diff --git a/CMakeLists.txt b/CMakeLists.txt
index e61c4d6..f5027ba 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,242 +1,245 @@
 # 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/>.
 ################################################################################
 cmake_minimum_required (VERSION 2.8 FATAL_ERROR)
 
 #Use the compilers found in the path
 find_program(CMAKE_C_COMPILER NAMES $ENV{CC} gcc PATHS ENV PATH NO_DEFAULT_PATH)
 find_program(CMAKE_CXX_COMPILER NAMES $ENV{CXX} g++ PATHS ENV PATH NO_DEFAULT_PATH)
 
 project(NUISANCE)
 
 include(ExternalProject)
 
 enable_language(Fortran)
 
 set (NUISANCE_VERSION_MAJOR 2)
 set (NUISANCE_VERSION_MINOR 7)
 set (NUISANCE_VERSION_REVISION 0)
 
 set (NUISANCE_VERSION_STRING "v${NUISANCE_VERSION_MAJOR}r${NUISANCE_VERSION_MINOR}")
 if(${NUISANCE_VERSION_REVISION} STRGREATER "0")
   set (NUISANCE_VERSION_STRING "${NUISANCE_VERSION_STRING}p${NUISANCE_VERSION_REVISION}")
 endif()
 
 #Set this to TRUE to enable build debugging messages
 set(BUILD_DEBUG_MSGS TRUE)
 include(${CMAKE_SOURCE_DIR}/cmake/cmessage.cmake)
 
 include(${CMAKE_SOURCE_DIR}/cmake/cacheVariables.cmake)
 
 cmessage(STATUS "CMAKE_INSTALL_PREFIX: \"${CMAKE_INSTALL_PREFIX}\"")
 cmessage(STATUS "CMAKE_BUILD_TYPE: \"${CMAKE_BUILD_TYPE}\"")
 
 ################################################################################
 #                            Check Dependencies
 ################################################################################
 
 ##################################  ROOT  ######################################
 include(${CMAKE_SOURCE_DIR}/cmake/ROOTSetup.cmake)
 
 #################################  HEPMC  ######################################
 include(${CMAKE_SOURCE_DIR}/cmake/HepMC.cmake)
 
 ############################  Reweight Engines  ################################
 include(${CMAKE_SOURCE_DIR}/cmake/ReweightEnginesSetup.cmake)
 
 ############################  Other Generators  ################################
 
 include(${CMAKE_SOURCE_DIR}/cmake/GiBUUSetup.cmake)
 
 if(USE_NUANCE)
   LIST(APPEND EXTRA_CXX_FLAGS -D__NUANCE_ENABLED__)
 endif()
 
 #################################  Pythia6/8  ####################################
 include(${CMAKE_SOURCE_DIR}/cmake/pythia6Setup.cmake)
 include(${CMAKE_SOURCE_DIR}/cmake/pythia8Setup.cmake)
 
 ################################# gperftools ###################################
 
 include(${CMAKE_SOURCE_DIR}/cmake/gperfSetup.cmake)
 
 if(NOT NOTEST)
   enable_testing()
 endif()
 
 SET(GENERATOR_SUPPORT)
 
 foreach(gen NEUT;NuWro;GENIE;GiBUU;NUANCE)
   if(USE_${gen})
     SET(GENERATOR_SUPPORT "${GENERATOR_SUPPORT}${gen} ")
   endif()
 endforeach(gen)
 
 cmessage(STATUS "Generator Input Support: ${GENERATOR_SUPPORT}")
 
 set(MINCODE
   Routines
   FCN)
 
 set(CORE
   MCStudies
   FitBase
   Config
   Logger
   InputHandler
   Splines
   Utils
   Statistical
   #Devel
   Smearceptance
   )
 
 LIST(APPEND ALLEXPERIMENTS
   ANL
   ArgoNeuT
   BEBC
   BNL
   Electron
   FNAL
   GGM
   K2K
   MINERvA
   MicroBooNE
   MiniBooNE
   SciBooNE
   T2K)
 
 foreach(exp ${ALLEXPERIMENTS})
   if(NOT NO_${exp})
     LIST(APPEND EXPERIMENTS_TO_BUILD ${exp})
   else()
     LIST(REVERSE EXTRA_CXX_FLAGS)
     LIST(APPEND EXTRA_CXX_FLAGS -D__NO_${exp}__)
     LIST(REVERSE EXTRA_CXX_FLAGS)
   endif()
 endforeach()
 
 ################################## COMPILER ####################################
 include(${CMAKE_SOURCE_DIR}/cmake/c++CompilerSetup.cmake)
 
 ################################### doxygen ###################################
 
 include(${CMAKE_SOURCE_DIR}/cmake/docsSetup.cmake)
 
 ################################################################################
 
 
 set(MINIMUM_INCLUDE_DIRECTORIES)
 LIST(APPEND MINIMUM_INCLUDE_DIRECTORIES
   ${RWENGINE_INCLUDE_DIRECTORIES}
   ${CMAKE_SOURCE_DIR}/src/FitBase
   ${CMAKE_SOURCE_DIR}/src/Reweight
   ${CMAKE_SOURCE_DIR}/src/InputHandler
   ${CMAKE_SOURCE_DIR}/src/Config
   ${CMAKE_SOURCE_DIR}/src/Logger
   ${CMAKE_SOURCE_DIR}/src/Statistical
   ${CMAKE_SOURCE_DIR}/src/Splines
   ${CMAKE_SOURCE_DIR}/src/Utils)
 
 #Not yet capable of just building without the rwdirs.
 #if(USE_REWEIGHT)
   LIST(APPEND MINIMUM_INCLUDE_DIRECTORIES
     ${CMAKE_SOURCE_DIR}/src/Reweight)
   LIST(APPEND CORE Reweight)
 #endif()
 
 cmessage(DEBUG "Base include directories: ${MINIMUM_INCLUDE_DIRECTORIES}")
 
 set(EXP_INCLUDE_DIRECTORIES)
 
 foreach(edir ${EXPERIMENTS_TO_BUILD})
   LIST(APPEND EXP_INCLUDE_DIRECTORIES ${CMAKE_SOURCE_DIR}/src/${edir})
 endforeach()
 cmessage(DEBUG "Included experiments: ${EXP_INCLUDE_DIRECTORIES}")
 
 foreach(mdir ${MINCODE})
   cmessage (DEBUG "Configuring directory: src/${mdir}")
   add_subdirectory(src/${mdir})
 endforeach()
 
 foreach(edir ${EXPERIMENTS_TO_BUILD})
   cmessage (DEBUG "Configuring directory: src/${edir}")
   add_subdirectory(src/${edir})
 endforeach()
 
 foreach(cdir ${CORE})
   cmessage (DEBUG "Configuring directory: src/${cdir}")
   add_subdirectory(src/${cdir})
 endforeach()
 
 cmessage(DEBUG "Module targets: ${MODULETargets}")
 
 LIST(APPEND MODULETargets -Wl,--end-group)
 LIST(REVERSE MODULETargets)
 LIST(APPEND MODULETargets -Wl,--start-group)
 LIST(REVERSE MODULETargets)
 
 add_subdirectory(app)
 add_subdirectory(src/Tests)
 
 configure_file(cmake/setup.sh.in
   "${PROJECT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/setup.sh" @ONLY)
 install(FILES
   "${PROJECT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/setup.sh" DESTINATION
   ${CMAKE_INSTALL_PREFIX})
 
 configure_file(cmake/MakeBinaryBlob.in
   "${PROJECT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/MakeBinaryBlob" @ONLY)
 install(PROGRAMS
   "${PROJECT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/MakeBinaryBlob" DESTINATION
   bin)
 
 if(USE_DYNSAMPLES)
   SET(ALL_INCLUDES ${MINIMUM_INCLUDE_DIRECTORIES})
   LIST(APPEND ALL_INCLUDES ${CMAKE_SOURCE_DIR}/src/Smearceptance)
   LIST(APPEND ALL_INCLUDES ${EXP_INCLUDE_DIRECTORIES})
 
   string(REPLACE ";" " -I" ALL_INCLUDES_STR "${ALL_INCLUDES}")
+  string(REPLACE "${CMAKE_SOURCE_DIR}/src" "${CMAKE_INSTALL_PREFIX}"
+                 ALL_INCLUDES_STR "${ALL_INCLUDES_STR}")
 
   cmessage(DEBUG ${CMAKE_DEPENDLIB_FLAGS})
   string(REPLACE "-levent " "" CMAKE_DEPENDLIB_FLAGS_NEW ${CMAKE_DEPENDLIB_FLAGS})
   set(CMAKE_DEPENDLIB_FLAGS ${CMAKE_DEPENDLIB_FLAGS_NEW})
   cmessage(DEBUG ${CMAKE_DEPENDLIB_FLAGS})
 
   string(REPLACE ";" " -l" ALL_MODULETARGETS_STR "${MODULETargets}")
+  string(REPLACE "-l-Wl" "-Wl" ALL_MODULETARGETS_STR "${ALL_MODULETARGETS_STR}")
 
   configure_file(cmake/BuildDynamicSample.in
     "${PROJECT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/BuildDynamicSample" @ONLY)
   install(PROGRAMS
     "${PROJECT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/BuildDynamicSample" DESTINATION
     bin)
 
   configure_file(cmake/BuildDynamicSmearcepter.in
     "${PROJECT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/BuildDynamicSmearcepter" @ONLY)
   install(PROGRAMS
     "${PROJECT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/BuildDynamicSmearcepter" DESTINATION
     bin)
 endif()
 
 install(PROGRAMS
   "${PROJECT_SOURCE_DIR}/scripts/nuiscardgen" DESTINATION
   bin)
 
 install(PROGRAMS
   "${PROJECT_SOURCE_DIR}/scripts/nuissamples" DESTINATION
   bin)
diff --git a/src/ANL/CMakeLists.txt b/src/ANL/CMakeLists.txt
index 34aecb7..ff37ba0 100644
--- a/src/ANL/CMakeLists.txt
+++ b/src/ANL/CMakeLists.txt
@@ -1,131 +1,130 @@
 # 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/>.
 ################################################################################
 set(IMPLFILES
 ANL_CCQE_Evt_1DQ2_nu.cxx
 ANL_CCQE_XSec_1DEnu_nu.cxx
 
 ANL_CC1npip_Evt_1DcosmuStar_nu.cxx
 ANL_CC1npip_Evt_1Dppi_nu.cxx
 ANL_CC1npip_Evt_1DQ2_nu.cxx
 ANL_CC1npip_XSec_1DEnu_nu.cxx
 
 ANL_CC1pi0_Evt_1DcosmuStar_nu.cxx
 ANL_CC1pi0_Evt_1DQ2_nu.cxx
 ANL_CC1pi0_XSec_1DEnu_nu.cxx
 
 ANL_CC1ppip_Evt_1DcosmuStar_nu.cxx
 ANL_CC1ppip_Evt_1Dppi_nu.cxx
 ANL_CC1ppip_Evt_1DQ2_nu.cxx
 ANL_CC1ppip_Evt_1Dthpr_nu.cxx
 ANL_CC1ppip_XSec_1DEnu_nu.cxx
 ANL_CC1ppip_XSec_1DQ2_nu.cxx
 ANL_CC1ppip_Evt_1DcosthAdler_nu.cxx
 ANL_CC1ppip_Evt_1Dphi_nu.cxx
 
