPLACE " $" "" CMAKE_DEPENDLIB_FLAGS "${CMAKE_DEPENDLIB_FLAGS}")
+
 if (VERBOSE)
   cmessage (STATUS "C++ Compiler      : ${CXX_COMPILER_NAME}")
   cmessage (STATUS "    flags         : ${CMAKE_CXX_FLAGS}")
   cmessage (STATUS "    Release flags : ${CMAKE_CXX_FLAGS_RELEASE}")
   cmessage (STATUS "    Debug flags   : ${CMAKE_CXX_FLAGS_DEBUG}")
   cmessage (STATUS "    Link Flags    : ${CMAKE_LINK_FLAGS}")
   cmessage (STATUS "    Lib Flags     : ${CMAKE_DEPENDLIB_FLAGS}")
 endif()
diff --git a/cmake/cacheVariables.cmake b/cmake/cacheVariables.cmake
index c7155b3..52d5ea1 100644
--- a/cmake/cacheVariables.cmake
+++ b/cmake/cacheVariables.cmake
@@ -1,217 +1,220 @@
 # Copyright 2016 L. Pickering, P Stowell, R. Terri, C. Wilkinson, C. Wret
 
 ################################################################################
 #    This file is part of NUISANCE.
 #
 #    NUISANCE is free software: you can redistribute it and/or modify
 #    it under the terms of the GNU General Public License as published by
 #    the Free Software Foundation, either version 3 of the License, or
 #    (at your option) any later version.
 #
 #    NUISANCE is distributed in the hope that it will be useful,
 #    but WITHOUT ANY WARRANTY; without even the implied warranty of
 #    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 #    GNU General Public License for more details.
 #
 #    You should have received a copy of the GNU General Public License
 #    along with NUISANCE.  If not, see <http://www.gnu.org/licenses/>.
 ################################################################################
 
 function(CheckAndSetDefaultEnv VARNAME DEFAULT CACHETYPE DOCSTRING ENVNAME)
   #cmessage(DEBUG "Trying to assign variable ${VARNAME} into the cache.")
   if(NOT DEFINED ${VARNAME})
     if(DEFINED ENV{${ENVNAME}} AND NOT $ENV{${ENVNAME}} STREQUAL "")
       set(${VARNAME} $ENV{${ENVNAME}} CACHE ${CACHETYPE} ${DOCSTRING})
       cmessage(DEBUG "    Read ${VARNAME} from ENVVAR ${ENVNAME} as $ENV{${ENVNAME}}.")
     else()
       set(${VARNAME} ${DEFAULT} CACHE ${CACHETYPE} ${DOCSTRING})
     endif()
   else()
     set(${VARNAME} ${${VARNAME}} CACHE ${CACHETYPE} ${DOCSTRING})
     unset(${VARNAME})
   endif()
   cmessage(CACHE "--Set cache variable: \"${VARNAME}\" to \"${${VARNAME}}\", in cache ${CACHETYPE}.")
 endfunction()
 
 function(CheckAndSetDefaultCache VARNAME DEFAULT CACHETYPE DOCSTRING)
 #  cmessage(DEBUG "Trying to assign variable ${VARNAME} into the cache.")
   if(NOT DEFINED ${VARNAME})
     set(${VARNAME} ${DEFAULT} CACHE ${CACHETYPE} ${DOCSTRING})
   else()
     set(${VARNAME} ${${VARNAME}} CACHE ${CACHETYPE} ${DOCSTRING})
     unset(${VARNAME})
   endif()
   cmessage(CACHE "--Set cache variable: \"${VARNAME}\" to \"${${VARNAME}}\", in cache ${CACHETYPE}.")
 endfunction()
 
 function(CheckAndSetDefault VARNAME DEFAULT)
 #  cmessage(DEBUG "Trying to assign variable ${VARNAME}.")
   if(NOT DEFINED ${VARNAME})
     set(${VARNAME} ${DEFAULT} PARENT_SCOPE)
     set(${VARNAME} ${DEFAULT})
   endif()
   cmessage(CACHE "--Set variable: \"${VARNAME}\" to \"${${VARNAME}}\".")
 endfunction()
 
