diff --git a/CMakeLists.txt b/CMakeLists.txt
index d2537af..38aae55 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,80 +1,82 @@
 # Copyright 2018 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)
 
 set (NUISANCE_VERSION_MAJOR 3)
 set (NUISANCE_VERSION_MINOR 0)
 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)
 
 ################################# InputHandler #################################
 include(${CMAKE_SOURCE_DIR}/cmake/InputHandlerSetup.cmake)
 
 #################################  Pythia6/8 ###################################
 include(${CMAKE_SOURCE_DIR}/cmake/pythia6Setup.cmake)
 
 ################################## FHICLCPP ####################################
 include(${CMAKE_SOURCE_DIR}/cmake/fhiclcppSetup.cmake)
 
 #Need this to be at the front
 LIST(REVERSE EXTRA_CXX_FLAGS)
 LIST(APPEND EXTRA_CXX_FLAGS -I${CMAKE_SOURCE_DIR}/src)
 LIST(REVERSE EXTRA_CXX_FLAGS)
 
 ################################## COMPILER ####################################
 include(${CMAKE_SOURCE_DIR}/cmake/c++CompilerSetup.cmake)
 
 ################################################################################
 
 add_subdirectory(src)
 
 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})
+
+add_subdirectory(config)
diff --git a/cmake/setup.sh.in b/cmake/setup.sh.in
index 44d8d3f..95e2b09 100644
--- a/cmake/setup.sh.in
+++ b/cmake/setup.sh.in
@@ -1,159 +1,112 @@
 # 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/>.
 ################################################################################
 
 #!/bin/sh
 
 ### Adapted from https://unix.stackexchange.com/questions/4965/keep-duplicates-out-of-path-on-source
 function add_to_PATH () {
   for d; do
 
     d=$(cd -- "$d" && { pwd -P || pwd; }) 2>/dev/null  # canonicalize symbolic links
     if [ -z "$d" ]; then continue; fi  # skip nonexistent directory
 
     if [ "$d" == "/usr/bin" ] || [ "$d" == "/usr/bin64" ] || [ "$d" == "/usr/local/bin" ] || [ "$d" == "/usr/local/bin64" ]; then
       case ":$PATH:" in
         *":$d:"*) :;;
         *) export PATH=$PATH:$d;;
       esac
     else
       case ":$PATH:" in
         *":$d:"*) :;;
         *) export PATH=$d:$PATH;;
       esac
     fi
   done
 }
 
 function add_to_LD_LIBRARY_PATH () {
   for d; do
 
     d=$(cd -- "$d" && { pwd -P || pwd; }) 2>/dev/null  # canonicalize symbolic links
     if [ -z "$d" ]; then continue; fi  # skip nonexistent directory
 
     if [ "$d" == "/usr/lib" ] || [ "$d" == "/usr/lib64" ] || [ "$d" == "/usr/local/lib" ] || [ "$d" == "/usr/local/lib64" ]; then
       case ":$LD_LIBRARY_PATH:" in
         *":$d:"*) :;;
         *) export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$d;;
       esac
     else
       case ":$LD_LIBRARY_PATH:" in
         *":$d:"*) :;;
         *) export LD_LIBRARY_PATH=$d:$LD_LIBRARY_PATH;;
       esac
     fi
   done
 }
 
 if [ "@EXTRA_SETUP_SCRIPT@" ]; then
   if [ ! -e @EXTRA_SETUP_SCRIPT@ ]; then
       echo "[WARN]: Extra setup script \"@EXTRA_SETUP_SCRIPT@\" requested, but could not be found. Skipping..."
   else
     echo "[INFO]: Sourcing extra setup from \"@EXTRA_SETUP_SCRIPT@\"."
     . @EXTRA_SETUP_SCRIPT@
   fi
 fi
 
 add_to_PATH "@CMAKE_INSTALL_PREFIX@/bin"
 
 add_to_LD_LIBRARY_PATH "@CMAKE_INSTALL_PREFIX@/lib"
 
 if [ ! "${ROOTSYS}" ]; then
   echo "[INFO]: Sourcing ROOT from: @CMAKE_ROOTSYS@"
   source "@CMAKE_ROOTSYS@/bin/thisroot.sh"
 fi
 
-if [ "@USE_T2K@" != "FALSE" ]; then
-  echo "[INFO]: Adding T2K paths to the environment."
-  export T2KREWEIGHT=@T2KREWEIGHT@
-  add_to_LD_LIBRARY_PATH "@T2KREWEIGHT@/lib"
-fi
-
-if [ "@USE_NIWG@" != "FALSE" ]; then
-  echo "[INFO]: Adding NIWG paths to the environment."
-  export NIWG=@NIWG_ROOT@
-  export NIWGREWEIGHT_INPUTS=@NIWG_ROOT@/inputs
-  add_to_LD_LIBRARY_PATH "@NIWG_ROOT@"
-fi
-
 if [ "@USE_NEUT@" != "FALSE" ]; then
   echo "[INFO]: Adding NEUT library paths to the environment."
   export NEUT_ROOT=@NEUT_ROOT@
   export CERN=@CERN@
   export CERN_LEVEL=@CERN_LEVEL@
   add_to_LD_LIBRARY_PATH "${NEUT_LIB_DIR}" "${NEUT_ROOT}/src/reweight"
 fi
 
 if [ "@USE_NuWro@" != "FALSE" ]; then
-  if [ "@NUWRO_BUILT_FROM_FILE@" == "FALSE" ]; then
-    echo "[INFO]: Adding NuWro library paths to the environment."
-    export NUWRO="@NUWRO@"
-
-    add_to_PATH "@NUWRO@/bin"
-    add_to_LD_LIBRARY_PATH "@NUWRO@/build/@CMAKE_SYSTEM_NAME@/lib"
+  echo "[INFO]: Adding NuWro library paths to the environment."
+  export NUWRO="@NUWRO@"
 
-    if [ "@NUWRO_INC@" ]; then
-      export NUWRO_INC=@NUWRO_INC@
-    fi
+  add_to_PATH "@NUWRO@/bin"
+  add_to_LD_LIBRARY_PATH "@NUWRO@/build/@CMAKE_SYSTEM_NAME@/lib"
 
-  else
-    echo "[INFO]: NuWro support included from input event file."
+  if [ "@NUWRO_INC@" ]; then
+    export NUWRO_INC=@NUWRO_INC@
   fi
 fi
 
 if [ "@NEED_PYTHIA6@" != "FALSE" ]; then
   echo "[INFO]: Adding PYTHIA6 library paths to the environment."
   export PYTHIA6="@PYTHIA6@"
 
   add_to_LD_LIBRARY_PATH "@PYTHIA6@"
 fi
 
-if [ "@USE_GENIE@" != "FALSE" ]; then
-  echo "[INFO]: Adding GENIE paths to the environment."
-
-  export GENIE="@GENIE@"
-
-  export LHAPDF_LIB="@LHAPDF_LIB@"
-  export LHAPDF_INC="@LHAPDF_INC@"
-
-  export LIBXML2_LIB="@LIBXML2_LIB@"
-  export LIBXML2_INC="@LIBXML2_INC@"
-
-  export LOG4CPP_LIB="@LOG4CPP_LIB@"
-  export LOG4CPP_INC="@LOG4CPP_INC@"
-
-  if [ "@LHAPATH@" ]; then
-    export LHAPATH="@LHAPATH@"
-  fi
-
-  add_to_PATH "@GENIE@/bin"
-
-  add_to_LD_LIBRARY_PATH "@GENIE@/lib" "@LHAPDF_LIB@" "@LIBXML2_LIB@" "@LOG4CPP_LIB@"
-
-fi
-
-if [ "@BUILD_GiBUU@" != "FALSE" ]; then
-  echo "[INFO]: Sourcing GiBUU tools."
-  source @CMAKE_BINARY_DIR@/GiBUUTools/src/GiBUUTools-build/Linux/setup.sh
-fi
+source @CMAKE_INSTALL_PREFIX@/fhiclcpp.setup.sh
 
-if [ "@NUSYST_ROOT@" != "" ]; then
-  source @NUSYST_ROOT@/setup.sh
-fi
+add_to_FHICL_FILE_PATH @CMAKE_INSTALL_PREFIX@/fcl
 