 ANL_NC1npip_Evt_1Dppi_nu.cxx
 
 ANL_NC1ppim_XSec_1DEnu_nu.cxx
 ANL_NC1ppim_Evt_1DcosmuStar_nu.cxx
 
 ANL_CC2pi_1pim1pip_XSec_1DEnu_nu.cxx
 ANL_CC2pi_1pim1pip_Evt_1Dpmu_nu.cxx
 ANL_CC2pi_1pim1pip_Evt_1Dppim_nu.cxx
 ANL_CC2pi_1pim1pip_Evt_1Dppip_nu.cxx
 ANL_CC2pi_1pim1pip_Evt_1Dpprot_nu.cxx
 
 ANL_CC2pi_1pip1pi0_XSec_1DEnu_nu.cxx
 ANL_CC2pi_1pip1pi0_Evt_1Dpmu_nu.cxx
 ANL_CC2pi_1pip1pi0_Evt_1Dppi0_nu.cxx
 ANL_CC2pi_1pip1pi0_Evt_1Dppip_nu.cxx
 ANL_CC2pi_1pip1pi0_Evt_1Dpprot_nu.cxx
 
 ANL_CC2pi_1pip1pip_XSec_1DEnu_nu.cxx
 ANL_CC2pi_1pip1pip_Evt_1Dpmu_nu.cxx
 ANL_CC2pi_1pip1pip_Evt_1Dpneut_nu.cxx
 ANL_CC2pi_1pip1pip_Evt_1DppipHigh_nu.cxx
 ANL_CC2pi_1pip1pip_Evt_1DppipLow_nu.cxx
 )
 
 set(HEADERFILES
 ANL_CCQE_Evt_1DQ2_nu.h
 ANL_CCQE_XSec_1DEnu_nu.h
 
 ANL_CC1npip_Evt_1DcosmuStar_nu.h
 ANL_CC1npip_Evt_1Dppi_nu.h
 ANL_CC1npip_Evt_1DQ2_nu.h
 ANL_CC1npip_XSec_1DEnu_nu.h
 
 ANL_CC1pi0_Evt_1DcosmuStar_nu.h
 ANL_CC1pi0_Evt_1DQ2_nu.h
 ANL_CC1pi0_XSec_1DEnu_nu.h
 
 ANL_CC1ppip_Evt_1DcosmuStar_nu.h
 ANL_CC1ppip_Evt_1Dppi_nu.h
 ANL_CC1ppip_Evt_1DQ2_nu.h
 ANL_CC1ppip_Evt_1Dthpr_nu.h
 ANL_CC1ppip_XSec_1DEnu_nu.h
 ANL_CC1ppip_XSec_1DQ2_nu.h
 ANL_CC1ppip_Evt_1DcosthAdler_nu.h
 ANL_CC1ppip_Evt_1Dphi_nu.h
 
 ANL_NC1npip_Evt_1Dppi_nu.h
 
 ANL_NC1ppim_XSec_1DEnu_nu.h
 ANL_NC1ppim_Evt_1DcosmuStar_nu.h
 
 ANL_CC2pi_1pim1pip_XSec_1DEnu_nu.h
 ANL_CC2pi_1pim1pip_Evt_1Dpmu_nu.h
 ANL_CC2pi_1pim1pip_Evt_1Dppim_nu.h
 ANL_CC2pi_1pim1pip_Evt_1Dppip_nu.h
 ANL_CC2pi_1pim1pip_Evt_1Dpprot_nu.h
 
 ANL_CC2pi_1pip1pi0_XSec_1DEnu_nu.h
 ANL_CC2pi_1pip1pi0_Evt_1Dpmu_nu.h
 ANL_CC2pi_1pip1pi0_Evt_1Dppi0_nu.h
 ANL_CC2pi_1pip1pi0_Evt_1Dppip_nu.h
 ANL_CC2pi_1pip1pi0_Evt_1Dpprot_nu.h
 
 ANL_CC2pi_1pip1pip_XSec_1DEnu_nu.h
 ANL_CC2pi_1pip1pip_Evt_1Dpmu_nu.h
 ANL_CC2pi_1pip1pip_Evt_1Dpneut_nu.h
 ANL_CC2pi_1pip1pip_Evt_1DppipHigh_nu.h
-ANL_CC2pi_1pip1pip_Evt_1DppipLow_nu.h
-)
+ANL_CC2pi_1pip1pip_Evt_1DppipLow_nu.h)
 
 set(LIBNAME expANL)
 
 if(CMAKE_BUILD_TYPE MATCHES DEBUG)
   add_library(${LIBNAME} STATIC ${IMPLFILES})
 else(CMAKE_BUILD_TYPE MATCHES RELEASE)
   add_library(${LIBNAME} SHARED ${IMPLFILES})
 endif()
 
 include_directories(${MINIMUM_INCLUDE_DIRECTORIES})
 
 set_target_properties(${LIBNAME} PROPERTIES VERSION
   "${NUISANCE_VERSION_MAJOR}.${NUISANCE_VERSION_MINOR}.${NUISANCE_VERSION_REVISION}")
 #set_target_properties(${LIBNAME} PROPERTIES LINK_FLAGS ${ROOT_LD_FLAGS})
 if(DEFINED PROJECTWIDE_EXTRA_DEPENDENCIES)
   add_dependencies(${LIBNAME} ${PROJECTWIDE_EXTRA_DEPENDENCIES})
 endif()
 install(TARGETS ${LIBNAME} DESTINATION lib)
 #Can uncomment this to install the headers... but is it really neccessary?
-#install(FILES ${HEADERFILES} DESTINATION include)
+install(FILES ${HEADERFILES} DESTINATION include/ANL)
 
 set(MODULETargets ${MODULETargets} ${LIBNAME} PARENT_SCOPE)
diff --git a/src/ArgoNeuT/CMakeLists.txt b/src/ArgoNeuT/CMakeLists.txt
index 34a20a2..40f9e95 100644
--- a/src/ArgoNeuT/CMakeLists.txt
+++ b/src/ArgoNeuT/CMakeLists.txt
@@ -1,72 +1,72 @@
 # 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/>.
 ################################################################################
 set(IMPLFILES
 ArgoNeuT_CC1Pi_XSec_1Dpmu_nu.cxx
 ArgoNeuT_CC1Pi_XSec_1Dpmu_antinu.cxx
 ArgoNeuT_CC1Pi_XSec_1Dthetamu_nu.cxx
 ArgoNeuT_CC1Pi_XSec_1Dthetamu_antinu.cxx
 ArgoNeuT_CC1Pi_XSec_1Dthetapi_nu.cxx
 ArgoNeuT_CC1Pi_XSec_1Dthetapi_antinu.cxx
 ArgoNeuT_CC1Pi_XSec_1Dthetamupi_nu.cxx
 ArgoNeuT_CC1Pi_XSec_1Dthetamupi_antinu.cxx
 ArgoNeuT_CCInc_XSec_1Dpmu_antinu.cxx
 ArgoNeuT_CCInc_XSec_1Dpmu_nu.cxx
 ArgoNeuT_CCInc_XSec_1Dthetamu_antinu.cxx
 ArgoNeuT_CCInc_XSec_1Dthetamu_nu.cxx
 )
 
 set(HEADERFILES
 ArgoNeuT_CC1Pi_XSec_1Dpmu_nu.h
 ArgoNeuT_CC1Pi_XSec_1Dpmu_antinu.h
 ArgoNeuT_CC1Pi_XSec_1Dthetamu_nu.h
 ArgoNeuT_CC1Pi_XSec_1Dthetamu_antinu.h
 ArgoNeuT_CC1Pi_XSec_1Dthetapi_nu.h
 ArgoNeuT_CC1Pi_XSec_1Dthetapi_antinu.h
 ArgoNeuT_CC1Pi_XSec_1Dthetamupi_nu.h
 ArgoNeuT_CC1Pi_XSec_1Dthetamupi_antinu.h
 ArgoNeuT_CCInc_XSec_1Dpmu_antinu.h
 ArgoNeuT_CCInc_XSec_1Dpmu_nu.h
 ArgoNeuT_CCInc_XSec_1Dthetamu_antinu.h
 ArgoNeuT_CCInc_XSec_1Dthetamu_nu.h
 )
 
 set(LIBNAME expArgoNeuT)
 
 if(CMAKE_BUILD_TYPE MATCHES DEBUG)
   add_library(${LIBNAME} STATIC ${IMPLFILES})
 else(CMAKE_BUILD_TYPE MATCHES RELEASE)
   add_library(${LIBNAME} SHARED ${IMPLFILES})
 endif()
 
 include_directories(${MINIMUM_INCLUDE_DIRECTORIES})
 
 set_target_properties(${LIBNAME} PROPERTIES VERSION
   "${NUISANCE_VERSION_MAJOR}.${NUISANCE_VERSION_MINOR}.${NUISANCE_VERSION_REVISION}")
 #set_target_properties(${LIBNAME} PROPERTIES LINK_FLAGS ${ROOT_LD_FLAGS})
 
 # Add Extra Links
 if(DEFINED PROJECTWIDE_EXTRA_DEPENDENCIES)
    add_dependencies(${LIBNAME} ${PROJECTWIDE_EXTRA_DEPENDENCIES})
 endif()
 
 install(TARGETS ${LIBNAME} DESTINATION lib)
 #Can uncomment this to install the headers... but is it really neccessary?
-#install(FILES ${HEADERFILES} DESTINATION include)
+install(FILES ${HEADERFILES} DESTINATION include/ArgoNeuT/)
 
 set(MODULETargets ${MODULETargets} ${LIBNAME} PARENT_SCOPE)
diff --git a/src/BEBC/CMakeLists.txt b/src/BEBC/CMakeLists.txt
index deffdc1..86dd94a 100644
--- a/src/BEBC/CMakeLists.txt
+++ b/src/BEBC/CMakeLists.txt
@@ -1,67 +1,67 @@
 # 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/>.
 ################################################################################
 set(IMPLFILES
 BEBC_CC1npim_XSec_1DEnu_antinu.cxx
 BEBC_CC1npim_XSec_1DQ2_antinu.cxx
 BEBC_CC1npip_XSec_1DEnu_nu.cxx
 BEBC_CC1npip_XSec_1DQ2_nu.cxx
 BEBC_CC1pi0_XSec_1DEnu_nu.cxx
 BEBC_CC1pi0_XSec_1DQ2_nu.cxx
 BEBC_CC1ppim_XSec_1DEnu_antinu.cxx
 BEBC_CC1ppim_XSec_1DQ2_antinu.cxx
 BEBC_CC1ppip_XSec_1DEnu_nu.cxx
 BEBC_CC1ppip_XSec_1DQ2_nu.cxx
 BEBC_CCQE_XSec_1DQ2_nu.cxx
 )
 
 set(HEADERFILES
 BEBC_CC1npim_XSec_1DEnu_antinu.h
 BEBC_CC1npim_XSec_1DQ2_antinu.h
 BEBC_CC1npip_XSec_1DEnu_nu.h
 BEBC_CC1npip_XSec_1DQ2_nu.h
 BEBC_CC1pi0_XSec_1DEnu_nu.h
 BEBC_CC1pi0_XSec_1DQ2_nu.h
 BEBC_CC1ppim_XSec_1DEnu_antinu.h
 BEBC_CC1ppim_XSec_1DQ2_antinu.h
 BEBC_CC1ppip_XSec_1DEnu_nu.h
 BEBC_CC1ppip_XSec_1DQ2_nu.h
 BEBC_CCQE_XSec_1DQ2_nu.h
 )
 