 CheckAndSetDefaultCache(VERBOSE TRUE BOOL "Whether to configure loudly.")
 
 set (CMAKE_SKIP_BUILD_RPATH TRUE)
 
 #Changes default install path to be a subdirectory of the build dir.
 #Can set build dir at configure time with -DCMAKE_INSTALL_PREFIX=/install/path
 if(CMAKE_INSTALL_PREFIX STREQUAL "" OR CMAKE_INSTALL_PREFIX STREQUAL
   "/usr/local")
   set(CMAKE_INSTALL_PREFIX "${CMAKE_BINARY_DIR}/${CMAKE_SYSTEM_NAME}")
 elseif(NOT DEFINED CMAKE_INSTALL_PREFIX)
   set(CMAKE_INSTALL_PREFIX "${CMAKE_BINARY_DIR}/${CMAKE_SYSTEM_NAME}")
 endif()
 
 if(CMAKE_BUILD_TYPE STREQUAL "")
   set(CMAKE_BUILD_TYPE DEBUG)
 elseif(NOT DEFINED CMAKE_BUILD_TYPE)
   set(CMAKE_BUILD_TYPE DEBUG)
 endif()
 
 CheckAndSetDefaultCache(EXTRA_SETUP_SCRIPT "" PATH "The path to an extra script to inject into the NUISANCE setup script. <>")
 
 CheckAndSetDefaultCache(USE_MINIMIZER TRUE INTERNAL "Whether we are using the ROOT minimization libraries. <TRUE>")
 
 CheckAndSetDefaultCache(USE_ROOT6 FALSE INTERNAL "Whether we are using the ROOT 6. <FALSE>")
 
 CheckAndSetDefaultCache(USE_HEPMC FALSE BOOL "Whether to enable HepMC input support. <FALSE>")
 CheckAndSetDefaultEnv(HEPMC "" PATH "Path to HepMC source tree root directory. Overrides environment variable \$HEPMC <>" HEPMC)
 CheckAndSetDefaultCache(HEPMC_MOMUNIT "GEV" STRING "HepMC momentum units [MEV|GEV]. <GEV>")
 CheckAndSetDefaultCache(HEPMC_LENUNIT "CM" STRING "HepMC momentum units [MM|CM]. <CM>")
 CheckAndSetDefaultCache(HEPMC_USED_EP FALSE INTERNAL "Whether we built HepMC or not. <FALSE>")
 
 CheckAndSetDefaultCache(USE_NEUT FALSE BOOL "Whether to enable NEUT (reweight) support. Requires external libraries. <FALSE>")
 CheckAndSetDefaultEnv(NEUT_VERSION FALSE STRING "NEUT version string, e.g. 5.4.0. <5.4.0>" NEUT_VERSION)
 CheckAndSetDefaultEnv(NEUT_ROOT "" PATH "Path to NEUT source tree root directory. Overrides environment variable \$NEUT_ROOT <>" NEUT_ROOT)
 CheckAndSetDefaultEnv(CERN "" PATH "Path to CERNLIB source tree root directory that NEUT was built against. Overrides environment variable \$CERN <>" CERN)
 CheckAndSetDefaultEnv(CERN_LEVEL "" STRING "CERNLIB Library version. Overrides environment variable \$CERN_LEVEL <>" CERN_LEVEL)
 
 CheckAndSetDefaultCache(USE_NuWro FALSE BOOL "Whether to enable NuWro support. <FALSE>")
 CheckAndSetDefaultEnv(NUWRO "" PATH "Path to NuWro source tree root directory. Overrides environment variable \$NUWRO <>" NUWRO)
 CheckAndSetDefaultEnv(NUWRO_INC "" PATH "Path to NuWro installed includes directory, needs to contain \"params_all.h\". Overrides environment variable \$NUWRO_INC <>" NUWRO_INC)
 CheckAndSetDefaultCache(NUWRO_INPUT_FILE "" FILEPATH "Path to an input NuWro event vector, which can be used to build NuWro i/o libraries. <>")
 CheckAndSetDefaultCache(NUWRO_BUILT_FROM_FILE FALSE INTERNAL "Whether the NuWro libraries were built by NUISANCE. <FALSE>")
 CheckAndSetDefaultCache(USE_NuWro_RW FALSE BOOL "Whether to try and build support for NuWro reweighting. <FALSE>")
 CheckAndSetDefaultCache(USE_NuWro_SRW_Event FALSE BOOL "Whether to use cut down NuWro reweight event format. Requires NuWro reweight. <FALSE>")
 