 export NUISANCE="@CMAKE_SOURCE_DIR@"
diff --git a/config/CMakeLists.txt b/config/CMakeLists.txt
new file mode 100644
index 0000000..c7af5ef
--- /dev/null
+++ b/config/CMakeLists.txt
@@ -0,0 +1 @@
+add_subdirectory(global)
diff --git a/config/global/CMakeLists.txt b/config/global/CMakeLists.txt
new file mode 100644
index 0000000..307d738
--- /dev/null
+++ b/config/global/CMakeLists.txt
@@ -0,0 +1,13 @@
+configure_file(nuis.global.config.fcl.in
+  "${PROJECT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/nuis.global.config.fcl" @ONLY)
+
+install(FILES
+  "${PROJECT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/nuis.global.config.fcl" DESTINATION
+${CMAKE_INSTALL_PREFIX}/fcl)
+
+configure_file(nuis.datacomparisons.fcl.in
+"${PROJECT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/nuis.datacomparisons.fcl" @ONLY)
+
+install(FILES
+  "${PROJECT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/nuis.datacomparisons.fcl" DESTINATION
+${CMAKE_INSTALL_PREFIX}/fcl)
diff --git a/config/global/nuis.datacomparisons.fcl.in b/config/global/nuis.datacomparisons.fcl.in
new file mode 100644
index 0000000..565e6e9
--- /dev/null
+++ b/config/global/nuis.datacomparisons.fcl.in
@@ -0,0 +1,6 @@
+data_comparisons: {
+  nuA: [@INuADataComparisons_List@]
+  eA: []
+  piA: []
+  NA: []
+}
diff --git a/config/global/nuis.global.config.fcl.in b/config/global/nuis.global.config.fcl.in
new file mode 100644
index 0000000..aeb5331
--- /dev/null
+++ b/config/global/nuis.global.config.fcl.in
@@ -0,0 +1,12 @@
+plugins: {
+  search_paths: {
+    #Default plugin install directory
+    installed_plugins: [ @CMAKE_INSTALL_PREFIX@/plugins ]
+  }
+}
+
+data_dir: @CMAKE_INSTALL_PREFIX@/data
+
+persistency: {
+  default_output_file: nuis.out.root
+}
diff --git a/data/ANL/ANL_CCQE_BinMask_PRD26_537.dat b/data_old/ANL/ANL_CCQE_BinMask_PRD26_537.dat
similarity index 100%
rename from data/ANL/ANL_CCQE_BinMask_PRD26_537.dat
rename to data_old/ANL/ANL_CCQE_BinMask_PRD26_537.dat
diff --git a/data/ANL/ANL_CCQE_Data_PRD16_3103.root b/data_old/ANL/ANL_CCQE_Data_PRD16_3103.root
similarity index 100%
rename from data/ANL/ANL_CCQE_Data_PRD16_3103.root
rename to data_old/ANL/ANL_CCQE_Data_PRD16_3103.root
diff --git a/data/ANL/ANL_CCQE_Data_PRL31_844.root b/data_old/ANL/ANL_CCQE_Data_PRL31_844.root
similarity index 100%
rename from data/ANL/ANL_CCQE_Data_PRL31_844.root
rename to data_old/ANL/ANL_CCQE_Data_PRL31_844.root
diff --git a/data/ANL/ANL_Data_PRD26_537.root b/data_old/ANL/ANL_Data_PRD26_537.root
similarity index 100%
rename from data/ANL/ANL_Data_PRD26_537.root
rename to data_old/ANL/ANL_Data_PRD26_537.root
diff --git a/data/ANL/CC1pi0_on_n/ANL_CC1pi0_cosmuStar.csv b/data_old/ANL/CC1pi0_on_n/ANL_CC1pi0_cosmuStar.csv
similarity index 100%
rename from data/ANL/CC1pi0_on_n/ANL_CC1pi0_cosmuStar.csv
rename to data_old/ANL/CC1pi0_on_n/ANL_CC1pi0_cosmuStar.csv
diff --git a/data/ANL/CC1pi0_on_n/ANL_CC1pi0_on_n_noEvents_Q2_W14GeV.txt b/data_old/ANL/CC1pi0_on_n/ANL_CC1pi0_on_n_noEvents_Q2_W14GeV.txt
similarity index 100%
rename from data/ANL/CC1pi0_on_n/ANL_CC1pi0_on_n_noEvents_Q2_W14GeV.txt
rename to data_old/ANL/CC1pi0_on_n/ANL_CC1pi0_on_n_noEvents_Q2_W14GeV.txt
diff --git a/data/ANL/CC1pi0_on_n/ANL_CC1pi0_on_n_noEvents_Q2_W14GeV_firstQ2rem.txt b/data_old/ANL/CC1pi0_on_n/ANL_CC1pi0_on_n_noEvents_Q2_W14GeV_firstQ2rem.txt
similarity index 100%
rename from data/ANL/CC1pi0_on_n/ANL_CC1pi0_on_n_noEvents_Q2_W14GeV_firstQ2rem.txt
rename to data_old/ANL/CC1pi0_on_n/ANL_CC1pi0_on_n_noEvents_Q2_W14GeV_firstQ2rem.txt
diff --git a/data/ANL/CC1pi0_on_n/ANL_CC1pi0_on_n_noEvents_Q2_W14GeV_rebin.txt b/data_old/ANL/CC1pi0_on_n/ANL_CC1pi0_on_n_noEvents_Q2_W14GeV_rebin.txt
similarity index 100%
rename from data/ANL/CC1pi0_on_n/ANL_CC1pi0_on_n_noEvents_Q2_W14GeV_rebin.txt
rename to data_old/ANL/CC1pi0_on_n/ANL_CC1pi0_on_n_noEvents_Q2_W14GeV_rebin.txt
diff --git a/data/ANL/CC1pi0_on_n/ANL_CC1pi0_on_n_noEvents_Q2_W14GeV_rebin_firstQ2rem.txt b/data_old/ANL/CC1pi0_on_n/ANL_CC1pi0_on_n_noEvents_Q2_W14GeV_rebin_firstQ2rem.txt
similarity index 100%
rename from data/ANL/CC1pi0_on_n/ANL_CC1pi0_on_n_noEvents_Q2_W14GeV_rebin_firstQ2rem.txt
rename to data_old/ANL/CC1pi0_on_n/ANL_CC1pi0_on_n_noEvents_Q2_W14GeV_rebin_firstQ2rem.txt
diff --git a/data/ANL/CC1pi0_on_n/ANL_CC1pi0_on_n_noEvents_Q2_noWcut.txt b/data_old/ANL/CC1pi0_on_n/ANL_CC1pi0_on_n_noEvents_Q2_noWcut.txt
similarity index 100%
rename from data/ANL/CC1pi0_on_n/ANL_CC1pi0_on_n_noEvents_Q2_noWcut.txt
rename to data_old/ANL/CC1pi0_on_n/ANL_CC1pi0_on_n_noEvents_Q2_noWcut.txt
diff --git a/data/ANL/CC1pi0_on_n/ANL_CC1pi0_on_n_noEvents_Q2_noWcut_HighQ2Gone.txt b/data_old/ANL/CC1pi0_on_n/ANL_CC1pi0_on_n_noEvents_Q2_noWcut_HighQ2Gone.txt
similarity index 100%
rename from data/ANL/CC1pi0_on_n/ANL_CC1pi0_on_n_noEvents_Q2_noWcut_HighQ2Gone.txt
rename to data_old/ANL/CC1pi0_on_n/ANL_CC1pi0_on_n_noEvents_Q2_noWcut_HighQ2Gone.txt
diff --git a/data/ANL/CC1pi0_on_n/ANL_CC1pi0_on_n_noEvents_Q2_noWcut_firstQ2rem.txt b/data_old/ANL/CC1pi0_on_n/ANL_CC1pi0_on_n_noEvents_Q2_noWcut_firstQ2rem.txt
similarity index 100%
rename from data/ANL/CC1pi0_on_n/ANL_CC1pi0_on_n_noEvents_Q2_noWcut_firstQ2rem.txt
rename to data_old/ANL/CC1pi0_on_n/ANL_CC1pi0_on_n_noEvents_Q2_noWcut_firstQ2rem.txt
diff --git a/data/ANL/CC1pi0_on_n/anl82-numu-cc1pi0-14Wcut.txt b/data_old/ANL/CC1pi0_on_n/anl82-numu-cc1pi0-14Wcut.txt
similarity index 100%
rename from data/ANL/CC1pi0_on_n/anl82-numu-cc1pi0-14Wcut.txt
rename to data_old/ANL/CC1pi0_on_n/anl82-numu-cc1pi0-14Wcut.txt
diff --git a/data/ANL/CC1pi0_on_n/anl82-numu-cc1pi0-16Wcut.txt b/data_old/ANL/CC1pi0_on_n/anl82-numu-cc1pi0-16Wcut.txt
similarity index 100%
rename from data/ANL/CC1pi0_on_n/anl82-numu-cc1pi0-16Wcut.txt
rename to data_old/ANL/CC1pi0_on_n/anl82-numu-cc1pi0-16Wcut.txt
diff --git a/data/ANL/CC1pi0_on_n/anl82-numu-cc1pi0-noWcut.txt b/data_old/ANL/CC1pi0_on_n/anl82-numu-cc1pi0-noWcut.txt
similarity index 100%
rename from data/ANL/CC1pi0_on_n/anl82-numu-cc1pi0-noWcut.txt
rename to data_old/ANL/CC1pi0_on_n/anl82-numu-cc1pi0-noWcut.txt
diff --git a/data/ANL/CC1pi0_on_n/anl82corr-numu-n-to-mu-p-pi0-lowW_edges.txt b/data_old/ANL/CC1pi0_on_n/anl82corr-numu-n-to-mu-p-pi0-lowW_edges.txt
similarity index 100%
rename from data/ANL/CC1pi0_on_n/anl82corr-numu-n-to-mu-p-pi0-lowW_edges.txt
rename to data_old/ANL/CC1pi0_on_n/anl82corr-numu-n-to-mu-p-pi0-lowW_edges.txt
diff --git a/data/ANL/CC1pi0_on_n/anl82corr-numu-n-to-mu-p-pi0-noW_edges.txt b/data_old/ANL/CC1pi0_on_n/anl82corr-numu-n-to-mu-p-pi0-noW_edges.txt
similarity index 100%
rename from data/ANL/CC1pi0_on_n/anl82corr-numu-n-to-mu-p-pi0-noW_edges.txt
rename to data_old/ANL/CC1pi0_on_n/anl82corr-numu-n-to-mu-p-pi0-noW_edges.txt
diff --git a/data/ANL/CC1pip_on_n/ANL_CC1npip_cosmuStar.csv b/data_old/ANL/CC1pip_on_n/ANL_CC1npip_cosmuStar.csv
similarity index 100%
rename from data/ANL/CC1pip_on_n/ANL_CC1npip_cosmuStar.csv
rename to data_old/ANL/CC1pip_on_n/ANL_CC1npip_cosmuStar.csv
diff --git a/data/ANL/CC1pip_on_n/ANL_CC1pip_on_n_noEvents_Q2_W14GeV.txt b/data_old/ANL/CC1pip_on_n/ANL_CC1pip_on_n_noEvents_Q2_W14GeV.txt
similarity index 100%
rename from data/ANL/CC1pip_on_n/ANL_CC1pip_on_n_noEvents_Q2_W14GeV.txt
rename to data_old/ANL/CC1pip_on_n/ANL_CC1pip_on_n_noEvents_Q2_W14GeV.txt
diff --git a/data/ANL/CC1pip_on_n/ANL_CC1pip_on_n_noEvents_Q2_W14GeV_firstQ2rem.txt b/data_old/ANL/CC1pip_on_n/ANL_CC1pip_on_n_noEvents_Q2_W14GeV_firstQ2rem.txt
similarity index 100%
rename from data/ANL/CC1pip_on_n/ANL_CC1pip_on_n_noEvents_Q2_W14GeV_firstQ2rem.txt
rename to data_old/ANL/CC1pip_on_n/ANL_CC1pip_on_n_noEvents_Q2_W14GeV_firstQ2rem.txt
diff --git a/data/ANL/CC1pip_on_n/ANL_CC1pip_on_n_noEvents_Q2_W14GeV_rebin.txt b/data_old/ANL/CC1pip_on_n/ANL_CC1pip_on_n_noEvents_Q2_W14GeV_rebin.txt
similarity index 100%
rename from data/ANL/CC1pip_on_n/ANL_CC1pip_on_n_noEvents_Q2_W14GeV_rebin.txt
rename to data_old/ANL/CC1pip_on_n/ANL_CC1pip_on_n_noEvents_Q2_W14GeV_rebin.txt
diff --git a/data/ANL/CC1pip_on_n/ANL_CC1pip_on_n_noEvents_Q2_W14GeV_rebin_firstQ2rem.txt b/data_old/ANL/CC1pip_on_n/ANL_CC1pip_on_n_noEvents_Q2_W14GeV_rebin_firstQ2rem.txt
similarity index 100%
rename from data/ANL/CC1pip_on_n/ANL_CC1pip_on_n_noEvents_Q2_W14GeV_rebin_firstQ2rem.txt
rename to data_old/ANL/CC1pip_on_n/ANL_CC1pip_on_n_noEvents_Q2_W14GeV_rebin_firstQ2rem.txt
diff --git a/data/ANL/CC1pip_on_n/ANL_CC1pip_on_n_noEvents_Q2_noWcut.txt b/data_old/ANL/CC1pip_on_n/ANL_CC1pip_on_n_noEvents_Q2_noWcut.txt
similarity index 100%
rename from data/ANL/CC1pip_on_n/ANL_CC1pip_on_n_noEvents_Q2_noWcut.txt
rename to data_old/ANL/CC1pip_on_n/ANL_CC1pip_on_n_noEvents_Q2_noWcut.txt
diff --git a/data/ANL/CC1pip_on_n/ANL_CC1pip_on_n_noEvents_Q2_noWcut_HighQ2Gone.txt b/data_old/ANL/CC1pip_on_n/ANL_CC1pip_on_n_noEvents_Q2_noWcut_HighQ2Gone.txt
similarity index 100%
rename from data/ANL/CC1pip_on_n/ANL_CC1pip_on_n_noEvents_Q2_noWcut_HighQ2Gone.txt
rename to data_old/ANL/CC1pip_on_n/ANL_CC1pip_on_n_noEvents_Q2_noWcut_HighQ2Gone.txt
diff --git a/data/ANL/CC1pip_on_n/ANL_CC1pip_on_n_noEvents_Q2_noWcut_firstQ2rem.txt b/data_old/ANL/CC1pip_on_n/ANL_CC1pip_on_n_noEvents_Q2_noWcut_firstQ2rem.txt
similarity index 100%
rename from data/ANL/CC1pip_on_n/ANL_CC1pip_on_n_noEvents_Q2_noWcut_firstQ2rem.txt
rename to data_old/ANL/CC1pip_on_n/ANL_CC1pip_on_n_noEvents_Q2_noWcut_firstQ2rem.txt
diff --git a/data/ANL/CC1pip_on_n/ANL_ppi_CC1npip.csv b/data_old/ANL/CC1pip_on_n/ANL_ppi_CC1npip.csv
similarity index 100%
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diff --git a/data/ANL/CC1pip_on_n/anl82-numu-cc1npip-14Wcut.txt b/data_old/ANL/CC1pip_on_n/anl82-numu-cc1npip-14Wcut.txt
similarity index 100%
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diff --git a/data/ANL/CC1pip_on_n/anl82-numu-cc1npip-16Wcut.txt b/data_old/ANL/CC1pip_on_n/anl82-numu-cc1npip-16Wcut.txt
similarity index 100%
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diff --git a/data/ANL/CC1pip_on_n/anl82-numu-cc1npip-noWcut.txt b/data_old/ANL/CC1pip_on_n/anl82-numu-cc1npip-noWcut.txt
similarity index 100%
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diff --git a/data/ANL/CC1pip_on_n/anl82corr-numu-n-to-mu-n-piplus-lowW_edges.txt b/data_old/ANL/CC1pip_on_n/anl82corr-numu-n-to-mu-n-piplus-lowW_edges.txt