 set(LIBNAME expBEBC)
 
 if(CMAKE_BUILD_TYPE MATCHES DEBUG)
   add_library(${LIBNAME} STATIC ${IMPLFILES})
 else(CMAKE_BUILD_TYPE MATCHES RELEASE)
   add_library(${LIBNAME} SHARED ${IMPLFILES})
 endif()
 
 include_directories(${MINIMUM_INCLUDE_DIRECTORIES})
 
 set_target_properties(${LIBNAME} PROPERTIES VERSION
   "${NUISANCE_VERSION_MAJOR}.${NUISANCE_VERSION_MINOR}.${NUISANCE_VERSION_REVISION}")
 #set_target_properties(${LIBNAME} PROPERTIES LINK_FLAGS ${ROOT_LD_FLAGS})
 if(DEFINED PROJECTWIDE_EXTRA_DEPENDENCIES)
   add_dependencies(${LIBNAME} ${PROJECTWIDE_EXTRA_DEPENDENCIES})
 endif()
 install(TARGETS ${LIBNAME} DESTINATION lib)
 #Can uncomment this to install the headers... but is it really neccessary?
-#install(FILES ${HEADERFILES} DESTINATION include)
+install(FILES ${HEADERFILES} DESTINATION include/BNL)
 
 set(MODULETargets ${MODULETargets} ${LIBNAME} PARENT_SCOPE)
diff --git a/src/Config/CMakeLists.txt b/src/Config/CMakeLists.txt
index 7577b9d..64464af 100644
--- a/src/Config/CMakeLists.txt
+++ b/src/Config/CMakeLists.txt
@@ -1,52 +1,52 @@
 # 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/>.
 ################################################################################
 set(HEADERFILES
 NuisConfig.h
 NuisKey.h
 )
 
 set(IMPLFILES
 NuisConfig.cxx
 NuisKey.cxx
 )
 
 set(LIBNAME Config)
 
 if(CMAKE_BUILD_TYPE MATCHES DEBUG)
   add_library(${LIBNAME} STATIC ${IMPLFILES})
 else(CMAKE_BUILD_TYPE MATCHES RELEASE)
   add_library(${LIBNAME} SHARED ${IMPLFILES})
 endif()
 
 include_directories(${MINIMUM_INCLUDE_DIRECTORIES})
 
 set_target_properties(${LIBNAME} PROPERTIES VERSION
   "${NUISANCE_VERSION_MAJOR}.${NUISANCE_VERSION_MINOR}.${NUISANCE_VERSION_REVISION}")
 
 #set_target_properties(${LIBNAME} PROPERTIES LINK_FLAGS ${ROOT_LD_FLAGS})
 
 if(DEFINED PROJECTWIDE_EXTRA_DEPENDENCIES)
   add_dependencies(${LIBNAME} ${PROJECTWIDE_EXTRA_DEPENDENCIES})
 endif()
 
 install(TARGETS ${LIBNAME} DESTINATION lib)
 #Can uncomment this to install the headers... but is it really neccessary?
-#install(FILES ${HEADERFILES} DESTINATION include)
+install(FILES ${HEADERFILES} DESTINATION include/Config)
 
 set(MODULETargets ${MODULETargets} ${LIBNAME} PARENT_SCOPE)
diff --git a/src/Electron/CMakeLists.txt b/src/Electron/CMakeLists.txt
index 73dddc7..a785720 100644
--- a/src/Electron/CMakeLists.txt
+++ b/src/Electron/CMakeLists.txt
@@ -1,48 +1,48 @@
 # 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/>.
 ################################################################################
 set(IMPLFILES
 ElectronScattering_DurhamData.cxx
 )
 
 set(HEADERFILES
 ElectronScattering_DurhamData.h
 )
 
 
 set(LIBNAME expElectron)
 
 if(CMAKE_BUILD_TYPE MATCHES DEBUG)
   add_library(${LIBNAME} STATIC ${IMPLFILES})
 else(CMAKE_BUILD_TYPE MATCHES RELEASE)
   add_library(${LIBNAME} SHARED ${IMPLFILES})
 endif()
 
 include_directories(${MINIMUM_INCLUDE_DIRECTORIES})
 
 set_target_properties(${LIBNAME} PROPERTIES VERSION
   "${ExtFit_VERSION_MAJOR}.${ExtFit_VERSION_MINOR}.${ExtFit_VERSION_REVISION}")
 #set_target_properties(${LIBNAME} PROPERTIES LINK_FLAGS ${ROOT_LD_FLAGS})
 if(DEFINED PROJECTWIDE_EXTRA_DEPENDENCIES)
   add_dependencies(${LIBNAME} ${PROJECTWIDE_EXTRA_DEPENDENCIES})
 endif()
 install(TARGETS ${LIBNAME} DESTINATION lib)
 #Can uncomment this to install the headers... but is it really neccessary?
-#install(FILES ${HEADERFILES} DESTINATION include)
+install(FILES ${HEADERFILES} DESTINATION include/Electron)
 
 set(MODULETargets ${MODULETargets} ${LIBNAME} PARENT_SCOPE)
diff --git a/src/FCN/CMakeLists.txt b/src/FCN/CMakeLists.txt
index 9f3230c..fe490d3 100644
--- a/src/FCN/CMakeLists.txt
+++ b/src/FCN/CMakeLists.txt
@@ -1,59 +1,59 @@
 # 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/>.
 ################################################################################
 set(IMPLFILES
 JointFCN.cxx
 SampleList.cxx
 )
 
 set(HEADERFILES
 JointFCN.h
 MinimizerFCN.h
 SampleList.h
 )
 
 set(LIBNAME FCN)
 
 if(CMAKE_BUILD_TYPE MATCHES DEBUG)
   add_library(${LIBNAME} STATIC ${IMPLFILES})
 else(CMAKE_BUILD_TYPE MATCHES RELEASE)
   add_library(${LIBNAME} SHARED ${IMPLFILES})
 endif()
 
 include_directories(${MINIMUM_INCLUDE_DIRECTORIES})
 include_directories(${EXP_INCLUDE_DIRECTORIES})
 
 include_directories(${CMAKE_SOURCE_DIR}/src/Electron)
 
 include_directories(${CMAKE_SOURCE_DIR}/src/MCStudies)
 include_directories(${CMAKE_CURRENT_SOURCE_DIR})
 
 
 set_target_properties(${LIBNAME} PROPERTIES VERSION
   "${NUISANCE_VERSION_MAJOR}.${NUISANCE_VERSION_MINOR}.${NUISANCE_VERSION_REVISION}")
 #set_target_properties(${LIBNAME} PROPERTIES LINK_FLAGS ${ROOT_LD_FLAGS})
 
 if(DEFINED PROJECTWIDE_EXTRA_DEPENDENCIES)
   add_dependencies(${LIBNAME} ${PROJECTWIDE_EXTRA_DEPENDENCIES})
 endif()
 
 install(TARGETS ${LIBNAME} DESTINATION lib)
 #Can uncomment this to install the headers... but is it really neccessary?
-#install(FILES ${HEADERFILES} DESTINATION include)
+install(FILES ${HEADERFILES} DESTINATION include/FCN)
 
 set(MODULETargets ${MODULETargets} ${LIBNAME} PARENT_SCOPE)
diff --git a/src/FNAL/CMakeLists.txt b/src/FNAL/CMakeLists.txt
index 0ccebcb..d5b2748 100644
--- a/src/FNAL/CMakeLists.txt
+++ b/src/FNAL/CMakeLists.txt
@@ -1,55 +1,55 @@
 # 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/>.
 ################################################################################
 set(IMPLFILES
 FNAL_CC1ppip_Evt_1DQ2_nu.cxx
 FNAL_CC1ppip_XSec_1DEnu_nu.cxx
 FNAL_CC1ppip_XSec_1DQ2_nu.cxx
 FNAL_CCQE_Evt_1DQ2_nu.cxx
 FNAL_CC1ppim_XSec_1DEnu_antinu.cxx
 )
 
 set(HEADERFILES
 FNAL_CC1ppim_XSec_1DEnu_antinu.h
 FNAL_CC1ppip_Evt_1DQ2_nu.h
 FNAL_CC1ppip_XSec_1DEnu_nu.h
 FNAL_CC1ppip_XSec_1DQ2_nu.h
 FNAL_CCQE_Evt_1DQ2_nu.h
 )
 
 set(LIBNAME expFNAL)
 
 if(CMAKE_BUILD_TYPE MATCHES DEBUG)
   add_library(${LIBNAME} STATIC ${IMPLFILES})
 else(CMAKE_BUILD_TYPE MATCHES RELEASE)
   add_library(${LIBNAME} SHARED ${IMPLFILES})
 endif()
 
 include_directories(${MINIMUM_INCLUDE_DIRECTORIES})
 
 set_target_properties(${LIBNAME} PROPERTIES VERSION
   "${NUISANCE_VERSION_MAJOR}.${NUISANCE_VERSION_MINOR}.${NUISANCE_VERSION_REVISION}")
 #set_target_properties(${LIBNAME} PROPERTIES LINK_FLAGS ${ROOT_LD_FLAGS})
 if(DEFINED PROJECTWIDE_EXTRA_DEPENDENCIES)
   add_dependencies(${LIBNAME} ${PROJECTWIDE_EXTRA_DEPENDENCIES})
 endif()
 install(TARGETS ${LIBNAME} DESTINATION lib)
 #Can uncomment this to install the headers... but is it really neccessary?
-#install(FILES ${HEADERFILES} DESTINATION include)
+install(FILES ${HEADERFILES} DESTINATION include/FNAL)
 
 set(MODULETargets ${MODULETargets} ${LIBNAME} PARENT_SCOPE)
diff --git a/src/FitBase/CMakeLists.txt b/src/FitBase/CMakeLists.txt
index 91bfe86..165b94e 100644
--- a/src/FitBase/CMakeLists.txt
+++ b/src/FitBase/CMakeLists.txt
@@ -1,76 +1,75 @@
 # 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/>.
 ################################################################################
 set(IMPLFILES
 ParamPull.cxx
 EventManager.cxx
 Measurement1D.cxx
 Measurement2D.cxx
 JointMeas1D.cxx
 MeasurementBase.cxx
 TemplateMeas1D.cxx
 SampleSettings.cxx
 MeasurementVariableBox.cxx
 MeasurementVariableBox2D.cxx
 MeasurementVariableBox1D.cxx
-CustomVariableBoxes.h
 StandardStacks.cxx
 StackBase.cxx
 )
 
 set(HEADERFILES
 ParamPull.h
 JointMeas1D.h
 Measurement2D.h
 EventManager.h
 MeasurementBase.h
 Measurement1D.h
 TemplateMeas1D.h
 SampleSettings.h
 MeasurementVariableBox.h
 MeasurementVariableBox2D.h
 MeasurementVariableBox1D.h
 CustomVariableBoxes.h
 StandardStacks.h
 StackBase.h
 )
 
 set(LIBNAME FitBase)
 