 CheckAndSetDefaultCache(USE_GENIE FALSE BOOL "Whether to enable GENIE (reweight) support. Requires external libraries. <FALSE>")
 CheckAndSetDefaultCache(GENIE_VERSION "AUTO" STRING "GENIE Version <AUTO>")
 CheckAndSetDefaultEnv(GENIE "" PATH "Path to GENIE source tree root directory. Overrides environment variable \$GENIE <>" GENIE)
+CheckAndSetDefaultEnv(GENIE_REWEIGHT "" PATH "Path to GENIE ReWeight directory. Only relevant for GENIE v3+. Overrides environment variable \$GENIE_REWEIGHT <>" GENIE_REWEIGHT)
 CheckAndSetDefaultCache(GENIE_EMPMEC_REWEIGHT FALSE BOOL "Whether to use GENIE EMP MEC reweight (requires custom GENIE) <FALSE>")
 CheckAndSetDefaultEnv(LHAPDF_LIB "" PATH "Path to pre-built LHAPDF libraries. Overrides environment variable \$LHAPDF_LIB. <>" LHAPDF_LIB)
 CheckAndSetDefaultEnv(LHAPDF_INC "" PATH "Path to installed LHAPDF headers. Overrides environment variable \$LHAPDF_INC. <>" LHAPDF_INC)
 CheckAndSetDefaultEnv(LHAPATH "" PATH "Path to LHA PDF inputs. Overrides environment variable \$LHAPATH. <>" LHAPATH)
 CheckAndSetDefaultEnv(LIBXML2_LIB "" PATH "Path to pre-built LIBXML2 libraries. Overrides environment variable \$LIBXML2_LIB. <>" LIBXML2_LIB)
 CheckAndSetDefaultEnv(LIBXML2_INC "" PATH "Path to installed LIBXML2 headers. Overrides environment variable \$LIBXML2_INC. <>" LIBXML2_INC)
 CheckAndSetDefaultEnv(LOG4CPP_LIB "" PATH "Path to pre-built LOG4CPP libraries. Overrides environment variable \$LOG4CPP_LIB. <>" LOG4CPP_LIB)
 CheckAndSetDefaultEnv(LOG4CPP_INC "" PATH "Path to installed LOG4CPP headers. Overrides environment variable \$LOG4CPP_INC. <>" LOG4CPP_INC)
+CheckAndSetDefaultEnv(GSL_LIB "" PATH "Path to pre-built gsl libraries. Overrides environment variable \$GSL_LIB. <>" GSL_LIB)
+CheckAndSetDefaultEnv(GSL_INC "" PATH "Path to installed gsl headers. Overrides environment variable \$GSL_INC. <>" GSL_INC)
 
 CheckAndSetDefaultCache(BUILD_GEVGEN FALSE BOOL "Whether to build nuisance_gevgen app.")
 
 CheckAndSetDefaultCache(USE_T2K FALSE BOOL "Whether to enable T2KReWeight support. Requires external libraries. <FALSE>")
 CheckAndSetDefaultEnv(T2KREWEIGHT "" PATH "Path to installed T2KREWEIGHTReWeight. Overrides environment variable \$T2KREWEIGHT. <>" T2KREWEIGHT)
 
 CheckAndSetDefaultCache(USE_NIWG FALSE BOOL "Whether to enable (T2K) NIWG ReWeight support. Requires external libraries. <FALSE>")
 CheckAndSetDefaultEnv(NIWG_ROOT "" PATH "Path to installed NIWGReWeight. Overrides environment variable \$NIWG. <>" NIWG)
 