similarity index 100%
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diff --git a/data/ANL/CC1pip_on_n/anl82corr-numu-n-to-mu-n-piplus-noW_edges.txt b/data_old/ANL/CC1pip_on_n/anl82corr-numu-n-to-mu-n-piplus-noW_edges.txt
similarity index 100%
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diff --git a/data/ANL/CC1pip_on_p/ANL_CC1pip_on_p_dSigdQ2_W14_1982.txt b/data_old/ANL/CC1pip_on_p/ANL_CC1pip_on_p_dSigdQ2_W14_1982.txt
similarity index 100%
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diff --git a/data/ANL/CC1pip_on_p/ANL_CC1pip_on_p_noEvents_Q2_W14GeV.txt b/data_old/ANL/CC1pip_on_p/ANL_CC1pip_on_p_noEvents_Q2_W14GeV.txt
similarity index 100%
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diff --git a/data/ANL/CC1pip_on_p/ANL_CC1pip_on_p_noEvents_Q2_W14GeV_firstQ2rem.txt b/data_old/ANL/CC1pip_on_p/ANL_CC1pip_on_p_noEvents_Q2_W14GeV_firstQ2rem.txt
similarity index 100%
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diff --git a/data/ANL/CC1pip_on_p/ANL_CC1pip_on_p_noEvents_Q2_W14GeV_rebin.txt b/data_old/ANL/CC1pip_on_p/ANL_CC1pip_on_p_noEvents_Q2_W14GeV_rebin.txt
similarity index 100%
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diff --git a/data/ANL/CC1pip_on_p/ANL_CC1pip_on_p_noEvents_Q2_W14GeV_rebin_Q2_1GeV.txt b/data_old/ANL/CC1pip_on_p/ANL_CC1pip_on_p_noEvents_Q2_W14GeV_rebin_Q2_1GeV.txt
similarity index 100%
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diff --git a/data/ANL/CC1pip_on_p/ANL_CC1pip_on_p_noEvents_Q2_W14GeV_rebin_firstQ2rem.txt b/data_old/ANL/CC1pip_on_p/ANL_CC1pip_on_p_noEvents_Q2_W14GeV_rebin_firstQ2rem.txt
similarity index 100%
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diff --git a/data/ANL/CC1pip_on_p/ANL_CC1pip_on_p_noEvents_Q2_W14GeV_rebin_min20.txt b/data_old/ANL/CC1pip_on_p/ANL_CC1pip_on_p_noEvents_Q2_W14GeV_rebin_min20.txt
similarity index 100%
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diff --git a/data/ANL/CC1pip_on_p/ANL_CC1pip_on_p_noEvents_Q2_W14_firstQ2rem.txt b/data_old/ANL/CC1pip_on_p/ANL_CC1pip_on_p_noEvents_Q2_W14_firstQ2rem.txt
similarity index 100%
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diff --git a/data/ANL/CC1pip_on_p/ANL_CC1pip_on_p_noEvents_Q2_noW.txt b/data_old/ANL/CC1pip_on_p/ANL_CC1pip_on_p_noEvents_Q2_noW.txt
similarity index 100%
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diff --git a/data/ANL/CC1pip_on_p/ANL_CC1pip_on_p_noEvents_Q2_noW_HighQ2Gone.txt b/data_old/ANL/CC1pip_on_p/ANL_CC1pip_on_p_noEvents_Q2_noW_HighQ2Gone.txt
similarity index 100%
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diff --git a/data/ANL/CC1pip_on_p/ANL_CC1pip_on_p_noEvents_Q2_noW_firstQ2rem.txt b/data_old/ANL/CC1pip_on_p/ANL_CC1pip_on_p_noEvents_Q2_noW_firstQ2rem.txt
similarity index 100%
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diff --git a/data/ANL/CC1pip_on_p/ANL_CC1pip_on_p_noEvents_cosmuStar_1982.csv b/data_old/ANL/CC1pip_on_p/ANL_CC1pip_on_p_noEvents_cosmuStar_1982.csv
similarity index 100%
rename from data/ANL/CC1pip_on_p/ANL_CC1pip_on_p_noEvents_cosmuStar_1982.csv
rename to data_old/ANL/CC1pip_on_p/ANL_CC1pip_on_p_noEvents_cosmuStar_1982.csv
diff --git a/data/ANL/CC1pip_on_p/ANL_CC1pip_on_p_noEvents_costhAdler_1982.csv b/data_old/ANL/CC1pip_on_p/ANL_CC1pip_on_p_noEvents_costhAdler_1982.csv
similarity index 100%
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diff --git a/data/ANL/CC1pip_on_p/ANL_CC1pip_on_p_noEvents_phiAdler_1982.csv b/data_old/ANL/CC1pip_on_p/ANL_CC1pip_on_p_noEvents_phiAdler_1982.csv
similarity index 100%
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diff --git a/data/ANL/CC1pip_on_p/ANL_CC1pip_on_p_noEvents_ppi.csv b/data_old/ANL/CC1pip_on_p/ANL_CC1pip_on_p_noEvents_ppi.csv
similarity index 100%
rename from data/ANL/CC1pip_on_p/ANL_CC1pip_on_p_noEvents_ppi.csv
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diff --git a/data/ANL/CC1pip_on_p/ANL_CC1pip_on_p_noEvents_thProt.csv b/data_old/ANL/CC1pip_on_p/ANL_CC1pip_on_p_noEvents_thProt.csv
similarity index 100%
rename from data/ANL/CC1pip_on_p/ANL_CC1pip_on_p_noEvents_thProt.csv
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diff --git a/data/ANL/CC1pip_on_p/README b/data_old/ANL/CC1pip_on_p/README
similarity index 100%
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diff --git a/data/ANL/CC1pip_on_p/anl82-numu-cc1ppip-14Wcut.txt b/data_old/ANL/CC1pip_on_p/anl82-numu-cc1ppip-14Wcut.txt
similarity index 100%
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diff --git a/data/ANL/CC1pip_on_p/anl82-numu-cc1ppip-16Wcut.txt b/data_old/ANL/CC1pip_on_p/anl82-numu-cc1ppip-16Wcut.txt
similarity index 100%
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diff --git a/data/ANL/CC1pip_on_p/anl82-numu-cc1ppip-noWcut.txt b/data_old/ANL/CC1pip_on_p/anl82-numu-cc1ppip-noWcut.txt
similarity index 100%
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diff --git a/data/ANL/CC1pip_on_p/anl82corr-numu-p-to-mu-p-piplus-lowW_edges.txt b/data_old/ANL/CC1pip_on_p/anl82corr-numu-p-to-mu-p-piplus-lowW_edges.txt
similarity index 100%
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diff --git a/data/ANL/CC1pip_on_p/anl82corr-numu-p-to-mu-p-piplus-noW_edges.txt b/data_old/ANL/CC1pip_on_p/anl82corr-numu-p-to-mu-p-piplus-noW_edges.txt
similarity index 100%
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rename to data_old/ANL/CC1pip_on_p/anl82corr-numu-p-to-mu-p-piplus-noW_edges.txt
diff --git a/data/ANL/CC2pi/1pim1pip/CC2pi_1pim1pip1p_xsec.csv b/data_old/ANL/CC2pi/1pim1pip/CC2pi_1pim1pip1p_xsec.csv
similarity index 100%
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diff --git a/data/ANL/CC2pi/1pim1pip/CC2pi_1pim1pip_pMu_unweight.csv b/data_old/ANL/CC2pi/1pim1pip/CC2pi_1pim1pip_pMu_unweight.csv
similarity index 100%
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diff --git a/data/ANL/CC2pi/1pim1pip/CC2pi_1pim1pip_pMu_weight.csv b/data_old/ANL/CC2pi/1pim1pip/CC2pi_1pim1pip_pMu_weight.csv
similarity index 100%
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diff --git a/data/ANL/CC2pi/1pim1pip/CC2pi_1pim1pip_pProt_unweight.csv b/data_old/ANL/CC2pi/1pim1pip/CC2pi_1pim1pip_pProt_unweight.csv
similarity index 100%
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diff --git a/data/ANL/CC2pi/1pim1pip/CC2pi_1pim1pip_pProt_weight.csv b/data_old/ANL/CC2pi/1pim1pip/CC2pi_1pim1pip_pProt_weight.csv
similarity index 100%
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diff --git a/data/ANL/CC2pi/1pim1pip/CC2pi_1pim1pip_ppim_unweight.csv b/data_old/ANL/CC2pi/1pim1pip/CC2pi_1pim1pip_ppim_unweight.csv
similarity index 100%
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diff --git a/data/ANL/CC2pi/1pim1pip/CC2pi_1pim1pip_ppim_weight.csv b/data_old/ANL/CC2pi/1pim1pip/CC2pi_1pim1pip_ppim_weight.csv
similarity index 100%
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diff --git a/data/ANL/CC2pi/1pim1pip/CC2pi_1pim1pip_ppip_unweight.csv b/data_old/ANL/CC2pi/1pim1pip/CC2pi_1pim1pip_ppip_unweight.csv
similarity index 100%
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diff --git a/data/ANL/CC2pi/1pim1pip/CC2pi_1pim1pip_ppip_weight.csv b/data_old/ANL/CC2pi/1pim1pip/CC2pi_1pim1pip_ppip_weight.csv
similarity index 100%
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diff --git a/data/ANL/CC2pi/1pip1pi0/CC2pi_1pip1pi01p_xsec.csv b/data_old/ANL/CC2pi/1pip1pi0/CC2pi_1pip1pi01p_xsec.csv
similarity index 100%
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diff --git a/data/ANL/CC2pi/1pip1pi0/CC2pi_1pip1pi0_pMu_unweight.csv b/data_old/ANL/CC2pi/1pip1pi0/CC2pi_1pip1pi0_pMu_unweight.csv
similarity index 100%
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diff --git a/data/ANL/CC2pi/1pip1pi0/CC2pi_1pip1pi0_pMu_weight.csv b/data_old/ANL/CC2pi/1pip1pi0/CC2pi_1pip1pi0_pMu_weight.csv
similarity index 100%
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diff --git a/data/ANL/CC2pi/1pip1pi0/CC2pi_1pip1pi0_pProt_unweight.csv b/data_old/ANL/CC2pi/1pip1pi0/CC2pi_1pip1pi0_pProt_unweight.csv
similarity index 100%
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diff --git a/data/ANL/CC2pi/1pip1pi0/CC2pi_1pip1pi0_pProt_weight.csv b/data_old/ANL/CC2pi/1pip1pi0/CC2pi_1pip1pi0_pProt_weight.csv
similarity index 100%
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diff --git a/data/ANL/CC2pi/1pip1pi0/CC2pi_1pip1pi0_ppi0_unweight.csv b/data_old/ANL/CC2pi/1pip1pi0/CC2pi_1pip1pi0_ppi0_unweight.csv
similarity index 100%
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diff --git a/data/ANL/CC2pi/1pip1pi0/CC2pi_1pip1pi0_ppi0_weight.csv b/data_old/ANL/CC2pi/1pip1pi0/CC2pi_1pip1pi0_ppi0_weight.csv
similarity index 100%
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diff --git a/data/ANL/CC2pi/1pip1pi0/CC2pi_1pip1pi0_ppip_unweight.csv b/data_old/ANL/CC2pi/1pip1pi0/CC2pi_1pip1pi0_ppip_unweight.csv
similarity index 100%
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diff --git a/data/ANL/CC2pi/1pip1pi0/CC2pi_1pip1pi0_ppip_weight.csv b/data_old/ANL/CC2pi/1pip1pi0/CC2pi_1pip1pi0_ppip_weight.csv
similarity index 100%
rename from data/ANL/CC2pi/1pip1pi0/CC2pi_1pip1pi0_ppip_weight.csv
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diff --git a/data/ANL/CC2pi/1pip1pip/CC2pi_1pip1pip1n_pHigh_unweight.csv b/data_old/ANL/CC2pi/1pip1pip/CC2pi_1pip1pip1n_pHigh_unweight.csv
similarity index 100%
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diff --git a/data/ANL/CC2pi/1pip1pip/CC2pi_1pip1pip1n_pHigh_weight.csv b/data_old/ANL/CC2pi/1pip1pip/CC2pi_1pip1pip1n_pHigh_weight.csv
similarity index 100%
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diff --git a/data/ANL/CC2pi/1pip1pip/CC2pi_1pip1pip1n_pLow_unweight.csv b/data_old/ANL/CC2pi/1pip1pip/CC2pi_1pip1pip1n_pLow_unweight.csv
similarity index 100%
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diff --git a/data/ANL/CC2pi/1pip1pip/CC2pi_1pip1pip1n_pLow_weight.csv b/data_old/ANL/CC2pi/1pip1pip/CC2pi_1pip1pip1n_pLow_weight.csv
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diff --git a/data/MINERvA/CCcoh/raw/t13_nu_diffxsec-pionAngle_stat_covmatrix.csv b/data_old/MINERvA/CCcoh/raw/t13_nu_diffxsec-pionAngle_stat_covmatrix.csv