 if(CMAKE_BUILD_TYPE MATCHES DEBUG)
   add_library(${LIBNAME} STATIC ${IMPLFILES})
 else(CMAKE_BUILD_TYPE MATCHES RELEASE)
   add_library(${LIBNAME} SHARED ${IMPLFILES})
 endif()
 
 include_directories(${MINIMUM_INCLUDE_DIRECTORIES})
 cmessage(DEBUG "FitBase includes: ${MINIMUM_INCLUDE_DIRECTORIES}")
 
 set_target_properties(${LIBNAME} PROPERTIES VERSION
   "${NUISANCE_VERSION_MAJOR}.${NUISANCE_VERSION_MINOR}.${NUISANCE_VERSION_REVISION}")
 #set_target_properties(${LIBNAME} PROPERTIES LINK_FLAGS ${ROOT_LD_FLAGS})
 
 if(DEFINED PROJECTWIDE_EXTRA_DEPENDENCIES)
   add_dependencies(${LIBNAME} ${PROJECTWIDE_EXTRA_DEPENDENCIES})
 endif()
 
 install(TARGETS ${LIBNAME} DESTINATION lib)
 #Can uncomment this to install the headers... but is it really neccessary?
-install(FILES ${HEADERFILES} DESTINATION include)
+install(FILES ${HEADERFILES} DESTINATION include/FitBase)
 
 set(MODULETargets ${MODULETargets} ${LIBNAME} PARENT_SCOPE)
diff --git a/src/GGM/CMakeLists.txt b/src/GGM/CMakeLists.txt
index 66bcead..39333e5 100644
--- a/src/GGM/CMakeLists.txt
+++ b/src/GGM/CMakeLists.txt
@@ -1,49 +1,49 @@
 # 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/>.
 ################################################################################
 set(IMPLFILES
 GGM_CC1ppip_Evt_1DQ2_nu.cxx
 GGM_CC1ppip_XSec_1DEnu_nu.cxx
 )
 
 set(HEADERFILES
 GGM_CC1ppip_Evt_1DQ2_nu.h
 GGM_CC1ppip_XSec_1DEnu_nu.h
 )
 
 set(LIBNAME expGGM)
 
 if(CMAKE_BUILD_TYPE MATCHES DEBUG)
   add_library(${LIBNAME} STATIC ${IMPLFILES})
 else(CMAKE_BUILD_TYPE MATCHES RELEASE)
   add_library(${LIBNAME} SHARED ${IMPLFILES})
 endif()
 
 include_directories(${MINIMUM_INCLUDE_DIRECTORIES})
 
 set_target_properties(${LIBNAME} PROPERTIES VERSION
   "${NUISANCE_VERSION_MAJOR}.${NUISANCE_VERSION_MINOR}.${NUISANCE_VERSION_REVISION}")
 #set_target_properties(${LIBNAME} PROPERTIES LINK_FLAGS ${ROOT_LD_FLAGS})
 if(DEFINED PROJECTWIDE_EXTRA_DEPENDENCIES)
   add_dependencies(${LIBNAME} ${PROJECTWIDE_EXTRA_DEPENDENCIES})
 endif()
 install(TARGETS ${LIBNAME} DESTINATION lib)
 #Can uncomment this to install the headers... but is it really neccessary?
-#install(FILES ${HEADERFILES} DESTINATION include)
+install(FILES ${HEADERFILES} DESTINATION include/GGM)
 
 set(MODULETargets ${MODULETargets} ${LIBNAME} PARENT_SCOPE)
diff --git a/src/InputHandler/CMakeLists.txt b/src/InputHandler/CMakeLists.txt
index 5b2cf1d..bf1f2a3 100644
--- a/src/InputHandler/CMakeLists.txt
+++ b/src/InputHandler/CMakeLists.txt
@@ -1,93 +1,92 @@
 # 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/>.
 ################################################################################
 set(IMPLFILES
 BaseFitEvt.cxx
 FitParticle.cxx
 FitEvent.cxx
 GeneratorUtils.cxx
 StdHepEvt.cxx
 InputUtils.cxx
 NEUTInputHandler.cxx
 GENIEInputHandler.cxx
 NuWroInputHandler.cxx
 GIBUUInputHandler.cxx
 NUANCEInputHandler.cxx
 InputHandler.cxx
 NuanceEvent.cxx
 FitEventInputHandler.cxx
 SplineInputHandler.cxx
 GeneratorInfoBase.h
-InputTypes.h
 HepMCTextInputHandler.cxx
 InputFactory.cxx
 SigmaQ0HistogramInputHandler.cxx
 HistogramInputHandler.cxx
 )
 
 set(HEADERFILES
-NuanceEvent.h
 BaseFitEvt.h
-FitEvent.h
 FitParticle.h
+FitEvent.h
 GeneratorUtils.h
 StdHepEvt.h
 InputUtils.h
 NEUTInputHandler.h
-HepMCTextInputHandler.h
 GENIEInputHandler.h
 NuWroInputHandler.h
-InputHandler.h
 GIBUUInputHandler.h
 NUANCEInputHandler.h
+InputHandler.h
+NuanceEvent.h
 FitEventInputHandler.h
 SplineInputHandler.h
 GeneratorInfoBase.h
+InputTypes.h
+HepMCTextInputHandler.h
 InputFactory.h
-InteractionModes.h
 SigmaQ0HistogramInputHandler.h
 HistogramInputHandler.h
 )
 
 set(LIBNAME InputHandler)
 
 if(CMAKE_BUILD_TYPE MATCHES DEBUG)
   add_library(${LIBNAME} STATIC ${IMPLFILES})
 else(CMAKE_BUILD_TYPE MATCHES RELEASE)
   add_library(${LIBNAME} SHARED ${IMPLFILES})
 endif()
 
 include_directories(${MINIMUM_INCLUDE_DIRECTORIES})
 
 set_target_properties(${LIBNAME} PROPERTIES VERSION
   "${ExtFit_VERSION_MAJOR}.${ExtFit_VERSION_MINOR}.${ExtFit_VERSION_REVISION}")
 #set_target_properties(${LIBNAME} PROPERTIES LINK_FLAGS ${ROOT_LD_FLAGS})
 
 if(DEFINED PROJECTWIDE_EXTRA_DEPENDENCIES)
   add_dependencies(${LIBNAME} ${PROJECTWIDE_EXTRA_DEPENDENCIES})
 endif()
 
 if(HEPMC_USED_EP)
   add_dependencies(${LIBNAME} HepMC)
 endif()
 
 install(TARGETS ${LIBNAME} DESTINATION lib)
 #Can uncomment this to install the headers... but is it really neccessary?
-install(FILES ${HEADERFILES} DESTINATION include)
+install(FILES ${HEADERFILES} DESTINATION include/InputHandler)
 
 set(MODULETargets ${MODULETargets} ${LIBNAME} PARENT_SCOPE)
diff --git a/src/K2K/CMakeLists.txt b/src/K2K/CMakeLists.txt
index 71ea0d5..6d0a3c5 100644
--- a/src/K2K/CMakeLists.txt
+++ b/src/K2K/CMakeLists.txt
@@ -1,47 +1,47 @@
 # 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/>.
 ################################################################################
 set(IMPLFILES
 K2K_NC1pi0_Evt_1Dppi0_nu.cxx
 )
 
 set(HEADERFILES
 K2K_NC1pi0_Evt_1Dppi0_nu.h
 )
 
 set(LIBNAME expK2K)
 
 if(CMAKE_BUILD_TYPE MATCHES DEBUG)
   add_library(${LIBNAME} STATIC ${IMPLFILES})
 else(CMAKE_BUILD_TYPE MATCHES RELEASE)
   add_library(${LIBNAME} SHARED ${IMPLFILES})
 endif()
 
 include_directories(${MINIMUM_INCLUDE_DIRECTORIES})
 
 set_target_properties(${LIBNAME} PROPERTIES VERSION
   "${NUISANCE_VERSION_MAJOR}.${NUISANCE_VERSION_MINOR}.${NUISANCE_VERSION_REVISION}")
 #set_target_properties(${LIBNAME} PROPERTIES LINK_FLAGS ${ROOT_LD_FLAGS})
 if(DEFINED PROJECTWIDE_EXTRA_DEPENDENCIES)
   add_dependencies(${LIBNAME} ${PROJECTWIDE_EXTRA_DEPENDENCIES})
 endif()
 install(TARGETS ${LIBNAME} DESTINATION lib)
 #Can uncomment this to install the headers... but is it really neccessary?
-#install(FILES ${HEADERFILES} DESTINATION include)
+install(FILES ${HEADERFILES} DESTINATION include/K2K)
 
 set(MODULETargets ${MODULETargets} ${LIBNAME} PARENT_SCOPE)
diff --git a/src/Logger/CMakeLists.txt b/src/Logger/CMakeLists.txt
index dee1fc1..f6c8e27 100644
--- a/src/Logger/CMakeLists.txt
+++ b/src/Logger/CMakeLists.txt
@@ -1,54 +1,53 @@
 # 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/>.
 ################################################################################
 set(HEADERFILES
 FitLogger.h
 Initialiser.h
 )
 
 set(IMPLFILES
 PythiaQuiet.f
 FitLogger.cxx
 Initialiser.cxx
 )
 
 set(LIBNAME Logger)
 
 if(CMAKE_BUILD_TYPE MATCHES DEBUG)
   add_library(${LIBNAME} STATIC ${IMPLFILES})
 else(CMAKE_BUILD_TYPE MATCHES RELEASE)
   add_library(${LIBNAME} SHARED ${IMPLFILES})
 endif()
 
 include_directories(${MINIMUM_INCLUDE_DIRECTORIES})
 
 set_target_properties(${LIBNAME} PROPERTIES VERSION
   "${NUISANCE_VERSION_MAJOR}.${NUISANCE_VERSION_MINOR}.${NUISANCE_VERSION_REVISION}")
 
 #set_target_properties(${LIBNAME} PROPERTIES LINK_FLAGS ${ROOT_LD_FLAGS})
 
 if(DEFINED PROJECTWIDE_EXTRA_DEPENDENCIES)
   add_dependencies(${LIBNAME} ${PROJECTWIDE_EXTRA_DEPENDENCIES})
 endif()
 
 install(TARGETS ${LIBNAME} DESTINATION lib)
 #Can uncomment this to install the headers... but is it really neccessary?
-#install(FILES ${HEADERFILES} DESTINATION include)
+install(FILES ${HEADERFILES} DESTINATION include/Logger)
 
 set(MODULETargets ${MODULETargets} ${LIBNAME} PARENT_SCOPE)
-
diff --git a/src/MCStudies/CMakeLists.txt b/src/MCStudies/CMakeLists.txt
index b77401f..0e979c2 100644
--- a/src/MCStudies/CMakeLists.txt
+++ b/src/MCStudies/CMakeLists.txt
@@ -1,81 +1,81 @@
 # 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/>.
 ################################################################################
 set(IMPLFILES
 ExpMultDist_CCQE_XSec_1DVar_FakeStudy.cxx
 ExpMultDist_CCQE_XSec_2DVar_FakeStudy.cxx
 GenericFlux_Tester.cxx
 GenericFlux_Vectors.cxx
 #MCStudy_KaonPreSelection.cxx
 MCStudy_MuonValidation.cxx
 ElectronFlux_FlatTree.cxx
 T2K2017_FakeData.cxx
 MCStudy_CCQEHistograms.cxx
 OfficialNIWGPlots.cxx
 Smearceptance_Tester.cxx
 Simple_Osc.cxx
 Smear_SVDUnfold_Propagation_Osc.cxx
 )
 
 set(HEADERFILES
 ExpMultDist_CCQE_XSec_1DVar_FakeStudy.h
 ExpMultDist_CCQE_XSec_2DVar_FakeStudy.h
 GenericFlux_Tester.h
 GenericFlux_Vectors.h
 #MCStudy_KaonPreSelection.h
 MCStudy_MuonValidation.h
 ElectronFlux_FlatTree.h
 T2K2017_FakeData.h
 MCStudy_CCQEHistograms.h
 OfficialNIWGPlots.h
 Smearceptance_Tester.h
 Simple_Osc.h
 Smear_SVDUnfold_Propagation_Osc.h
 )
 
 set(LIBNAME MCStudies)
 
 if(CMAKE_BUILD_TYPE MATCHES DEBUG)
   add_library(${LIBNAME} STATIC ${IMPLFILES})
 else(CMAKE_BUILD_TYPE MATCHES RELEASE)
   add_library(${LIBNAME} SHARED ${IMPLFILES})
 endif()
 
 include_directories(${MINIMUM_INCLUDE_DIRECTORIES})
 