 CheckAndSetDefaultCache(USE_MINERvA_RW FALSE BOOL "Whether to enable MINERvA ReWeight support. <FALSE>")
 
 CheckAndSetDefaultEnv(PYTHIA6 "" PATH "Path to directory containing libPythia6.so. Overrides environment variable \$PYTHIA6 <>" PYTHIA6)
 
 CheckAndSetDefaultEnv(PYTHIA8 "" PATH "Path to directory containing libPythia8.so. Overrides environment variable \$PYTHIA8 <>" PYTHIA8)
 CheckAndSetDefaultCache(USE_PYTHIA8 FALSE BOOL "Whether to enable PYTHIA8 event support. <FALSE>")
 
 CheckAndSetDefaultCache(USE_GiBUU TRUE BOOL "Whether to enable GiBUU event support. <TRUE>")
 CheckAndSetDefaultCache(BUILD_GiBUU FALSE BOOL "Whether to build supporting GiBUU event tools along with a patched version of GiBUU. <FALSE>")
 
 CheckAndSetDefaultCache(USE_NUANCE TRUE BOOL "Whether to enable NUANCE event support. <TRUE>")
 
 CheckAndSetDefaultCache(USE_PROB3PP FALSE BOOL "Whether to download and compile in Prob3++ support. <FALSE>")
 
 CheckAndSetDefaultCache(NO_EXTERNAL_UPDATE FALSE BOOL "Whether to perform the update target for external dependencies. Note this may produce errors for CMake < 3.8 where a bug was fixed for the feature that this option invokes. <FALSE>")
 
 CheckAndSetDefaultCache(USE_GPERFTOOLS FALSE BOOL "Whether to compile in google performance tools. <FALSE>")
 
 CheckAndSetDefault(NEED_PYTHIA6 FALSE)
 CheckAndSetDefault(NEED_PYTHIA8 FALSE)
 
 CheckAndSetDefault(NEED_ROOTEVEGEN FALSE)
 CheckAndSetDefault(NEED_ROOTPYTHIA6 FALSE)
 
 CheckAndSetDefaultCache(USE_OMP FALSE BOOL "Whether to enable multicore features (there currently are none...). <FALSE>")
 
 CheckAndSetDefaultCache(USE_DYNSAMPLES TRUE BOOL "Whether to enable the dynamic sample loader. <TRUE>")
 
 CheckAndSetDefault(NO_EXPERIMENTS FALSE)
 
 cmessage(STATUS "NO_EXPERIMENTS: ${NO_EXPERIMENTS}")
 
 CheckAndSetDefaultCache(NO_ANL ${NO_EXPERIMENTS} BOOL "Whether to *NOT* build ANL samples. <-DNO_EXPERIMENTS=FALSE>")
 CheckAndSetDefaultCache(NO_ArgoNeuT ${NO_EXPERIMENTS} BOOL "Whether to *NOT* build ArgoNeuT samples. <-DNO_EXPERIMENTS=FALSE>")
 CheckAndSetDefaultCache(NO_BEBC ${NO_EXPERIMENTS} BOOL "Whether to *NOT* build BEBC samples. <-DNO_EXPERIMENTS=FALSE>")
 CheckAndSetDefaultCache(NO_BNL ${NO_EXPERIMENTS} BOOL "Whether to *NOT* build BNL samples. <-DNO_EXPERIMENTS=FALSE>")
 CheckAndSetDefaultCache(NO_FNAL ${NO_EXPERIMENTS} BOOL "Whether to *NOT* build FNAL samples. <-DNO_EXPERIMENTS=FALSE>")
 CheckAndSetDefaultCache(NO_GGM ${NO_EXPERIMENTS} BOOL "Whether to *NOT* build GGM samples. <-DNO_EXPERIMENTS=FALSE>")
 CheckAndSetDefaultCache(NO_K2K ${NO_EXPERIMENTS} BOOL "Whether to *NOT* build K2K samples. <-DNO_EXPERIMENTS=FALSE>")
 CheckAndSetDefaultCache(NO_MINERvA ${NO_EXPERIMENTS} BOOL "Whether to *NOT* build MINERvA samples. <-DNO_EXPERIMENTS=FALSE>")
 CheckAndSetDefaultCache(NO_MiniBooNE ${NO_EXPERIMENTS} BOOL "Whether to *NOT* build MiniBooNE samples. <-DNO_EXPERIMENTS=FALSE>")
 CheckAndSetDefaultCache(NO_T2K ${NO_EXPERIMENTS} BOOL "Whether to *NOT* build T2K samples. <-DNO_EXPERIMENTS=FALSE>")
 CheckAndSetDefaultCache(NO_SciBooNE ${NO_EXPERIMENTS} BOOL "Whether to *NOT* build SciBooNE samples. <-DNO_EXPERIMENTS=FALSE>")
 