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diff --git a/data/MINERvA/CCcoh/raw/t19_nu_xsec-nuEnergy_stat_covmatrix.csv b/data_old/MINERvA/CCcoh/raw/t19_nu_xsec-nuEnergy_stat_covmatrix.csv
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diff --git a/data/MINERvA/CCinc/CCinc_C12_CH_ratio_Enu_covar.csv b/data_old/MINERvA/CCinc/CCinc_C12_CH_ratio_Enu_covar.csv
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diff --git a/data/MiniBooNE/CC1pi0/README b/data_old/MiniBooNE/CC1pi0/README
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diff --git a/data/MiniBooNE/CC1pi0/dxsecdq2.txt b/data_old/MiniBooNE/CC1pi0/dxsecdq2.txt
similarity index 100%
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diff --git a/data/MiniBooNE/CC1pi0/dxsecdq2_covar.txt b/data_old/MiniBooNE/CC1pi0/dxsecdq2_covar.txt
similarity index 100%
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diff --git a/data/MiniBooNE/CC1pi0/dxsecdq2_edit.txt b/data_old/MiniBooNE/CC1pi0/dxsecdq2_edit.txt
similarity index 100%
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diff --git a/data/MiniBooNE/CC1pi0/numuflux.txt b/data_old/MiniBooNE/CC1pi0/numuflux.txt
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diff --git a/data/MiniBooNE/CC1pi0/totalxsec.txt b/data_old/MiniBooNE/CC1pi0/totalxsec.txt
similarity index 100%
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diff --git a/data/MiniBooNE/CC1piRat/cc1pipccqerat_corr.txt b/data_old/MiniBooNE/CC1piRat/cc1pipccqerat_corr.txt
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diff --git a/data/MiniBooNE/CC1piRat/cc1pipccqerat_like.txt b/data_old/MiniBooNE/CC1piRat/cc1pipccqerat_like.txt
similarity index 100%
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diff --git a/data/MiniBooNE/CC1piRat/cc1pipccqerat_like_edit.txt b/data_old/MiniBooNE/CC1piRat/cc1pipccqerat_like_edit.txt
similarity index 100%
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diff --git a/data/MiniBooNE/CC1pip/ccpipXSecTables.txt b/data_old/MiniBooNE/CC1pip/ccpipXSecTables.txt
similarity index 100%
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diff --git a/data/MiniBooNE/CC1pip/ccpipXSec_KEmu.txt b/data_old/MiniBooNE/CC1pip/ccpipXSec_KEmu.txt
similarity index 100%
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similarity index 100%
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diff --git a/data/MiniBooNE/CC1pip/ccpipXSec_Q2.txt b/data_old/MiniBooNE/CC1pip/ccpipXSec_Q2.txt
similarity index 100%
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diff --git a/data/MiniBooNE/CC1pip/ccpipXSec_cosmu_KEmu.txt b/data_old/MiniBooNE/CC1pip/ccpipXSec_cosmu_KEmu.txt
similarity index 100%
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diff --git a/data/MiniBooNE/CC1pip/ccpipXSec_enu.txt b/data_old/MiniBooNE/CC1pip/ccpipXSec_enu.txt
similarity index 100%
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similarity index 100%
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diff --git a/data/MiniBooNE/NC1pi0/combinedsignnubarmodecosthetapi0binedges.txt b/data_old/MiniBooNE/NC1pi0/combinedsignnubarmodecosthetapi0binedges.txt
similarity index 100%
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diff --git a/data/MiniBooNE/NC1pi0/combinedsignnubarmodecosthetapi0xsec.txt b/data_old/MiniBooNE/NC1pi0/combinedsignnubarmodecosthetapi0xsec.txt
similarity index 100%
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diff --git a/data/MiniBooNE/NC1pi0/combinedsignnubarmodecosthetapi0xsec_edit.txt b/data_old/MiniBooNE/NC1pi0/combinedsignnubarmodecosthetapi0xsec_edit.txt
similarity index 100%
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diff --git a/data/MiniBooNE/NC1pi0/combinedsignnubarmodecosthetapi0xsecerrormatrix.txt b/data_old/MiniBooNE/NC1pi0/combinedsignnubarmodecosthetapi0xsecerrormatrix.txt
similarity index 100%
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diff --git a/data/MiniBooNE/NC1pi0/combinedsignnubarmodeppi0binedges.txt b/data_old/MiniBooNE/NC1pi0/combinedsignnubarmodeppi0binedges.txt
similarity index 100%
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diff --git a/data/MiniBooNE/NC1pi0/combinedsignnubarmodeppi0xsec.txt b/data_old/MiniBooNE/NC1pi0/combinedsignnubarmodeppi0xsec.txt
similarity index 100%
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diff --git a/data/MiniBooNE/NC1pi0/combinedsignnubarmodeppi0xsec_edit.txt b/data_old/MiniBooNE/NC1pi0/combinedsignnubarmodeppi0xsec_edit.txt
similarity index 100%
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diff --git a/data/MiniBooNE/NC1pi0/combinedsignnubarmodeppi0xsecerrormatrix.txt b/data_old/MiniBooNE/NC1pi0/combinedsignnubarmodeppi0xsecerrormatrix.txt
similarity index 100%
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diff --git a/data/MiniBooNE/NC1pi0/combinedsignnumodecosthetapi0binedges.txt b/data_old/MiniBooNE/NC1pi0/combinedsignnumodecosthetapi0binedges.txt
similarity index 100%
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diff --git a/data/MiniBooNE/NC1pi0/combinedsignnumodecosthetapi0xsec.txt b/data_old/MiniBooNE/NC1pi0/combinedsignnumodecosthetapi0xsec.txt
similarity index 100%
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diff --git a/data/MiniBooNE/NC1pi0/combinedsignnumodecosthetapi0xsec_edit.txt b/data_old/MiniBooNE/NC1pi0/combinedsignnumodecosthetapi0xsec_edit.txt
similarity index 100%
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diff --git a/data/MiniBooNE/NC1pi0/combinedsignnumodecosthetapi0xsecerrormatrix.txt b/data_old/MiniBooNE/NC1pi0/combinedsignnumodecosthetapi0xsecerrormatrix.txt
similarity index 100%
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diff --git a/data/MiniBooNE/NC1pi0/combinedsignnumodeppi0binedges.txt b/data_old/MiniBooNE/NC1pi0/combinedsignnumodeppi0binedges.txt
similarity index 100%
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diff --git a/data/MiniBooNE/NC1pi0/combinedsignnumodeppi0xsec.txt b/data_old/MiniBooNE/NC1pi0/combinedsignnumodeppi0xsec.txt
similarity index 100%
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diff --git a/data/MiniBooNE/NC1pi0/combinedsignnumodeppi0xsec_edit.txt b/data_old/MiniBooNE/NC1pi0/combinedsignnumodeppi0xsec_edit.txt
similarity index 100%
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diff --git a/data/MiniBooNE/NC1pi0/combinedsignnumodeppi0xsecerrormatrix.txt b/data_old/MiniBooNE/NC1pi0/combinedsignnumodeppi0xsecerrormatrix.txt
similarity index 100%
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diff --git a/data/MiniBooNE/NC1pi0/nubarcosthetapi0binedges.txt b/data_old/MiniBooNE/NC1pi0/nubarcosthetapi0binedges.txt
similarity index 100%
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diff --git a/data/MiniBooNE/NC1pi0/nubarcosthetapi0xsec.txt b/data_old/MiniBooNE/NC1pi0/nubarcosthetapi0xsec.txt
similarity index 100%
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diff --git a/data/MiniBooNE/NC1pi0/nubarcosthetapi0xsec_edit.txt b/data_old/MiniBooNE/NC1pi0/nubarcosthetapi0xsec_edit.txt
similarity index 100%
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diff --git a/data/MiniBooNE/NC1pi0/nubarcosthetapi0xsecerrormatrix.txt b/data_old/MiniBooNE/NC1pi0/nubarcosthetapi0xsecerrormatrix.txt
similarity index 100%
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diff --git a/data/MiniBooNE/NC1pi0/nubarppi0binedges.txt b/data_old/MiniBooNE/NC1pi0/nubarppi0binedges.txt
similarity index 100%
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diff --git a/data/MiniBooNE/NC1pi0/nubarppi0xsec.txt b/data_old/MiniBooNE/NC1pi0/nubarppi0xsec.txt
similarity index 100%
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diff --git a/data/MiniBooNE/NC1pi0/nubarppi0xsec_edit.txt b/data_old/MiniBooNE/NC1pi0/nubarppi0xsec_edit.txt
similarity index 100%
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diff --git a/data/MiniBooNE/NC1pi0/nubarppi0xsecerrormatrix.txt b/data_old/MiniBooNE/NC1pi0/nubarppi0xsecerrormatrix.txt
similarity index 100%
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diff --git a/data/MiniBooNE/NC1pi0/nucosthetapi0binedges.txt b/data_old/MiniBooNE/NC1pi0/nucosthetapi0binedges.txt
similarity index 100%
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diff --git a/data/MiniBooNE/NC1pi0/nucosthetapi0xsec.txt b/data_old/MiniBooNE/NC1pi0/nucosthetapi0xsec.txt
similarity index 100%
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diff --git a/data/MiniBooNE/NC1pi0/nucosthetapi0xsec_edit.txt b/data_old/MiniBooNE/NC1pi0/nucosthetapi0xsec_edit.txt
similarity index 100%
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diff --git a/data/MiniBooNE/NC1pi0/nucosthetapi0xsecerrormatrix.txt b/data_old/MiniBooNE/NC1pi0/nucosthetapi0xsecerrormatrix.txt
similarity index 100%
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diff --git a/data/MiniBooNE/NC1pi0/nuppi0binedges.txt b/data_old/MiniBooNE/NC1pi0/nuppi0binedges.txt
similarity index 100%
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diff --git a/data/MiniBooNE/NC1pi0/nuppi0xsec.txt b/data_old/MiniBooNE/NC1pi0/nuppi0xsec.txt
similarity index 100%
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similarity index 100%
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similarity index 100%
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diff --git a/data/MiniBooNE/anti-ccqe/aski_bkg_ccpim.txt b/data_old/MiniBooNE/anti-ccqe/aski_bkg_ccpim.txt
similarity index 100%
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diff --git a/data/MiniBooNE/anti-ccqe/aski_bkg_ccqe.txt b/data_old/MiniBooNE/anti-ccqe/aski_bkg_ccqe.txt
similarity index 100%
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diff --git a/data/MiniBooNE/anti-ccqe/aski_con.txt b/data_old/MiniBooNE/anti-ccqe/aski_con.txt
similarity index 100%
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similarity index 100%
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diff --git a/data/MiniBooNE/anti-ccqe/asqq_bkg_ccpim.txt b/data_old/MiniBooNE/anti-ccqe/asqq_bkg_ccpim.txt
similarity index 100%
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similarity index 100%
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diff --git a/data/MiniBooNE/anti-ccqe/asqq_con.txt b/data_old/MiniBooNE/anti-ccqe/asqq_con.txt
similarity index 100%