 # Needed for experiment specific signal flags
 include_directories(${CMAKE_SOURCE_DIR}/src/T2K)
 include_directories(${CMAKE_SOURCE_DIR}/src/MINERvA)
 include_directories(${CMAKE_SOURCE_DIR}/src/Smearceptance)
 
 set_target_properties(${LIBNAME} PROPERTIES VERSION
   "${NUISANCE_VERSION_MAJOR}.${NUISANCE_VERSION_MINOR}.${NUISANCE_VERSION_REVISION}")
 #set_target_properties(${LIBNAME} PROPERTIES LINK_FLAGS ${ROOT_LD_FLAGS})
 if(DEFINED PROJECTWIDE_EXTRA_DEPENDENCIES)
   add_dependencies(${LIBNAME} ${PROJECTWIDE_EXTRA_DEPENDENCIES})
 endif()
 
 if(USE_PROB3PP)
   add_dependencies(${LIBNAME} prob3pp)
 endif()
 
 install(TARGETS ${LIBNAME} DESTINATION lib)
 #Can uncomment this to install the headers... but is it really neccessary?
-#install(FILES ${HEADERFILES} DESTINATION include)
+install(FILES ${HEADERFILES} DESTINATION include/MCStudies)
 
 set(MODULETargets ${MODULETargets} ${LIBNAME} PARENT_SCOPE)
diff --git a/src/MINERvA/CMakeLists.txt b/src/MINERvA/CMakeLists.txt
index a1e50b8..fb420a0 100644
--- a/src/MINERvA/CMakeLists.txt
+++ b/src/MINERvA/CMakeLists.txt
@@ -1,180 +1,180 @@
 # 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/>.
 ################################################################################
 set(IMPLFILES
 MINERvA_CCQE_XSec_1DQ2_antinu.cxx
 MINERvA_CCQE_XSec_1DQ2_joint.cxx
 MINERvA_CCQE_XSec_1DQ2_nu.cxx
 
 MINERvA_CC0pi_XSec_1DEe_nue.cxx
 MINERvA_CC0pi_XSec_1DQ2_nue.cxx
 MINERvA_CC0pi_XSec_1DQ2_nu_proton.cxx
 MINERvA_CC0pi_XSec_1DThetae_nue.cxx
 
 MINERvA_CC0pinp_STV_XSec_1D_nu.cxx
 
 MINERvA_CC1pi0_XSec_1DEnu_antinu.cxx
 MINERvA_CC1pi0_XSec_1DQ2_antinu.cxx
 MINERvA_CC1pi0_XSec_1Dpmu_antinu.cxx
 MINERvA_CC1pi0_XSec_1Dppi0_antinu.cxx
 MINERvA_CC1pi0_XSec_1DTpi0_antinu.cxx
 MINERvA_CC1pi0_XSec_1Dth_antinu.cxx
 MINERvA_CC1pi0_XSec_1Dthmu_antinu.cxx
 
 MINERvA_CC1pi0_XSec_1D_nu.cxx
 
 MINERvA_CC1pip_XSec_1DTpi_20deg_nu.cxx
 MINERvA_CC1pip_XSec_1DTpi_nu.cxx
 MINERvA_CC1pip_XSec_1Dth_20deg_nu.cxx
 MINERvA_CC1pip_XSec_1Dth_nu.cxx
 MINERvA_CC1pip_XSec_1D_2017Update.cxx
 
 MINERvA_CCNpip_XSec_1DEnu_nu.cxx
 MINERvA_CCNpip_XSec_1DQ2_nu.cxx
 MINERvA_CCNpip_XSec_1DTpi_nu.cxx
 MINERvA_CCNpip_XSec_1Dpmu_nu.cxx
 MINERvA_CCNpip_XSec_1Dth_nu.cxx
 MINERvA_CCNpip_XSec_1Dthmu_nu.cxx
 
 MINERvA_CCinc_XSec_2DEavq3_nu.cxx
 MINERvA_CCinc_XSec_1Dx_ratio.cxx
 MINERvA_CCinc_XSec_1DEnu_ratio.cxx
 MINERvA_CCinc_XSec_1Dx_nu.cxx
 MINERvA_CCinc_XSec_1DEnu_nu.cxx
 
 MINERvA_CCDIS_XSec_1Dx_ratio.cxx
 MINERvA_CCDIS_XSec_1DEnu_ratio.cxx
 MINERvA_CCDIS_XSec_1Dx_nu.cxx
 MINERvA_CCDIS_XSec_1DEnu_nu.cxx
 
 MINERvA_CC0pi_XSec_1DQ2_Tgt_nu.cxx
 MINERvA_CC0pi_XSec_1DQ2_TgtRatio_nu.cxx
 
 MINERvA_CC0pi_XSec_2D_antinu.cxx
 MINERvA_CC0pi_XSec_2D_nu.cxx
 # MINERvA_CC0pi_XSec_3DptpzTp_nu.cxx
 MINERvA_CC0pi_XSec_1D_2018_nu.cxx
 
 MINERvA_CCCOHPI_XSec_1DEnu_nu.cxx
 MINERvA_CCCOHPI_XSec_1DEpi_nu.cxx
 MINERvA_CCCOHPI_XSec_1Dth_nu.cxx
 MINERvA_CCCOHPI_XSec_1DQ2_nu.cxx
 
 MINERvA_CCCOHPI_XSec_1DEnu_antinu.cxx
 MINERvA_CCCOHPI_XSec_1DEpi_antinu.cxx
 MINERvA_CCCOHPI_XSec_1Dth_antinu.cxx
 MINERvA_CCCOHPI_XSec_1DQ2_antinu.cxx
 
 MINERvA_CCCOHPI_XSec_joint.cxx
 
 MINERvAUtils.cxx
 MINERvA_SignalDef.cxx
 )
 
 set(HEADERFILES
 MINERvA_CCQE_XSec_1DQ2_antinu.h
 MINERvA_CCQE_XSec_1DQ2_joint.h
 MINERvA_CCQE_XSec_1DQ2_nu.h
 
 MINERvA_CC0pi_XSec_1DEe_nue.h
 MINERvA_CC0pi_XSec_1DQ2_nue.h
 MINERvA_CC0pi_XSec_1DQ2_nu_proton.h
 MINERvA_CC0pi_XSec_1DThetae_nue.h
 
 MINERvA_CC0pinp_STV_XSec_1D_nu.h
 
 MINERvA_CC1pi0_XSec_1DEnu_antinu.h
 MINERvA_CC1pi0_XSec_1DQ2_antinu.h
 MINERvA_CC1pi0_XSec_1Dpmu_antinu.h
 MINERvA_CC1pi0_XSec_1Dppi0_antinu.h
 MINERvA_CC1pi0_XSec_1DTpi0_antinu.h
 MINERvA_CC1pi0_XSec_1Dth_antinu.h
 MINERvA_CC1pi0_XSec_1Dthmu_antinu.h
 
 MINERvA_CC1pip_XSec_1DTpi_20deg_nu.h
 MINERvA_CC1pip_XSec_1DTpi_nu.h
 MINERvA_CC1pip_XSec_1Dth_20deg_nu.h
 MINERvA_CC1pip_XSec_1Dth_nu.h
 
 MINERvA_CCNpip_XSec_1DEnu_nu.h
 MINERvA_CCNpip_XSec_1DQ2_nu.h
 MINERvA_CCNpip_XSec_1DTpi_nu.h
 MINERvA_CCNpip_XSec_1Dpmu_nu.h
 MINERvA_CCNpip_XSec_1Dth_nu.h
 MINERvA_CCNpip_XSec_1Dthmu_nu.h
 
 MINERvA_CCinc_XSec_2DEavq3_nu.h
 MINERvA_CCinc_XSec_1Dx_ratio.h
 MINERvA_CCinc_XSec_1DEnu_ratio.h
 MINERvA_CCinc_XSec_1Dx_nu.h
 MINERvA_CCinc_XSec_1DEnu_nu.h
 
 MINERvA_CCDIS_XSec_1Dx_ratio.h
 MINERvA_CCDIS_XSec_1DEnu_ratio.h
 MINERvA_CCDIS_XSec_1Dx_nu.h
 MINERvA_CCDIS_XSec_1DEnu_nu.h
 
 MINERvA_CC0pi_XSec_1DQ2_Tgt_nu.h
 MINERvA_CC0pi_XSec_1DQ2_TgtRatio_nu.h
 
 MINERvA_CC0pi_XSec_2D_antinu.h
 MINERvA_CC0pi_XSec_2D_nu.h
 # MINERvA_CC0pi_XSec_3DptpzTp_nu.h
 MINERvA_CC0pi_XSec_1D_2018_nu.h
 
 MINERvA_CC1pip_XSec_1D_2017Update.h
 
 MINERvA_CCCOHPI_XSec_1DEnu_nu.h
 MINERvA_CCCOHPI_XSec_1DEpi_nu.h
 MINERvA_CCCOHPI_XSec_1Dth_nu.h
 MINERvA_CCCOHPI_XSec_1DQ2_nu.h
 
 MINERvA_CCCOHPI_XSec_1DEnu_antinu.h
 MINERvA_CCCOHPI_XSec_1DEpi_antinu.h
 MINERvA_CCCOHPI_XSec_1Dth_antinu.h
 MINERvA_CCCOHPI_XSec_1DQ2_antinu.h
 