 
 function(SAYVARS)
 
 LIST(APPEND VARS
   USE_HEPMC
   HEPMC
   HEPMC_MOMUNIT
   HEPMC_LENUNIT
   HEPMC_USED_EP
   USE_NEUT
   NEUT_ROOT
   CERN
   CERN_LEVEL
   USE_NuWro
   NUWRO
   NUWRO_INC
   NUWRO_INPUT_FILE
   NUWRO_BUILT_FROM_FILE
   USE_GENIE
   GENIE
   LHAPDF_LIB
   LHAPDF_INC
   LIBXML2_LIB
   LIBXML2_INC
   LOG4CPP_LIB
   GENIE_LOG4CPP_INC
   BUILD_GEVGEN
   USE_T2K
   USE_NIWG
   USE_GiBUU
   BUILD_GiBUU
   USE_NUANCE
   NO_EXTERNAL_UPDATE
   USE_GPERFTOOLS
   NO_ANL
   NO_ArgoNeuT
   NO_BEBC
   NO_BNL
   NO_FNAL
   NO_GGM
   NO_K2K
   NO_MINERvA
   NO_MiniBooNE
   NO_T2K
   NO_SciBooNE)
 
   foreach(v ${VARS})
     if(DEFINED ${v})
       cmessage(DEBUG "VARIABLE: \"${v}\" = \"${${v}}\"")
     endif()
   endforeach(v)
 