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similarity index 100%
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diff --git a/data/MiniBooNE/anti-ccqe/asqq_like.txt b/data_old/MiniBooNE/anti-ccqe/asqq_like.txt
similarity index 100%
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diff --git a/data/MiniBooNE/ccqe/MB_numu_1D_data_rebin_data.txt b/data_old/MiniBooNE/ccqe/MB_numu_1D_data_rebin_data.txt
similarity index 100%
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diff --git a/data/MiniBooNE/ccqe/all.xls b/data_old/MiniBooNE/ccqe/all.xls
similarity index 100%
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diff --git a/data/MiniBooNE/ccqe/aski_bkg.txt b/data_old/MiniBooNE/ccqe/aski_bkg.txt
similarity index 100%
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similarity index 100%
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similarity index 100%
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rename from data/T2K/CC0pi/rps_systCov_analysis2.txt
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diff --git a/data/T2K/CC1pip/H2O/README b/data_old/T2K/CC1pip/H2O/README
similarity index 100%
rename from data/T2K/CC1pip/H2O/README
rename to data_old/T2K/CC1pip/H2O/README
diff --git a/data/T2K/CC1pip/H2O/nd280data-numu-cc1pi-xs-on-h2o-2015.root b/data_old/T2K/CC1pip/H2O/nd280data-numu-cc1pi-xs-on-h2o-2015.root
similarity index 100%
rename from data/T2K/CC1pip/H2O/nd280data-numu-cc1pi-xs-on-h2o-2015.root
rename to data_old/T2K/CC1pip/H2O/nd280data-numu-cc1pi-xs-on-h2o-2015.root
diff --git a/data/T2K/CC1pip/H2O/raw/README.pdf b/data_old/T2K/CC1pip/H2O/raw/README.pdf
similarity index 100%
rename from data/T2K/CC1pip/H2O/raw/README.pdf
rename to data_old/T2K/CC1pip/H2O/raw/README.pdf
diff --git a/data/T2K/CC1pip/H2O/raw/nd280data-numu-cc1pi-xs-on-h2o-2015-EnuRec_Delta.csv b/data_old/T2K/CC1pip/H2O/raw/nd280data-numu-cc1pi-xs-on-h2o-2015-EnuRec_Delta.csv
similarity index 100%
rename from data/T2K/CC1pip/H2O/raw/nd280data-numu-cc1pi-xs-on-h2o-2015-EnuRec_Delta.csv
rename to data_old/T2K/CC1pip/H2O/raw/nd280data-numu-cc1pi-xs-on-h2o-2015-EnuRec_Delta.csv
diff --git a/data/T2K/CC1pip/H2O/raw/nd280data-numu-cc1pi-xs-on-h2o-2015-EnuRec_MB.csv b/data_old/T2K/CC1pip/H2O/raw/nd280data-numu-cc1pi-xs-on-h2o-2015-EnuRec_MB.csv
similarity index 100%
rename from data/T2K/CC1pip/H2O/raw/nd280data-numu-cc1pi-xs-on-h2o-2015-EnuRec_MB.csv
rename to data_old/T2K/CC1pip/H2O/raw/nd280data-numu-cc1pi-xs-on-h2o-2015-EnuRec_MB.csv
diff --git a/data/T2K/CC1pip/H2O/raw/nd280data-numu-cc1pi-xs-on-h2o-2015-MuCos.csv b/data_old/T2K/CC1pip/H2O/raw/nd280data-numu-cc1pi-xs-on-h2o-2015-MuCos.csv
similarity index 100%
rename from data/T2K/CC1pip/H2O/raw/nd280data-numu-cc1pi-xs-on-h2o-2015-MuCos.csv
rename to data_old/T2K/CC1pip/H2O/raw/nd280data-numu-cc1pi-xs-on-h2o-2015-MuCos.csv
diff --git a/data/T2K/CC1pip/H2O/raw/nd280data-numu-cc1pi-xs-on-h2o-2015-MuMom.csv b/data_old/T2K/CC1pip/H2O/raw/nd280data-numu-cc1pi-xs-on-h2o-2015-MuMom.csv
similarity index 100%
rename from data/T2K/CC1pip/H2O/raw/nd280data-numu-cc1pi-xs-on-h2o-2015-MuMom.csv
rename to data_old/T2K/CC1pip/H2O/raw/nd280data-numu-cc1pi-xs-on-h2o-2015-MuMom.csv
diff --git a/data/T2K/CC1pip/H2O/raw/nd280data-numu-cc1pi-xs-on-h2o-2015-MuPiCos.csv b/data_old/T2K/CC1pip/H2O/raw/nd280data-numu-cc1pi-xs-on-h2o-2015-MuPiCos.csv
similarity index 100%
rename from data/T2K/CC1pip/H2O/raw/nd280data-numu-cc1pi-xs-on-h2o-2015-MuPiCos.csv
rename to data_old/T2K/CC1pip/H2O/raw/nd280data-numu-cc1pi-xs-on-h2o-2015-MuPiCos.csv
diff --git a/data/T2K/CC1pip/H2O/raw/nd280data-numu-cc1pi-xs-on-h2o-2015-PosPionCos.csv b/data_old/T2K/CC1pip/H2O/raw/nd280data-numu-cc1pi-xs-on-h2o-2015-PosPionCos.csv
similarity index 100%
rename from data/T2K/CC1pip/H2O/raw/nd280data-numu-cc1pi-xs-on-h2o-2015-PosPionCos.csv
rename to data_old/T2K/CC1pip/H2O/raw/nd280data-numu-cc1pi-xs-on-h2o-2015-PosPionCos.csv
diff --git a/data/T2K/CC1pip/H2O/raw/nd280data-numu-cc1pi-xs-on-h2o-2015-PosPionMom.csv b/data_old/T2K/CC1pip/H2O/raw/nd280data-numu-cc1pi-xs-on-h2o-2015-PosPionMom.csv
similarity index 100%
rename from data/T2K/CC1pip/H2O/raw/nd280data-numu-cc1pi-xs-on-h2o-2015-PosPionMom.csv
rename to data_old/T2K/CC1pip/H2O/raw/nd280data-numu-cc1pi-xs-on-h2o-2015-PosPionMom.csv
diff --git a/data/T2K/CC1pip/H2O/raw/nd280data-numu-cc1pi-xs-on-h2o-2015-flux.csv b/data_old/T2K/CC1pip/H2O/raw/nd280data-numu-cc1pi-xs-on-h2o-2015-flux.csv
similarity index 100%
rename from data/T2K/CC1pip/H2O/raw/nd280data-numu-cc1pi-xs-on-h2o-2015-flux.csv
rename to data_old/T2K/CC1pip/H2O/raw/nd280data-numu-cc1pi-xs-on-h2o-2015-flux.csv
diff --git a/data/T2K/T2K_CC0pinp_STV_XSec_1Ddpt_nu.dat b/data_old/T2K/T2K_CC0pinp_STV_XSec_1Ddpt_nu.dat
similarity index 100%
rename from data/T2K/T2K_CC0pinp_STV_XSec_1Ddpt_nu.dat
rename to data_old/T2K/T2K_CC0pinp_STV_XSec_1Ddpt_nu.dat
diff --git a/data/Winter2016/NUISANCE_beamlist.tar.gz b/data_old/Winter2016/NUISANCE_beamlist.tar.gz
similarity index 100%
rename from data/Winter2016/NUISANCE_beamlist.tar.gz
rename to data_old/Winter2016/NUISANCE_beamlist.tar.gz
diff --git a/data/flux/ANL_1977_2horn_rescan.root b/data_old/flux/ANL_1977_2horn_rescan.root
similarity index 100%
rename from data/flux/ANL_1977_2horn_rescan.root
rename to data_old/flux/ANL_1977_2horn_rescan.root
diff --git a/data/flux/ArgoNeut_numu_flux.root b/data_old/flux/ArgoNeut_numu_flux.root
similarity index 100%
rename from data/flux/ArgoNeut_numu_flux.root
rename to data_old/flux/ArgoNeut_numu_flux.root
diff --git a/data/flux/ArgoNeut_numub_flux.root b/data_old/flux/ArgoNeut_numub_flux.root
similarity index 100%
rename from data/flux/ArgoNeut_numub_flux.root
rename to data_old/flux/ArgoNeut_numub_flux.root
diff --git a/data/flux/BEBC_Wachsmuth_numu_table.root b/data_old/flux/BEBC_Wachsmuth_numu_table.root
similarity index 100%
rename from data/flux/BEBC_Wachsmuth_numu_table.root
rename to data_old/flux/BEBC_Wachsmuth_numu_table.root
diff --git a/data/flux/BEBC_Wachsmuth_numubar_table.root b/data_old/flux/BEBC_Wachsmuth_numubar_table.root
similarity index 100%
rename from data/flux/BEBC_Wachsmuth_numubar_table.root
rename to data_old/flux/BEBC_Wachsmuth_numubar_table.root
diff --git a/data/flux/BNL_1986_flux-ALTERNATIVE.root b/data_old/flux/BNL_1986_flux-ALTERNATIVE.root
similarity index 100%
rename from data/flux/BNL_1986_flux-ALTERNATIVE.root
rename to data_old/flux/BNL_1986_flux-ALTERNATIVE.root
diff --git a/data/flux/BNL_CCQE_1981_rescan-ALTERNATIVE.root b/data_old/flux/BNL_CCQE_1981_rescan-ALTERNATIVE.root
similarity index 100%
rename from data/flux/BNL_CCQE_1981_rescan-ALTERNATIVE.root
rename to data_old/flux/BNL_CCQE_1981_rescan-ALTERNATIVE.root
diff --git a/data/flux/BNL_NuInt02_rescan.root b/data_old/flux/BNL_NuInt02_rescan.root
similarity index 100%
rename from data/flux/BNL_NuInt02_rescan.root
rename to data_old/flux/BNL_NuInt02_rescan.root
diff --git a/data/flux/FNAL_CCinc_1982_nu_MCadj.root b/data_old/flux/FNAL_CCinc_1982_nu_MCadj.root
similarity index 100%
rename from data/flux/FNAL_CCinc_1982_nu_MCadj.root
rename to data_old/flux/FNAL_CCinc_1982_nu_MCadj.root
diff --git a/data/flux/FNAL_coh_1993_anu.root b/data_old/flux/FNAL_coh_1993_anu.root
similarity index 100%
rename from data/flux/FNAL_coh_1993_anu.root
rename to data_old/flux/FNAL_coh_1993_anu.root
diff --git a/data/flux/GGM_nu_flux_1979_rescan.root b/data_old/flux/GGM_nu_flux_1979_rescan.root
similarity index 100%
rename from data/flux/GGM_nu_flux_1979_rescan.root
rename to data_old/flux/GGM_nu_flux_1979_rescan.root
diff --git a/data/flux/K2K_flux.root b/data_old/flux/K2K_flux.root
similarity index 100%
rename from data/flux/K2K_flux.root
rename to data_old/flux/K2K_flux.root
diff --git a/data/flux/MiniBooNE_numu_flux.root b/data_old/flux/MiniBooNE_numu_flux.root
similarity index 100%
rename from data/flux/MiniBooNE_numu_flux.root
rename to data_old/flux/MiniBooNE_numu_flux.root
diff --git a/data/flux/MiniBooNE_numubar_flux.root b/data_old/flux/MiniBooNE_numubar_flux.root
similarity index 100%
rename from data/flux/MiniBooNE_numubar_flux.root
rename to data_old/flux/MiniBooNE_numubar_flux.root
diff --git a/data/flux/input-flux.root b/data_old/flux/input-flux.root
similarity index 100%
rename from data/flux/input-flux.root
rename to data_old/flux/input-flux.root
diff --git a/data/flux/minerva_flux.root b/data_old/flux/minerva_flux.root
similarity index 100%
rename from data/flux/minerva_flux.root
rename to data_old/flux/minerva_flux.root
diff --git a/data/flux/t2kflux_2016_minus250kA.root b/data_old/flux/t2kflux_2016_minus250kA.root
similarity index 100%
rename from data/flux/t2kflux_2016_minus250kA.root
rename to data_old/flux/t2kflux_2016_minus250kA.root
diff --git a/data/flux/t2kflux_2016_plus250kA.root b/data_old/flux/t2kflux_2016_plus250kA.root
similarity index 100%
rename from data/flux/t2kflux_2016_plus250kA.root
rename to data_old/flux/t2kflux_2016_plus250kA.root
diff --git a/data/neut/neut_default.card b/data_old/neut/neut_default.card
similarity index 100%
rename from data/neut/neut_default.card
rename to data_old/neut/neut_default.card
diff --git a/data/nuwro/default_params.txt b/data_old/nuwro/default_params.txt
similarity index 100%
rename from data/nuwro/default_params.txt
rename to data_old/nuwro/default_params.txt
diff --git a/data/priors/philcallums-bctune/bctuneprior_WithNormRES.root b/data_old/priors/philcallums-bctune/bctuneprior_WithNormRES.root
similarity index 100%
rename from data/priors/philcallums-bctune/bctuneprior_WithNormRES.root
rename to data_old/priors/philcallums-bctune/bctuneprior_WithNormRES.root
diff --git a/data/priors/philcallums-bctune/makeprior_normres.py b/data_old/priors/philcallums-bctune/makeprior_normres.py
similarity index 100%
rename from data/priors/philcallums-bctune/makeprior_normres.py
rename to data_old/priors/philcallums-bctune/makeprior_normres.py
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 6a69ff2..5fd3a7e 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -1,9 +1,12 @@
 add_subdirectory(config)
-add_subdirectory(core)
+add_subdirectory(event)
+add_subdirectory(input)
 add_subdirectory(plugins)
 add_subdirectory(utility)
 add_subdirectory(generator)
+add_subdirectory(persistency)
 