 MINERvA_CCCOHPI_XSec_joint.h
 
 MINERvAUtils.h
 MINERvA_SignalDef.h
 MINERvAVariableBoxes.h
 )
 
 set(LIBNAME expMINERvA)
 
 if(CMAKE_BUILD_TYPE MATCHES DEBUG)
   add_library(${LIBNAME} STATIC ${IMPLFILES})
 else(CMAKE_BUILD_TYPE MATCHES RELEASE)
   add_library(${LIBNAME} SHARED ${IMPLFILES})
 endif()
 
 include_directories(${MINIMUM_INCLUDE_DIRECTORIES})
 
 set_target_properties(${LIBNAME} PROPERTIES VERSION
   "${NUISANCE_VERSION_MAJOR}.${NUISANCE_VERSION_MINOR}.${NUISANCE_VERSION_REVISION}")
 #set_target_properties(${LIBNAME} PROPERTIES LINK_FLAGS ${ROOT_LD_FLAGS})
 if(DEFINED PROJECTWIDE_EXTRA_DEPENDENCIES)
   add_dependencies(${LIBNAME} ${PROJECTWIDE_EXTRA_DEPENDENCIES})
 endif()
 
 install(TARGETS ${LIBNAME} DESTINATION lib)
 #Can uncomment this to install the headers... but is it really neccessary?
-#install(FILES ${HEADERFILES} DESTINATION include)
+install(FILES ${HEADERFILES} DESTINATION include/MINERvA)
 
 set(MODULETargets ${MODULETargets} ${LIBNAME} PARENT_SCOPE)
diff --git a/src/MicroBooNE/CMakeLists.txt b/src/MicroBooNE/CMakeLists.txt
index 775d829..e5b18d4 100644
--- a/src/MicroBooNE/CMakeLists.txt
+++ b/src/MicroBooNE/CMakeLists.txt
@@ -1,48 +1,48 @@
 # 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/>.
 ################################################################################
 set(IMPLFILES
 MicroBooNE_CCInc_XSec_2DPcos_nu.cxx
 )
 
 set(HEADERFILES
 MicroBooNE_CCInc_XSec_2DPcos_nu.h
 )
 
 set(LIBNAME expMicroBooNE)
 
 if(CMAKE_BUILD_TYPE MATCHES DEBUG)
   add_library(${LIBNAME} STATIC ${IMPLFILES})
 else(CMAKE_BUILD_TYPE MATCHES RELEASE)
   add_library(${LIBNAME} SHARED ${IMPLFILES})
 endif()
 
 include_directories(${MINIMUM_INCLUDE_DIRECTORIES})
 
 set_target_properties(${LIBNAME} PROPERTIES VERSION
   "${NUISANCE_VERSION_MAJOR}.${NUISANCE_VERSION_MINOR}.${NUISANCE_VERSION_REVISION}")
 #set_target_properties(${LIBNAME} PROPERTIES LINK_FLAGS ${ROOT_LD_FLAGS})
 if(DEFINED PROJECTWIDE_EXTRA_DEPENDENCIES)
   add_dependencies(${LIBNAME} ${PROJECTWIDE_EXTRA_DEPENDENCIES})
 endif()
 
 install(TARGETS ${LIBNAME} DESTINATION lib)
 #Can uncomment this to install the headers... but is it really neccessary?
-#install(FILES ${HEADERFILES} DESTINATION include)
+install(FILES ${HEADERFILES} DESTINATION include/MicroBooNE)
 
 set(MODULETargets ${MODULETargets} ${LIBNAME} PARENT_SCOPE)
diff --git a/src/MiniBooNE/CMakeLists.txt b/src/MiniBooNE/CMakeLists.txt
index cf5e9a6..8d50ae3 100644
--- a/src/MiniBooNE/CMakeLists.txt
+++ b/src/MiniBooNE/CMakeLists.txt
@@ -1,95 +1,95 @@
 # 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/>.
 ################################################################################
 set(IMPLFILES
 MiniBooNE_CC1pi0_XSec_1Dcosmu_nu.cxx
 MiniBooNE_CC1pip_XSec_2DTpiCospi_nu.cxx
 MiniBooNE_CC1pi0_XSec_1Dcospi0_nu.cxx
 MiniBooNE_CC1pip_XSec_2DTpiEnu_nu.cxx
 MiniBooNE_CC1pi0_XSec_1DEnu_nu.cxx
 MiniBooNE_CC1pip_XSec_2DTuCosmu_nu.cxx
 MiniBooNE_CC1pi0_XSec_1Dppi0_nu.cxx
 MiniBooNE_CC1pip_XSec_2DTuEnu_nu.cxx
 MiniBooNE_CC1pi0_XSec_1DQ2_nu.cxx
 MiniBooNE_CCQE_XSec_1DQ2_antinu.cxx
 MiniBooNE_CC1pi0_XSec_1DTu_nu.cxx
 MiniBooNE_CC1pip_XSec_1DEnu_nu.cxx
 MiniBooNE_CCQE_XSec_1DQ2_nu.cxx
 MiniBooNE_CC1pip_XSec_1DQ2_nu.cxx
 MiniBooNE_CCQE_XSec_2DTcos_antinu.cxx
 MiniBooNE_CC1pip_XSec_1DTpi_nu.cxx
 MiniBooNE_CCQE_XSec_2DTcos_nu.cxx
 MiniBooNE_CC1pip_XSec_1DTu_nu.cxx
 MiniBooNE_NCEL_XSec_Treco_nu.cxx
 MiniBooNE_CC1pip_XSec_2DQ2Enu_nu.cxx
 MiniBooNE_NC1pi0_XSec_1Dppi0_nu.cxx
 MiniBooNE_NC1pi0_XSec_1Dcospi0_nu.cxx
 MiniBooNE_NC1pi0_XSec_1Dppi0_antinu.cxx
 MiniBooNE_NC1pi0_XSec_1Dcospi0_antinu.cxx
 )
 
 set(HEADERFILES
 MiniBooNE_CC1pi0_XSec_1Dcosmu_nu.h
 MiniBooNE_CC1pip_XSec_2DTpiCospi_nu.h
 MiniBooNE_CC1pi0_XSec_1Dcospi0_nu.h
 MiniBooNE_CC1pip_XSec_2DTpiEnu_nu.h
 MiniBooNE_CC1pi0_XSec_1DEnu_nu.h
 MiniBooNE_CC1pip_XSec_2DTuCosmu_nu.h
 MiniBooNE_CC1pi0_XSec_1Dppi0_nu.h
 MiniBooNE_CC1pip_XSec_2DTuEnu_nu.h
 MiniBooNE_CC1pi0_XSec_1DQ2_nu.h
 MiniBooNE_CCQE_XSec_1DQ2_antinu.h
 MiniBooNE_CC1pi0_XSec_1DTu_nu.h
 MiniBooNE_CC1pip_XSec_1DEnu_nu.h
 MiniBooNE_CCQE_XSec_1DQ2_nu.h
 MiniBooNE_CC1pip_XSec_1DQ2_nu.h
 MiniBooNE_CCQE_XSec_2DTcos_antinu.h
 MiniBooNE_CC1pip_XSec_1DTpi_nu.h
 MiniBooNE_CCQE_XSec_2DTcos_nu.h
 MiniBooNE_CC1pip_XSec_1DTu_nu.h
 MiniBooNE_NCEL_XSec_Treco_nu.h
 MiniBooNE_CC1pip_XSec_2DQ2Enu_nu.h
 MiniBooNE_NC1pi0_XSec_1Dppi0_nu.h
 MiniBooNE_NC1pi0_XSec_1Dcospi0_nu.h
 MiniBooNE_NC1pi0_XSec_1Dppi0_antinu.h
 MiniBooNE_NC1pi0_XSec_1Dcospi0_antinu.h
 MiniBooNE_Boxes.h
 )
 
 set(LIBNAME expMiniBooNE)
 
 if(CMAKE_BUILD_TYPE MATCHES DEBUG)
   add_library(${LIBNAME} STATIC ${IMPLFILES})
 else(CMAKE_BUILD_TYPE MATCHES RELEASE)
   add_library(${LIBNAME} SHARED ${IMPLFILES})
 endif()
 
 include_directories(${MINIMUM_INCLUDE_DIRECTORIES})
 
 set_target_properties(${LIBNAME} PROPERTIES VERSION
   "${NUISANCE_VERSION_MAJOR}.${NUISANCE_VERSION_MINOR}.${NUISANCE_VERSION_REVISION}")
 #set_target_properties(${LIBNAME} PROPERTIES LINK_FLAGS ${ROOT_LD_FLAGS})
 if(DEFINED PROJECTWIDE_EXTRA_DEPENDENCIES)
   add_dependencies(${LIBNAME} ${PROJECTWIDE_EXTRA_DEPENDENCIES})
 endif()
 
 install(TARGETS ${LIBNAME} DESTINATION lib)
 #Can uncomment this to install the headers... but is it really neccessary?
-#install(FILES ${HEADERFILES} DESTINATION include)
+install(FILES ${HEADERFILES} DESTINATION include/MiniBooNE)
 
 set(MODULETargets ${MODULETargets} ${LIBNAME} PARENT_SCOPE)
diff --git a/src/Reweight/CMakeLists.txt b/src/Reweight/CMakeLists.txt
index 00f4bda..2684e27 100644
--- a/src/Reweight/CMakeLists.txt
+++ b/src/Reweight/CMakeLists.txt
@@ -1,92 +1,92 @@
 # 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/>.
 ################################################################################
 set(IMPLFILES
 GlobalDialList.cxx
 FitWeight.cxx
 WeightEngineBase.cxx
 NEUTWeightEngine.cxx
 NuWroWeightEngine.cxx
 GENIEWeightEngine.cxx
 WeightUtils.cxx
 SampleNormEngine.cxx
 LikelihoodWeightEngine.cxx
 SplineWeightEngine.cxx
 NUISANCESyst.cxx
 T2KWeightEngine.cxx
 NUISANCEWeightEngine.cxx
 NUISANCEWeightCalcs.cxx
 NIWGWeightEngine.cxx
 OscWeightEngine.cxx
 MINERvAWeightCalcs.cxx
 weightRPA.h
 )
 
 if(USE_NOvARwgt)
   LIST(APPEND IMPLFILES NOvARwgtEngine.cxx)
 endif()
 
 set(HEADERFILES
 GlobalDialList.h
 FitWeight.h
 WeightEngineBase.h
 NEUTWeightEngine.h
 NuWroWeightEngine.h
 GENIEWeightEngine.h
 WeightUtils.h
 SampleNormEngine.h
 LikelihoodWeightEngine.h
 SplineWeightEngine.h
 NUISANCESyst.h
 T2KWeightEngine.h
 NUISANCEWeightEngine.h
 NUISANCEWeightCalcs.h
 NIWGWeightEngine.h
 OscWeightEngine.h
 MINERvAWeightCalcs.h
 weightRPA.h
 BeRPA.h
 )
 
 if(USE_NOvARwgt)
   LIST(APPEND HEADERFILES NOvARwgtEngine.h)
 endif()
 
 set(LIBNAME Reweight)
 
 if(CMAKE_BUILD_TYPE MATCHES DEBUG)
   add_library(${LIBNAME} STATIC ${IMPLFILES})
 else(CMAKE_BUILD_TYPE MATCHES RELEASE)
   add_library(${LIBNAME} SHARED ${IMPLFILES})
 endif()
 
 include_directories(${MINIMUM_INCLUDE_DIRECTORIES})
 
 set_target_properties(${LIBNAME} PROPERTIES VERSION
   "${ExtFit_VERSION_MAJOR}.${ExtFit_VERSION_MINOR}.${ExtFit_VERSION_REVISION}")
 #set_target_properties(${LIBNAME} PROPERTIES LINK_FLAGS ${ROOT_LD_FLAGS})
 