 endfunction()
diff --git a/cmake/parseConfigApp.cmake b/cmake/parseConfigApp.cmake
new file mode 100644
index 0000000..222b0ec
--- /dev/null
+++ b/cmake/parseConfigApp.cmake
@@ -0,0 +1,141 @@
+function(GETFIRSTMATCHINGDELMIMMEDDIR DELIM CONFIGAPP ARG DIR_OUT FAILURE_IS_NOT_ERROR)
+
+  cmessage(DEBUG "CONFIGAPP: ${CONFIGAPP}, ARG: ${ARG} DIR_OUT: ${DIR_OUT}, FAILURE_IS_NOT_ERROR: ${FAILURE_IS_NOT_ERROR}")
+
+  if(DELIM STREQUAL "")
+    cmessage(FATAL_ERROR "GETFIRSTMATCHINGDELMIMMEDDIR Passed no delimiter. This is a build configuration bug in NUISANCE, please report to the developers.")
+  endif()
+
+  if(CONFIGAPP STREQUAL "")
+    cmessage(FATAL_ERROR "GETFIRSTMATCHINGDELMIMMEDDIR Passed no configuration application. This is a build configuration bug in NUISANCE, please report to the developers.")
+  endif()
+
+  SET(CONFIGAPP_LOCATION "CONFIGAPP_LOCATION-NOTFOUND")
+  find_program(CONFIGAPP_LOCATION ${CONFIGAPP})
+  if(NOT CONFIGAPP_LOCATION STREQUAL "CONFIGAPP_LOCATION-NOTFOUND")
+    execute_process (COMMAND ${CONFIGAPP_LOCATION}
+    ${ARG} OUTPUT_VARIABLE CONFIGAPP_RESPONSE_RAW OUTPUT_STRIP_TRAILING_WHITESPACE)
+
+    cmessage(DEBUG "${CONFIGAPP_LOCATION} ${ARG} responded with: \"${CONFIGAPP_RESPONSE_RAW}\"")
+
+    if(CONFIGAPP_RESPONSE_RAW STREQUAL "")
+      if(FAILURE_IS_NOT_ERROR)
+        cmessage(DEBUG "\"${CONFIGAPP_LOCATION} ${ARG}\" produced no output and was expected to.")
+        set(${DIR_OUT} "" PARENT_SCOPE)
+      else()
+        cmessage(FATAL_ERROR "\"${CONFIGAPP_LOCATION} ${ARG}\" produced no output and was required to.")
+      endif()
+    else()
+      string(REGEX MATCH "${DELIM}\([^ ]+\)" PARSE_CONFIGAPP_RESPONSE_MATCH ${CONFIGAPP_RESPONSE_RAW})
+
+      if(NOT PARSE_CONFIGAPP_RESPONSE_MATCH)
+        if(FAILURE_IS_NOT_ERROR)
+          cmessage(DEBUG "Couldn't find ${DELIM} flag, found: \"${CONFIGAPP_RESPONSE_RAW}\"")
+          set(${CMAKE_MATCH_1} "")
+        else()
+          cmessage(FATAL_ERROR "Expected to be able to parse the result of ${CONFIGAPP} ${ARG} to a lib directory, but couldn't find a ${DELIM} flag, found: \"${CONFIGAPP_RESPONSE_RAW}\"")
+        endif()
+      endif()
+
+      set(${DIR_OUT} ${CMAKE_MATCH_1} PARENT_SCOPE)
+    endif()
+  else()
+    cmessage(FATAL_ERROR "[ERROR]: Failed to find dependency configuration application: \"${CONFIGAPP}\"")
+  endif()
+endfunction()
+
+#Uselike GETLIBDIR(gsl-config --libs GSL_LIB_DIR)
+function(GETLIBDIR CONFIGAPP ARG LIBDIR_OUT)
+  if(ARGN)
+    set(FAILURE_IS_NOT_ERROR TRUE)
+  else()
+    set(FAILURE_IS_NOT_ERROR FALSE)
+  endif()
+  GETFIRSTMATCHINGDELMIMMEDDIR(
+    "-L"
+    ${CONFIGAPP}
+    ${ARG}
+    MATCHING_DIR
+    ${FAILURE_IS_NOT_ERROR})
+  set(${LIBDIR_OUT} ${MATCHING_DIR} PARENT_SCOPE)
+endfunction()
+
+#Uselike GETINCDIR(gsl-config --cflags GSL_INC_DIR)
+function(GETINCDIR CONFIGAPP ARG INCDIR_OUT)
+  if(ARGN)
+    set(FAILURE_IS_NOT_ERROR TRUE)
+  else()
+    set(FAILURE_IS_NOT_ERROR FALSE)
+  endif()
+  GETFIRSTMATCHINGDELMIMMEDDIR(
+    "-I"
+    ${CONFIGAPP}
+    ${ARG}
+    MATCHING_DIR
+    ${FAILURE_IS_NOT_ERROR})
+  set(${INCDIR_OUT} ${MATCHING_DIR} PARENT_SCOPE)
+endfunction()
+
+function(GETALLMATCHINGDELMIMMEDDIR DELIM CONFIGAPP ARG LIST_OUT)
+  if(DELIM STREQUAL "")
+    cmessage(FATAL_ERROR "GETALLMATCHINGDELMIMMEDDIR Passed no delimiter. This is a build configuration bug in NUISANCE, please report to the developers.")
+  endif()
+
+  if(CONFIGAPP STREQUAL "")
+    cmessage(FATAL_ERROR "GETALLMATCHINGDELMIMMEDDIR Passed no configuration application. This is a build configuration bug in NUISANCE, please report to the developers.")
+  endif()
+
+  find_program(CONFIGAPP_LOCATION ${CONFIGAPP})
+  if(NOT CONFIGAPP_LOCATION STREQUAL "CONFIGAPP_LOCATION-NOTFOUND")
+    execute_process (COMMAND ${CONFIGAPP_LOCATION}
+    ${ARG} OUTPUT_VARIABLE CONFIGAPP_RESPONSE_RAW OUTPUT_STRIP_TRAILING_WHITESPACE)
+
+    string(REPLACE " " ";" CONFIGAPP_RESPONSE_LIST "${CONFIGAPP_RESPONSE_RAW}")
+
+    set(LIST_BUILD)
+
+    foreach(I ${CONFIGAPP_RESPONSE_LIST})
+      if(I)
+        string(REGEX MATCH "^${DELIM}" WASMATCHED ${I})
+        if(WASMATCHED)
+          string(REPLACE "${DELIM}" "" I_STRIPPED "${I}")
+          LIST(APPEND LIST_BUILD ${I_STRIPPED})
+        endif()
+      endif()
+    endforeach()
+
+    set(${LIST_OUT} ${LIST_BUILD} PARENT_SCOPE)
+  else()
+    cmessage(FATAL_ERROR "[ERROR]: Failed to find dependency configuration application: \"${CONFIGAPP}\"")
+  endif()
+endfunction()
+
+#Uselike GETLIBDIRS(gsl-config --libs GSL_LIB_DIR)
+function(GETLIBDIRS CONFIGAPP ARG LIBDIR_OUT)
+  GETALLMATCHINGDELMIMMEDDIR(
+    "-L"
+    ${CONFIGAPP}
+    ${ARG}
+    MATCHING_DIR)
+  set(${LIBDIR_OUT} ${MATCHING_DIR} PARENT_SCOPE)
+endfunction()
+
+#Uselike GETINCDIRS(gsl-config --cflags GSL_INC_DIR)
+function(GETINCDIRS CONFIGAPP ARG INCDIR_OUT)
+  GETALLMATCHINGDELMIMMEDDIR(
+    "-I"
+    ${CONFIGAPP}
+    ${ARG}
+    MATCHING_DIR)
+  set(${INCDIR_OUT} ${MATCHING_DIR} PARENT_SCOPE)
+endfunction()
+
+#Uselike GETLIBS(gsl-config --libs GSL_LIB_DIR)
+function(GETLIBS CONFIGAPP ARG LIBLIST_OUT)
+  GETALLMATCHINGDELMIMMEDDIR(
+    "-l"
+    ${CONFIGAPP}
+    ${ARG}
+    MATCHING_ITEMS)
+  set(${LIBLIST_OUT} ${MATCHING_ITEMS} PARENT_SCOPE)
+endfunction()
diff --git a/cmake/pythia6Setup.cmake b/cmake/pythia6Setup.cmake
index 012fa34..1a89b0c 100644
--- a/cmake/pythia6Setup.cmake
+++ b/cmake/pythia6Setup.cmake
@@ -1,31 +1,29 @@
 # Copyright 2016 L. Pickering, P Stowell, R. Terri, C. Wilkinson, C. Wret
 