 add_subdirectory(samples)
+SET(INuADataComparisons_List ${INuADataComparisons_List} PARENT_SCOPE)
 
 add_subdirectory(app)
diff --git a/src/app/CMakeLists.txt b/src/app/CMakeLists.txt
index 4cb7ad3..6b6fc31 100644
--- a/src/app/CMakeLists.txt
+++ b/src/app/CMakeLists.txt
@@ -1,9 +1,13 @@
-add_executable(DumpEventInfo DumpEventInfo.cxx)
-target_link_libraries(DumpEventInfo nuis_core nuis_config)
-target_link_libraries(DumpEventInfo ${CMAKE_DEPENDLIB_FLAGS})
+SET(APPS nuissamples DumpEventInfo)
 
-if(NOT "${CMAKE_LINK_FLAGS}" STREQUAL "")
-  set_target_properties(DumpEventInfo PROPERTIES LINK_FLAGS ${CMAKE_LINK_FLAGS})
-endif()
+foreach(a ${APPS})
+  add_executable(${a} ${a}.cxx)
+  target_link_libraries(${a} nuis_event nuis_input nuis_utility nuis_config nuis_persistency)
+  target_link_libraries(${a} ${CMAKE_DEPENDLIB_FLAGS})
 
-install(TARGETS DumpEventInfo DESTINATION bin)
+  if(NOT "${CMAKE_LINK_FLAGS}" STREQUAL "")
+    set_target_properties(${a} PROPERTIES LINK_FLAGS ${CMAKE_LINK_FLAGS})
+  endif()
+
+  install(TARGETS ${a} DESTINATION bin)
+endforeach()
diff --git a/src/app/DumpEventInfo.cxx b/src/app/DumpEventInfo.cxx
index b65b10c..a602fec 100644
--- a/src/app/DumpEventInfo.cxx
+++ b/src/app/DumpEventInfo.cxx
@@ -1,34 +1,52 @@
-
 #include "config/GlobalConfiguration.hxx"
 
-#include "core/IInputHandler.hxx"
-#include "core/MinimalEvent.hxx"
+#include "input/IInputHandler.hxx"
+
+#include "event/MinimalEvent.hxx"
 
 #include "samples/ISample.hxx"
 
 #include "plugins/Instantiate.hxx"
 
+#include "exception/exception.hxx"
+
 #include "fhiclcpp/make_ParameterSet.h"
 
 #include <string>
 
-int main() {
-  nuis::config::EnsureConfigurationRead("./nuis.global.config.fcl");
+NEW_NUIS_EXCEPT(invalid_cli_arguments);
 
-  fhicl::ParameterSet ps = fhicl::make_ParameterSet("./test.fcl");
+int main(int argc, char const *argv[]) {
+  nuis::config::EnsureConfigurationRead("nuis.global.config.fcl");
+
+  if (argc != 2) {
+    throw invalid_cli_arguments()
+        << "[ERROR]: Expected to be passed a single FHiCL file name or "
+           "absolute or relative path. N.B. Files in the local directory must "
+           "be fully qualified like \"$ "
+        << argv[0] << " ./myconf.fcl\".";
+  }
+
+  fhicl::ParameterSet ps = fhicl::make_ParameterSet(argv[1]);
+
+  size_t NMax = std::numeric_limits<size_t>::max();
+
+  if (ps.has_key("nmax")) {
+    NMax = ps.get<size_t>("nmax");
+  }
 
   for (fhicl::ParameterSet const &samp_config :
        ps.get<std::vector<fhicl::ParameterSet>>("samples")) {
 
     std::cout << "[INFO]: Reading sample: "
               << samp_config.get<std::string>("name") << std::endl;
 
     nuis::plugins::plugin_traits<ISample>::unique_ptr_t sample =
         nuis::plugins::Instantiate<ISample>(
             samp_config.get<std::string>("name"));
-            
 