 if(DEFINED PROJECTWIDE_EXTRA_DEPENDENCIES)
   add_dependencies(${LIBNAME} ${PROJECTWIDE_EXTRA_DEPENDENCIES})
 endif()
 
 install(TARGETS ${LIBNAME} DESTINATION lib)
 #Can uncomment this to install the headers... but is it really neccessary?
-install(FILES ${HEADERFILES} DESTINATION include)
+install(FILES ${HEADERFILES} DESTINATION include/Reweight)
 
 set(MODULETargets ${MODULETargets} ${LIBNAME} PARENT_SCOPE)
diff --git a/src/Routines/CMakeLists.txt b/src/Routines/CMakeLists.txt
index a87e4a0..f55444f 100644
--- a/src/Routines/CMakeLists.txt
+++ b/src/Routines/CMakeLists.txt
@@ -1,68 +1,68 @@
 # 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/>.
 ################################################################################
 set(IMPLFILES
 ComparisonRoutines.cxx
 SystematicRoutines.cxx
 SplineRoutines.cxx
 BayesianRoutines.cxx
 )
 
 if(USE_MINIMIZER)
   set(IMPLFILES ${IMPLFILES};MinimizerRoutines.cxx)
 endif()
 
 set(HEADERFILES
 ComparisonRoutines.h
 SystematicRoutines.h
 BayesianRoutines.h
 SplineRoutines.h
 )
 
 if(USE_MINIMIZER)
   set(HEADERFILES ${HEADERFILES};MinimizerRoutines.h)
 endif()
 
 set(LIBNAME Routines)
 
 if(CMAKE_BUILD_TYPE MATCHES DEBUG)
   add_library(${LIBNAME} STATIC ${IMPLFILES})
 else(CMAKE_BUILD_TYPE MATCHES RELEASE)
   add_library(${LIBNAME} SHARED ${IMPLFILES})
 endif()
 
 include_directories(${EXP_INCLUDE_DIRECTORIES})
 
 include_directories(${MINIMUM_INCLUDE_DIRECTORIES})
 
 include_directories(${CMAKE_SOURCE_DIR}/src/FCN)
 include_directories(${CMAKE_SOURCE_DIR}/src/MCStudies)
 
 set_target_properties(${LIBNAME} PROPERTIES VERSION
   "${NUISANCE_VERSION_MAJOR}.${NUISANCE_VERSION_MINOR}.${NUISANCE_VERSION_REVISION}")
 #set_target_properties(${LIBNAME} PROPERTIES LINK_FLAGS ${ROOT_LD_FLAGS})
 
 if(DEFINED PROJECTWIDE_EXTRA_DEPENDENCIES)
   add_dependencies(${LIBNAME} ${PROJECTWIDE_EXTRA_DEPENDENCIES})
 endif()
 
 install(TARGETS ${LIBNAME} DESTINATION lib)
 #Can uncomment this to install the headers... but is it really neccessary?
-#install(FILES ${HEADERFILES} DESTINATION include)
+install(FILES ${HEADERFILES} DESTINATION include/Routines)
 
 set(MODULETargets ${MODULETargets} ${LIBNAME} PARENT_SCOPE)
diff --git a/src/SciBooNE/CMakeLists.txt b/src/SciBooNE/CMakeLists.txt
index 437afe9..9255c9f 100644
--- a/src/SciBooNE/CMakeLists.txt
+++ b/src/SciBooNE/CMakeLists.txt
@@ -1,77 +1,77 @@
 # 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/>.
 ################################################################################
 set(IMPLFILES
 SciBooNE_CCCOH_STOP_NTrks_nu.cxx
 SciBooNE_CCCOH_1TRK_1DQ2_nu.cxx
 SciBooNE_CCCOH_1TRK_1Dpmu_nu.cxx
-SciBooNE_CCCOH_1TRK_1Dthetamu_nu.cxx	
+SciBooNE_CCCOH_1TRK_1Dthetamu_nu.cxx
 SciBooNE_CCCOH_MuPr_1DQ2_nu.cxx
 SciBooNE_CCCOH_MuPr_1Dthetamu_nu.cxx
 SciBooNE_CCCOH_MuPr_1Dpmu_nu.cxx
 SciBooNE_CCCOH_MuPiVA_1DQ2_nu.cxx
 SciBooNE_CCCOH_MuPiVA_1Dthetamu_nu.cxx
 SciBooNE_CCCOH_MuPiVA_1Dpmu_nu.cxx
 SciBooNE_CCCOH_MuPiNoVA_1DQ2_nu.cxx
 SciBooNE_CCCOH_MuPiNoVA_1Dthetapr_nu.cxx
 SciBooNE_CCCOH_MuPiNoVA_1Dthetapi_nu.cxx
 SciBooNE_CCCOH_MuPiNoVA_1Dthetamu_nu.cxx
 SciBooNE_CCCOH_MuPiNoVA_1Dpmu_nu.cxx
 SciBooNE_CCCOH_STOPFINAL_1DQ2_nu.cxx
 SciBooNEUtils.cxx
 )
 
 set(HEADERFILES
 SciBooNE_CCCOH_STOP_NTrks_nu.h
 SciBooNE_CCCOH_1TRK_1DQ2_nu.h
 SciBooNE_CCCOH_1TRK_1Dpmu_nu.h
 SciBooNE_CCCOH_1TRK_1Dthetamu_nu.h
 SciBooNE_CCCOH_MuPr_1DQ2_nu.h
 SciBooNE_CCCOH_MuPr_1Dthetamu_nu.h
 SciBooNE_CCCOH_MuPr_1Dpmu_nu.h
 SciBooNE_CCCOH_MuPiVA_1DQ2_nu.h
 SciBooNE_CCCOH_MuPiVA_1Dthetamu_nu.h
 SciBooNE_CCCOH_MuPiVA_1Dpmu_nu.h
 SciBooNE_CCCOH_MuPiNoVA_1DQ2_nu.h
 SciBooNE_CCCOH_MuPiNoVA_1Dthetapr_nu.h
 SciBooNE_CCCOH_MuPiNoVA_1Dthetapi_nu.h
 SciBooNE_CCCOH_MuPiNoVA_1Dthetamu_nu.h
 SciBooNE_CCCOH_MuPiNoVA_1Dpmu_nu.h
 SciBooNE_CCCOH_STOPFINAL_1DQ2_nu.h
 SciBooNEUtils.h
 )
 
 set(LIBNAME expSciBooNE)
 
 if(CMAKE_BUILD_TYPE MATCHES DEBUG)
   add_library(${LIBNAME} STATIC ${IMPLFILES})
 else(CMAKE_BUILD_TYPE MATCHES RELEASE)
   add_library(${LIBNAME} SHARED ${IMPLFILES})
 endif()
 
 include_directories(${MINIMUM_INCLUDE_DIRECTORIES})
 
 set_target_properties(${LIBNAME} PROPERTIES VERSION
   "${ExtFit_VERSION_MAJOR}.${ExtFit_VERSION_MINOR}.${ExtFit_VERSION_REVISION}")
 #set_target_properties(${LIBNAME} PROPERTIES LINK_FLAGS ${ROOT_LD_FLAGS})
 
 install(TARGETS ${LIBNAME} DESTINATION lib)
 #Can uncomment this to install the headers... but is it really neccessary?
-#install(FILES ${HEADERFILES} DESTINATION include)
+install(FILES ${HEADERFILES} DESTINATION include/SciBooNE)
 
 set(MODULETargets ${MODULETargets} ${LIBNAME} PARENT_SCOPE)
diff --git a/src/Smearceptance/CMakeLists.txt b/src/Smearceptance/CMakeLists.txt
index cea1034..e8b2fb8 100644
--- a/src/Smearceptance/CMakeLists.txt
+++ b/src/Smearceptance/CMakeLists.txt
@@ -1,70 +1,70 @@
 # 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/>.
 ################################################################################
 set(HEADERFILES
 ISmearcepter.h
 Smearcepterton.h
 
 EfficiencyApplicator.h
 ThresholdAccepter.h
 TrackedMomentumMatrixSmearer.h
 GaussianSmearer.h
 
 EnergyShuffler.h
 
 MetaSimpleSmearcepter.h
 SmearceptanceUtils.h
 )
 
 set(IMPLFILES
 ISmearcepter.cxx
 Smearcepterton.cxx
 
 EfficiencyApplicator.cxx
 ThresholdAccepter.cxx
 TrackedMomentumMatrixSmearer.cxx
 GaussianSmearer.cxx
 
 EnergyShuffler.cxx
 
 MetaSimpleSmearcepter.cxx
 SmearceptanceUtils.cxx
 )
 
 set(LIBNAME Smearceptance)
 
 if(CMAKE_BUILD_TYPE MATCHES DEBUG)
   add_library(${LIBNAME} STATIC ${IMPLFILES})
 else(CMAKE_BUILD_TYPE MATCHES RELEASE)
   add_library(${LIBNAME} SHARED ${IMPLFILES})
 endif()
 
 include_directories(${MINIMUM_INCLUDE_DIRECTORIES})
 
 set_target_properties(${LIBNAME} PROPERTIES VERSION
   "${NUISANCE_VERSION_MAJOR}.${NUISANCE_VERSION_MINOR}.${NUISANCE_VERSION_REVISION}")
 
 if(DEFINED PROJECTWIDE_EXTRA_DEPENDENCIES)
   add_dependencies(${LIBNAME} ${PROJECTWIDE_EXTRA_DEPENDENCIES})
 endif()
 
 install(TARGETS ${LIBNAME} DESTINATION lib)
 #Can uncomment this to install the headers... but is it really neccessary?
-#install(FILES ${HEADERFILES} DESTINATION include)
+install(FILES ${HEADERFILES} DESTINATION include/Smearceptance)
 
 set(MODULETargets ${MODULETargets} ${LIBNAME} PARENT_SCOPE)
diff --git a/src/Splines/CMakeLists.txt b/src/Splines/CMakeLists.txt
index 58788d8..e02dd6a 100644
--- a/src/Splines/CMakeLists.txt
+++ b/src/Splines/CMakeLists.txt
@@ -1,56 +1,56 @@
 # 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/>.
 ################################################################################
 set(IMPLFILES
 SplineReader.cxx
 SplineWriter.cxx
 SplineMerger.cxx
 SplineUtils.cxx
 Spline.cxx
 )
 
 set(HEADERFILES
 SplineReader.h
 SplineWriter.h
 SplineUtils.h
 SplineMerger.h
 Spline.h
 )
 
 set(LIBNAME Splines)
 
 if(CMAKE_BUILD_TYPE MATCHES DEBUG)
   add_library(${LIBNAME} STATIC ${IMPLFILES})
 else(CMAKE_BUILD_TYPE MATCHES RELEASE)
   add_library(${LIBNAME} SHARED ${IMPLFILES})
 endif()
 
 include_directories(${MINIMUM_INCLUDE_DIRECTORIES})
 
 set_target_properties(${LIBNAME} PROPERTIES VERSION
   "${NUISANCE_VERSION_MAJOR}.${NUISANCE_VERSION_MINOR}.${NUISANCE_VERSION_REVISION}")
 #set_target_properties(${LIBNAME} PROPERTIES LINK_FLAGS ${ROOT_LD_FLAGS})
 if(DEFINED PROJECTWIDE_EXTRA_DEPENDENCIES)
   add_dependencies(${LIBNAME} ${PROJECTWIDE_EXTRA_DEPENDENCIES})
 endif()
 
 install(TARGETS ${LIBNAME} DESTINATION lib)
 #Can uncomment this to install the headers... but is it really neccessary?
-install(FILES ${HEADERFILES} DESTINATION include)
+install(FILES ${HEADERFILES} DESTINATION include/Splines)
 
 set(MODULETargets ${MODULETargets} ${LIBNAME} PARENT_SCOPE)
diff --git a/src/Statistical/CMakeLists.txt b/src/Statistical/CMakeLists.txt
index 7512473..5acd985 100644
--- a/src/Statistical/CMakeLists.txt
+++ b/src/Statistical/CMakeLists.txt
@@ -1,50 +1,50 @@
 # 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/>.
 ################################################################################
 set(HEADERFILES
 StatUtils.h
 )
 
 set(IMPLFILES
 StatUtils.cxx
 )
 
 set(LIBNAME Statistical)
 
 if(CMAKE_BUILD_TYPE MATCHES DEBUG)
   add_library(${LIBNAME} STATIC ${IMPLFILES})
 else(CMAKE_BUILD_TYPE MATCHES RELEASE)
   add_library(${LIBNAME} SHARED ${IMPLFILES})
 endif()
 
 include_directories(${MINIMUM_INCLUDE_DIRECTORIES})
 
 set_target_properties(${LIBNAME} PROPERTIES VERSION
   "${NUISANCE_VERSION_MAJOR}.${NUISANCE_VERSION_MINOR}.${NUISANCE_VERSION_REVISION}")
 