 ################################################################################
 #    This file is part of NUISANCE.
 #
 #    NUISANCE is free software: you can redistribute it and/or modify
 #    it under the terms of the GNU General Public License as published by
 #    the Free Software Foundation, either version 3 of the License, or
 #    (at your option) any later version.
 #
 #    NUISANCE is distributed in the hope that it will be useful,
 #    but WITHOUT ANY WARRANTY; without even the implied warranty of
 #    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 #    GNU General Public License for more details.
 #
 #    You should have received a copy of the GNU General Public License
 #    along with NUISANCE.  If not, see <http://www.gnu.org/licenses/>.
 ################################################################################
 
 if(NEED_PYTHIA6)
   if(PYTHIA6 STREQUAL "")
     cmessage(FATAL_ERROR "Variable PYTHIA6 is not defined. This must be set to point to a prebuilt PYTHIA6 instance, please set the \$PYTHIA6 environment variable or configure with -DPYTHIA6=/path/to/pythia6.")
   endif()
 
   LIST(APPEND EXTRA_LINK_DIRS ${PYTHIA6})
 
-  LIST(REVERSE EXTRA_LIBS)
   LIST(APPEND EXTRA_LIBS Pythia6 gfortran)
-  LIST(REVERSE EXTRA_LIBS)
 
 endif()