     sample->Initialize(samp_config);
-    sample->ProcessSample();
+    sample->ProcessSample(NMax);
+    sample->Write();
   }
 }
diff --git a/src/app/nuissamples.cxx b/src/app/nuissamples.cxx
new file mode 100644
index 0000000..68a17bc
--- /dev/null
+++ b/src/app/nuissamples.cxx
@@ -0,0 +1,36 @@
+#include "config/GlobalConfiguration.hxx"
+
+#include "input/IInputHandler.hxx"
+
+#include "plugins/Instantiate.hxx"
+
+#include "samples/IDataComparison.hxx"
+
+#include <iostream>
+#include <string>
+
+int main() {
+  nuis::config::EnsureConfigurationRead("nuis.global.config.fcl");
+  nuis::config::EnsureConfigurationRead("nuis.datacomparisons.fcl");
+
+  for (std::string const &comparison_set_key :
+       nuis::config::GetDocument()
+           .get<fhicl::ParameterSet>("data_comparisons")
+           .get_names()) {
+    for (std::string const &sample_name :
+         nuis::config::GetDocument().get<std::vector<std::string>>(
+             std::string("data_comparisons.") + comparison_set_key)) {
+
+      nuis::plugins::plugin_traits<IDataComparison>::unique_ptr_t sample =
+          nuis::plugins::Instantiate<IDataComparison>(sample_name);
+      //
+      // std::cout << sample->Name() << std::endl;
+      // std::cout << "\tJournal: " << sample->GetJournalReference() << std::endl;
+      // std::cout << "\tTarget: " << sample->GetTargetMaterial() << std::endl;
+      // std::cout << "\tFlux: " << sample->GetFluxDescription() << std::endl;
+      // std::cout << "\tSignal: " << sample->GetSignalDescription() << std::endl;
+      // std::cout << "\tDocs: " << sample->GetDocumentation() << std::endl;
+
+    }
+  }
+}
diff --git a/src/core/CMakeLists.txt b/src/core/CMakeLists.txt
deleted file mode 100644
index 1aa7703..0000000
--- a/src/core/CMakeLists.txt
+++ /dev/null
@@ -1,19 +0,0 @@
-set(core_implementation_files
-FullEvent.cxx
-InputManager.cxx
-MinimalEvent.cxx
-Particle.cxx)
-
-set(core_header_files
-FullEvent.hxx
-InputManager.hxx
-MinimalEvent.hxx
-Particle.hxx
-IInputHandler.hxx
-types.hxx)
-
-add_library(nuis_core SHARED ${core_implementation_files})
-target_link_libraries(nuis_core)
-
-install(TARGETS nuis_core DESTINATION lib)
-install(FILES ${core_header_files} DESTINATION include/core)
diff --git a/src/core/Particle.cxx b/src/core/Particle.cxx
deleted file mode 100644
index b3a856e..0000000
--- a/src/core/Particle.cxx
+++ /dev/null
@@ -1,11 +0,0 @@
-#include "core/Particle.hxx"
-
-#include "TLorentzVector.h"
-
-namespace nuis {
-namespace core {
-Particle::Particle() : pdg(0), status(Status_t::kUnknown), P4(0, 0, 0, 0) {}
-Particle::Particle(Particle const &other)
-    : pdg(other.pdg), status(other.status), P4(other.P4) {}
-} // namespace core
-} // namespace nuis
diff --git a/src/event/CMakeLists.txt b/src/event/CMakeLists.txt
new file mode 100644
index 0000000..cde1449
--- /dev/null
+++ b/src/event/CMakeLists.txt
@@ -0,0 +1,15 @@
+SET(event_implementation_files
+  FullEvent.cxx
+  MinimalEvent.cxx
+  Particle.cxx)
+
+SET(event_header_files
+  FullEvent.hxx
+  MinimalEvent.hxx
+  Particle.hxx
+  types.hxx)
+
+add_library(nuis_event SHARED ${event_implementation_files})
+
+install(TARGETS nuis_event DESTINATION lib)
+install(FILES ${event_header_files} DESTINATION include/event)
diff --git a/src/core/FullEvent.cxx b/src/event/FullEvent.cxx
similarity index 92%
rename from src/core/FullEvent.cxx
rename to src/event/FullEvent.cxx
index f0fdad0..8d77987 100644
--- a/src/core/FullEvent.cxx
+++ b/src/event/FullEvent.cxx
@@ -1,24 +1,24 @@
-#include "core/FullEvent.hxx"
+#include "event/FullEvent.hxx"
 
 namespace nuis {
-namespace core {
+namespace event {
 FullEvent::FullEvent() : MinimalEvent() {
 
   for (size_t status_it = 0;
        status_it < static_cast<size_t>(Particle::Status_t::kNParticleStatus);
        ++status_it) {
     ParticleStack.push_back({static_cast<Particle::Status_t>(status_it), {}});
   }
 }
 FullEvent::FullEvent(FullEvent &&other)
     : MinimalEvent(std::move(other)),
       ParticleStack(std::move(other.ParticleStack)) {}
 
 void FullEvent::ClearParticleStack() {
   for (auto &status_stack : ParticleStack) {
     status_stack.particles.clear();
   }
 }
 
 } // namespace core
 } // namespace nuis
diff --git a/src/core/FullEvent.hxx b/src/event/FullEvent.hxx
similarity index 90%
rename from src/core/FullEvent.hxx
rename to src/event/FullEvent.hxx
index d351550..12cbfe9 100644
--- a/src/core/FullEvent.hxx
+++ b/src/event/FullEvent.hxx
@@ -1,48 +1,47 @@
 // Copyright 2018 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/>.
  *******************************************************************************/
 
-#ifndef CORE_FULLEVENT_HXX_SEEN
-#define CORE_FULLEVENT_HXX_SEEN
-
-#include "core/MinimalEvent.hxx"
-#include "core/Particle.hxx"
+#ifndef EVENT_FULLEVENT_HXX_SEEN
+#define EVENT_FULLEVENT_HXX_SEEN
 
+#include "event/MinimalEvent.hxx"
+#include "event/Particle.hxx"
 
 namespace nuis {
-namespace core {
+namespace event {
 
 ///\brief The full, internal event format.
 class FullEvent : public MinimalEvent {
 public:
   struct StatusParticles {
     Particle::Status_t status;
     std::vector<Particle> particles;
   };
 
   FullEvent();
   FullEvent(FullEvent const&) = delete;
   FullEvent(FullEvent&&);
   std::vector<StatusParticles> ParticleStack;
 
   void ClearParticleStack();
 };
 
 } // namespace core
 } // namespace nuis
 #endif
diff --git a/src/core/MinimalEvent.cxx b/src/event/MinimalEvent.cxx
similarity index 91%
rename from src/core/MinimalEvent.cxx
rename to src/event/MinimalEvent.cxx
index 31a5332..1e78ed6 100644
--- a/src/core/MinimalEvent.cxx
+++ b/src/event/MinimalEvent.cxx
@@ -1,22 +1,22 @@
-#include "core/MinimalEvent.hxx"
+#include "event/MinimalEvent.hxx"
 
 namespace nuis {
-namespace core {
+namespace event {
 MinimalEvent::MinimalEvent()
     : mode(Channel_t::kUndefined), probe_E(0), probe_pdg(0), XSecWeight(1),
       RWWeight(1) {
 #ifdef __NUWRO_ENABLED__
   fNuWroEvent = nullptr;
 #endif
 }
 
 MinimalEvent::MinimalEvent(MinimalEvent &&other)
     : mode(other.mode), probe_E(other.probe_E), probe_pdg(other.probe_pdg),
       XSecWeight(other.XSecWeight), RWWeight(other.RWWeight) {
 #ifdef __NUWRO_ENABLED__
   fNuWroEvent = other.fNuWroEvent;
   other.fNuWroEvent = nullptr;
 #endif
 }
 } // namespace core
 } // namespace nuis
diff --git a/src/core/MinimalEvent.hxx b/src/event/MinimalEvent.hxx
similarity index 91%
rename from src/core/MinimalEvent.hxx
rename to src/event/MinimalEvent.hxx
index 92e0dc2..328965d 100644
--- a/src/core/MinimalEvent.hxx
+++ b/src/event/MinimalEvent.hxx
@@ -1,72 +1,73 @@
 // Copyright 2018 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/>.
  *******************************************************************************/
 
-#ifndef CORE_MINIMALEVENT_HXX_SEEN
-#define CORE_MINIMALEVENT_HXX_SEEN
+#ifndef EVENT_MINIMALEVENT_HXX_SEEN
+#define EVENT_MINIMALEVENT_HXX_SEEN
 
 #ifdef NUWRO_ENABLED
 #include "event1.h"
+typedef ::event NuWroEvent;
 #endif
 
 #ifdef NEUT_ENABLED
 #include "neutpart.h"
 #include "neutvect.h"
 #endif
 
-#include "core/types.hxx"
+#include "event/types.hxx"
 
 namespace nuis {
-namespace core {
+namespace event {
 ///\brief The minimal event information needed to perform reweights.
 ///
 /// Most often, event selections cannot be applied using this reduced format.
 class MinimalEvent {
 public:
   MinimalEvent();
   MinimalEvent(MinimalEvent const &) = delete;
   MinimalEvent(MinimalEvent &&);
   /// True interaction mode
   Channel_t mode;
   /// True probe energy
   double probe_E;
   /// True probe particle code
   PDG_t probe_pdg;
 
   PDG_t target_pdg;
 
   /// Event-weight that can be used to scale to a cross-section prediction
   double XSecWeight;
   /// Event weight incurred from current reweight engine state.
   double RWWeight;
 
 #ifdef NUWRO_ENABLED
   ///\brief Pointer to Nuwro event
   ///
   /// This will usually be tied to a TTree and so we are not responsible for
   /// deleting it
-  event *fNuWroEvent;
+  NuWroEvent *fNuWroEvent;
 #endif
 
 #ifdef NEUT_ENABLED
   NeutVect *fNeutVect;
 #endif
 };
 } // namespace core
 } // namespace nuis
 #endif
diff --git a/src/event/Particle.cxx b/src/event/Particle.cxx
new file mode 100644
index 0000000..bcbabd8
--- /dev/null
+++ b/src/event/Particle.cxx
@@ -0,0 +1,12 @@
+#include "event/Particle.hxx"
+
+#include "TLorentzVector.h"
+
+#include <limits>
+
+namespace nuis {
+namespace event {
+Particle::Particle() : pdg(std::numeric_limits<PDG_t>::max()), P4(0, 0, 0, 0) {}
+Particle::Particle(Particle const &other) : pdg(other.pdg), P4(other.P4) {}
+} // namespace core
+} // namespace nuis
diff --git a/src/core/Particle.hxx b/src/event/Particle.hxx
similarity index 85%
rename from src/core/Particle.hxx
rename to src/event/Particle.hxx
index 88a9528..accfe51 100644
--- a/src/core/Particle.hxx
+++ b/src/event/Particle.hxx
@@ -1,67 +1,68 @@
 // Copyright 2018 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/>.
  *******************************************************************************/
 
-#ifndef CORE_PARTICLE_HXX_SEEN
-#define CORE_PARTICLE_HXX_SEEN
+#ifndef EVENT_PARTICLE_HXX_SEEN
+#define EVENT_PARTICLE_HXX_SEEN
 
-#include "core/types.hxx"
+#include "event/types.hxx"
 
 #include "TLorentzVector.h"
 
 namespace nuis {
-namespace core {
+namespace event {
 class Particle {
 public:
 #define STATUS_LIST                                                            \
   X(kNuclearLeaving, 0)                                                        \
   X(kPrimaryInitialState, 1)                                                   \
   X(kPrimaryFinalState, 2)                                                     \
   X(kIntermediate, 3)                                                          \
   X(kUnknown, 4)                                                               \
   X(kBlocked, 5)                                                               \
   X(kNParticleStatus, 6)
 
 #define X(A, B) A = B,
   enum class Status_t { STATUS_LIST };
 #undef X
 
   Particle();
   Particle(Particle const &);
 
   PDG_t pdg;
-  Status_t status;
   TLorentzVector P4;
+
+  bool operator!() { return (pdg == std::numeric_limits<PDG_t>::max()); }
 };
-} // namespace core
+} // namespace event
 } // namespace nuis
 
 #define X(A, B)                                                                \
-  case nuis::core::Particle::Status_t::A: {                                    \
+  case nuis::event::Particle::Status_t::A: {                                    \
     return os << #A;                                                           \
   }
 
 inline std::ostream &operator<<(std::ostream &os,
-                                nuis::core::Particle::Status_t te) {
+                                nuis::event::Particle::Status_t te) {
   switch (te) { STATUS_LIST }
   return os;
 }
 #undef X
 #undef STATUS_LIST
 
 #endif
diff --git a/src/core/types.hxx b/src/event/types.hxx
similarity index 93%
rename from src/core/types.hxx
rename to src/event/types.hxx
index 3891185..5553f8c 100644
--- a/src/core/types.hxx
+++ b/src/event/types.hxx
@@ -1,104 +1,104 @@
 // Copyright 2018 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/>.
  *******************************************************************************/
-#ifndef CORE_TYPES_HXX_SEEN
-#define CORE_TYPES_HXX_SEEN
+#ifndef EVENT_TYPES_HXX_SEEN
+#define EVENT_TYPES_HXX_SEEN
 