 #set_target_properties(${LIBNAME} PROPERTIES LINK_FLAGS ${ROOT_LD_FLAGS})
 
 if(DEFINED PROJECTWIDE_EXTRA_DEPENDENCIES)
   add_dependencies(${LIBNAME} ${PROJECTWIDE_EXTRA_DEPENDENCIES})
 endif()
 
 install(TARGETS ${LIBNAME} DESTINATION lib)
 #Can uncomment this to install the headers... but is it really neccessary?
-#install(FILES ${HEADERFILES} DESTINATION include)
+install(FILES ${HEADERFILES} DESTINATION include/Statistical)
 
 set(MODULETargets ${MODULETargets} ${LIBNAME} PARENT_SCOPE)
diff --git a/src/T2K/CMakeLists.txt b/src/T2K/CMakeLists.txt
index e410de2..6246dfe 100644
--- a/src/T2K/CMakeLists.txt
+++ b/src/T2K/CMakeLists.txt
@@ -1,102 +1,102 @@
 # 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/>.
 ################################################################################
 set(IMPLFILES
 T2K_CC0pi_XSec_2DPcos_nu_I.cxx
 T2K_CC0pi_XSec_2DPcos_nu_II.cxx
 T2K_CCinc_XSec_2DPcos_nu_nonuniform.cxx
 
 T2K_CC1pip_CH_XSec_2Dpmucosmu_nu.cxx
 T2K_CC1pip_CH_XSec_1Dppi_nu.cxx
 T2K_CC1pip_CH_XSec_1Dthpi_nu.cxx
 T2K_CC1pip_CH_XSec_1Dthmupi_nu.cxx
 T2K_CC1pip_CH_XSec_1DQ2_nu.cxx
 T2K_CC1pip_CH_XSec_1DAdlerPhi_nu.cxx
 T2K_CC1pip_CH_XSec_1DCosThAdler_nu.cxx
 
 T2K_CC1pip_H2O_XSec_1DEnuDelta_nu.cxx
 T2K_CC1pip_H2O_XSec_1DEnuMB_nu.cxx
 T2K_CC1pip_H2O_XSec_1Dcosmu_nu.cxx
 T2K_CC1pip_H2O_XSec_1Dcosmupi_nu.cxx
 T2K_CC1pip_H2O_XSec_1Dcospi_nu.cxx
 T2K_CC1pip_H2O_XSec_1Dpmu_nu.cxx
 T2K_CC1pip_H2O_XSec_1Dppi_nu.cxx
 
 T2K_CC0pinp_STV_XSec_1Ddpt_nu.cxx
 T2K_CC0pinp_STV_XSec_1Ddphit_nu.cxx
 T2K_CC0pinp_STV_XSec_1Ddat_nu.cxx
 T2K_CC0pi1p_XSec_3DPcoscos_nu_nonuniform.cxx
 T2K_CC0pinp_ifk_XSec_3Dinfp_nu.cxx
 T2K_CC0pinp_ifk_XSec_3Dinfa_nu.cxx
 T2K_CC0pinp_ifk_XSec_3Dinfip_nu.cxx
 T2K_SignalDef.cxx
 )
 
 set(HEADERFILES
 T2K_CC0pi_XSec_2DPcos_nu_I.h
 T2K_CC0pi_XSec_2DPcos_nu_II.h
 T2K_CCinc_XSec_2DPcos_nu_nonuniform.h
 
 T2K_CC1pip_CH_XSec_2Dpmucosmu_nu.h
 T2K_CC1pip_CH_XSec_1Dppi_nu.h
 T2K_CC1pip_CH_XSec_1Dthpi_nu.h
 T2K_CC1pip_CH_XSec_1Dthmupi_nu.h
 T2K_CC1pip_CH_XSec_1DQ2_nu.h
 T2K_CC1pip_CH_XSec_1DAdlerPhi_nu.h
 T2K_CC1pip_CH_XSec_1DCosThAdler_nu.h
 
 T2K_CC1pip_H2O_XSec_1DEnuDelta_nu.h
 T2K_CC1pip_H2O_XSec_1DEnuMB_nu.h
 T2K_CC1pip_H2O_XSec_1Dcosmu_nu.h
 T2K_CC1pip_H2O_XSec_1Dcosmupi_nu.h
 T2K_CC1pip_H2O_XSec_1Dcospi_nu.h
 T2K_CC1pip_H2O_XSec_1Dpmu_nu.h
 T2K_CC1pip_H2O_XSec_1Dppi_nu.h
 
 T2K_CC0pinp_STV_XSec_1Ddpt_nu.h
 T2K_CC0pinp_STV_XSec_1Ddphit_nu.h
 T2K_CC0pinp_STV_XSec_1Ddat_nu.h
 T2K_CC0pi1p_XSec_3DPcoscos_nu_nonuniform.h
 T2K_CC0pinp_ifk_XSec_3Dinfp_nu.h
 T2K_CC0pinp_ifk_XSec_3Dinfa_nu.h
 T2K_CC0pinp_ifk_XSec_3Dinfip_nu.h
 T2K_SignalDef.h
 )
 
 set(LIBNAME expT2K)
 
 if(CMAKE_BUILD_TYPE MATCHES DEBUG)
   add_library(${LIBNAME} STATIC ${IMPLFILES})
 else(CMAKE_BUILD_TYPE MATCHES RELEASE)
   add_library(${LIBNAME} SHARED ${IMPLFILES})
 endif()
 
 include_directories(${MINIMUM_INCLUDE_DIRECTORIES})
 
 set_target_properties(${LIBNAME} PROPERTIES VERSION
   "${NUISANCE_VERSION_MAJOR}.${NUISANCE_VERSION_MINOR}.${NUISANCE_VERSION_REVISION}")
 #set_target_properties(${LIBNAME} PROPERTIES LINK_FLAGS ${ROOT_LD_FLAGS})
 if(DEFINED PROJECTWIDE_EXTRA_DEPENDENCIES)
   add_dependencies(${LIBNAME} ${PROJECTWIDE_EXTRA_DEPENDENCIES})
 endif()
 
 install(TARGETS ${LIBNAME} DESTINATION lib)
 #Can uncomment this to install the headers... but is it really neccessary?
-#install(FILES ${HEADERFILES} DESTINATION include)
+install(FILES ${HEADERFILES} DESTINATION include/T2K)
 
 set(MODULETargets ${MODULETargets} ${LIBNAME} PARENT_SCOPE)
diff --git a/src/Utils/CMakeLists.txt b/src/Utils/CMakeLists.txt
index 25a22c4..a1dad16 100644
--- a/src/Utils/CMakeLists.txt
+++ b/src/Utils/CMakeLists.txt
@@ -1,77 +1,77 @@
 # 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/>.
 ################################################################################
 set(HEADERFILES
 FitUtils.h
 GeneralUtils.h
 ParserUtils.h
 PlotUtils.h
 SignalDef.h
 BeamUtils.h
 TargetUtils.h
 OpenMPWrapper.h
 PhysConst.h
 )
 
 set(IMPLFILES
 FitUtils.cxx
 GeneralUtils.cxx
 PlotUtils.cxx
 SignalDef.cxx
 BeamUtils.cxx
 TargetUtils.cxx
 ParserUtils.cxx
 )
 
 set(LIBNAME Utils)
 
 if(CMAKE_BUILD_TYPE MATCHES DEBUG)
   add_library(${LIBNAME} STATIC ${IMPLFILES})
 else(CMAKE_BUILD_TYPE MATCHES RELEASE)
   add_library(${LIBNAME} SHARED ${IMPLFILES})
 endif()
 
 include_directories(${MINIMUM_INCLUDE_DIRECTORIES})
 include_directories(${CMAKE_SOURCE_DIR}/src/Logger)
 include_directories(${CMAKE_SOURCE_DIR}/src/Statistical)
 
 set_target_properties(${LIBNAME} PROPERTIES VERSION
   "${NUISANCE_VERSION_MAJOR}.${NUISANCE_VERSION_MINOR}.${NUISANCE_VERSION_REVISION}")
 
 #set_target_properties(${LIBNAME} PROPERTIES LINK_FLAGS ${ROOT_LD_FLAGS})
 
 if(DEFINED PROJECTWIDE_EXTRA_DEPENDENCIES)
   add_dependencies(${LIBNAME} ${PROJECTWIDE_EXTRA_DEPENDENCIES})
 endif()
 
 install(TARGETS ${LIBNAME} DESTINATION lib)
 #Can uncomment this to install the headers... but is it really neccessary?
-#install(FILES ${HEADERFILES} DESTINATION include)
+install(FILES ${HEADERFILES} DESTINATION include/Utils)
 
 set(MODULETargets ${MODULETargets} ${LIBNAME} PARENT_SCOPE)
 
 #add_executable(DumpROOTClassesFromVector DumpROOTClassesFromVector.cxx GeneralUtils.cxx FitLogger.cxx PythiaQuiet.f)
 #
 #  #Strip out -lNuWro_event1
 #  string(REPLACE "-lNuWro_event1" "" NWEVSTRIPPED_CDF ${CMAKE_DEPENDLIB_FLAGS})
 #  cmessage(DEBUG "Attempted to strip out nuwro library: \"${CMAKE_DEPENDLIB_FLAGS}\" -> \"${NWEVSTRIPPED_CDF}\"")
 #  target_link_libraries(DumpROOTClassesFromVector ${NWEVSTRIPPED_CDF})
 #  if(NOT CMAKE_LINK_FLAGS STREQUAL "")
 #    set_target_properties(DumpROOTClassesFromVector PROPERTIES LINK_FLAGS ${CMAKE_LINK_FLAGS})
 #  endif()
 #install(TARGETS DumpROOTClassesFromVector DESTINATION bin)