 #include "exception/exception.hxx"
 
 namespace nuis {
-namespace core {
+namespace event {
 
 #define NUIS_INTERACTION_CHANNEL_LIST                                          \
   X(kCCQE, 1)                                                                  \
   X(kCC2p2h, 2)                                                                \
   X(kCCSPP_PPip, 11)                                                           \
   X(kCCSPP_PPi0, 12)                                                           \
   X(kCCSPP_NPip, 13)                                                           \
   X(kCCCohPi, 16)                                                              \
   X(kCCResGamma, 17)                                                           \
   X(kCCTransitionMPi, 21)                                                      \
   X(kCCResEta0, 22)                                                            \
   X(kCCResK, 23)                                                               \
   X(kCCDIS, 26)                                                                \
                                                                                \
   X(kNCSPP_NPi0, 31)                                                           \
   X(kNCSPP_PPi0, 32)                                                           \
   X(kNCSPP_PPim, 33)                                                           \
   X(kNCSPP_NPip, 34)                                                           \
   X(kNCCohPi, 36)                                                              \
   X(kNCResNGamma, 38)                                                          \
   X(kNCResPGamma, 39)                                                          \
   X(kNCTransitionMPi, 41)                                                      \
   X(kNCResNEta0, 42)                                                           \
   X(kNCResPEta0, 43)                                                           \
   X(kNCResK0, 44)                                                              \
   X(kNCResKp, 45)                                                              \
   X(kNCDIS, 46)                                                                \
   X(kNCELP, 51)                                                                \
   X(kNCELN, 52)                                                                \
                                                                                \
   X(kCCQE_nub, -1)                                                             \
   X(kCC2p2h_nub, -2)                                                           \
   X(kCCSPP_NPim_nub, -11)                                                      \
   X(kCCSPP_NPi0_nub, -12)                                                      \
   X(kCCSPP_PPim_nub, -13)                                                      \
   X(kCCCohPi_nub, -16)                                                         \
   X(kCCResGamma_nub, -17)                                                      \
   X(kCCTransitionMPi_nub, -21)                                                 \
   X(kCCResEta0_nub, -22)                                                       \
   X(kCCResK_nub, -23)                                                          \
   X(kCCDIS_nub, -26)                                                           \
                                                                                \
   X(kNCSPP_NPi0_nub, -31)                                                      \
   X(kNCSPP_PPi0_nub, -32)                                                      \
   X(kNCSPP_PPim_nub, -33)                                                      \
   X(kNCSPP_NPip_nub, -34)                                                      \
   X(kNCCohPi_nub, -36)                                                         \
   X(kNCResNGamma_nub, -38)                                                     \
   X(kNCResPGamma_nub, -39)                                                     \
   X(kNCTransitionMPi_nub, -41)                                                 \
   X(kNCResNEta0_nub, -42)                                                      \
   X(kNCResPEta0_nub, -43)                                                      \
   X(kNCResK0_nub, -44)                                                         \
   X(kNCResKp_nub, -45)                                                         \
   X(kNCDIS_nub, -46)                                                           \
   X(kNCELP_nub, -51)                                                           \
-  X(kNCELN_nub, -52)\
-  \
+  X(kNCELN_nub, -52)                                                           \
+                                                                               \
   X(kUndefined, 0)
 
 #define X(A, B) A = B,
 enum class Channel_t { NUIS_INTERACTION_CHANNEL_LIST };
 #undef X
 
 typedef long PDG_t;
-} // namespace core
+} // namespace event
 } // namespace nuis
 
 #define X(A, B)                                                                \
-  case nuis::core::Channel_t::A: {                                             \
+  case nuis::event::Channel_t::A: {                                            \
     return os << #A;                                                           \
   }
 
-inline std::ostream &operator<<(std::ostream &os, nuis::core::Channel_t te) {
+inline std::ostream &operator<<(std::ostream &os, nuis::event::Channel_t te) {
   switch (te) { NUIS_INTERACTION_CHANNEL_LIST }
   return os;
 }
 #undef X
 #endif
diff --git a/src/generator/CMakeLists.txt b/src/generator/CMakeLists.txt
index 0b35aad..84e4aea 100644
--- a/src/generator/CMakeLists.txt
+++ b/src/generator/CMakeLists.txt
@@ -1,12 +1,2 @@
-if(USE_NuWro)
-  LIST(APPEND INPUT_HANDLERS_IMPL NuWroInputHandler.cxx)
-endif(USE_NuWro)
-
-if(USE_NEUT)
-  LIST(APPEND INPUT_HANDLERS_IMPL NEUTInputHandler.cxx)
-endif(USE_NEUT)
-
-add_library(InputHandlers SHARED ${INPUT_HANDLERS_IMPL})
-target_link_libraries(InputHandlers nuis_core nuis_config)
-
-install(TARGETS InputHandlers DESTINATION plugins)
+add_subdirectory(input)
+add_subdirectory(utility)
diff --git a/src/generator/input/CMakeLists.txt b/src/generator/input/CMakeLists.txt
new file mode 100644
index 0000000..e84aa10
--- /dev/null
+++ b/src/generator/input/CMakeLists.txt
@@ -0,0 +1,17 @@
+LIST(APPEND INPUT_HANDLERS_LINK_LIBS nuis_event nuis_config)
+
+if(USE_NuWro)
+  LIST(APPEND INPUT_HANDLERS_IMPL NuWroInputHandler.cxx)
+endif(USE_NuWro)
+
+if(USE_NEUT)
+  LIST(APPEND INPUT_HANDLERS_IMPL NEUTInputHandler.cxx)
+  LIST(APPEND INPUT_HANDLERS_LINK_LIBS nuis_generator_utility)
+endif(USE_NEUT)
+
+if(INPUT_HANDLERS_IMPL)
+  add_library(InputHandlers SHARED ${INPUT_HANDLERS_IMPL})
+  target_link_libraries(InputHandlers ${INPUT_HANDLERS_LINK_LIBS})
+
+  install(TARGETS InputHandlers DESTINATION plugins)
+endif()
diff --git a/src/generator/NEUTInputHandler.cxx b/src/generator/input/NEUTInputHandler.cxx
similarity index 63%
rename from src/generator/NEUTInputHandler.cxx
rename to src/generator/input/NEUTInputHandler.cxx
index 70bf5ce..f1b4920 100644
--- a/src/generator/NEUTInputHandler.cxx
+++ b/src/generator/input/NEUTInputHandler.cxx
@@ -1,85 +1,106 @@
-#include "NEUTInputHandler.hxx"
-
-#include "core/FullEvent.hxx"
+#include "generator/input/NEUTInputHandler.hxx"
 
 #include "utility/ROOTUtility.hxx"
+#include "utility/PDGCodeUtility.hxx"
+#include "utility/InteractionChannelUtility.hxx"
 
-#include "generator/NEUTUtility.hxx"
+#include "generator/utility/NEUTUtility.hxx"
 
 #include "fhiclcpp/ParameterSet.h"
 
-using namespace nuis::core;
+using namespace nuis::event;
 using namespace nuis::utility;
 
 NEUTInputHandler::NEUTInputHandler() : fInputTree(nullptr) {}
 NEUTInputHandler::NEUTInputHandler(NEUTInputHandler &&other)
     : fInputTree(std::move(other.fInputTree)),
       fReaderEvent(std::move(other.fReaderEvent)) {}
 
 void NEUTInputHandler::Initialize(fhicl::ParameterSet const &ps) {
 
   fInputTree = CheckGetTTree(ps.get<std::string>("file"), "neuttree");
 
   fReaderEvent.fNeutVect = nullptr;
   fInputTree->tree->SetBranchAddress("vectorbranch", &fReaderEvent.fNeutVect);
 }
 
 MinimalEvent const &NEUTInputHandler::GetMinimalEvent(ev_index_t idx) const {
   if (idx >= GetNEvents()) {
     throw IInputHandler::invalid_entry()
         << "[ERROR]: Attempted to get entry " << idx
         << " from an InputHandler with only " << GetNEvents();
   }
   fInputTree->tree->GetEntry(idx);
 
   fReaderEvent.mode = IntToChannel(fReaderEvent.fNeutVect->Mode);
 
   size_t NPart = fReaderEvent.fNeutVect->Npart();
   for (size_t part_it = 0; part_it < NPart; part_it++) {
     NeutPart const &part = (*fReaderEvent.fNeutVect->PartInfo(part_it));
     if ((part.fIsAlive == false) && (part.fStatus == -1) &&
         IsNeutralLepton(part.fPID)) {
       fReaderEvent.probe_E = part.fP.T();
       fReaderEvent.probe_pdg = part.fPID;
       break;
     }
   }
 
   return fReaderEvent;
 }
 
 FullEvent const &NEUTInputHandler::GetFullEvent(ev_index_t idx) const {
   (void)GetMinimalEvent(idx);
 
   fReaderEvent.ClearParticleStack();
 
   if (fReaderEvent.fNeutVect->Ibound) {
     fReaderEvent.target_pdg = MakeNuclearPDG(fReaderEvent.fNeutVect->TargetA,
                                              fReaderEvent.fNeutVect->TargetZ);
   } else {
     fReaderEvent.target_pdg = MakeNuclearPDG(1, 1);
   }
 
   size_t NPart = fReaderEvent.fNeutVect->Npart();
+  bool FoundIntermediateStateParticle = false;
   for (size_t part_it = 0; part_it < NPart; part_it++) {
     NeutPart const &part = (*fReaderEvent.fNeutVect->PartInfo(part_it));
 
-    nuis::core::Particle nuis_part;
+    Particle nuis_part;
     nuis_part.pdg = part.fPID;
-    nuis_part.status = GetNeutParticleStatus(part, fReaderEvent.mode);
     nuis_part.P4 = part.fP;
 
-    size_t state_int = static_cast<size_t>(nuis_part.status);
+    Particle::Status_t state = GetNeutParticleStatus(part, fReaderEvent.mode);
+    size_t state_int = static_cast<size_t>(state);
+
+    if ((!FoundIntermediateStateParticle) &&
+        (state == Particle::Status_t::kIntermediate)) {
+      FoundIntermediateStateParticle = true;
+    }
+
+    // Add status == 0 particles as pre-FSI particles until we find an
+    // intermediate state particle
+    if (!IsCoh(fReaderEvent.mode) && (part_it > 1) && (state_int == 0) &&
+        (!FoundIntermediateStateParticle)) {
+      fReaderEvent
+          .ParticleStack[static_cast<size_t>(
+              Particle::Status_t::kPrimaryFinalState)]
+          .particles.push_back(nuis_part);
+    }
+
+    // Intermediate particles should be pushed onto the primary final state
+    // stack for NEUT
+    if (state == Particle::Status_t::kIntermediate) {
+      state_int = static_cast<size_t>(Particle::Status_t::kPrimaryFinalState);
+    }
 
-    fReaderEvent.ParticleStack[state_int].particles.push_back(
-        std::move(nuis_part));
+    fReaderEvent.ParticleStack[state_int].particles.push_back(nuis_part);
   }
 
   return fReaderEvent;
 }
 
 size_t NEUTInputHandler::GetNEvents() const {
   return fInputTree->tree->GetEntries();
 }
 
 DECLARE_PLUGIN(IInputHandler, NEUTInputHandler);
diff --git a/src/generator/NEUTInputHandler.hxx b/src/generator/input/NEUTInputHandler.hxx
similarity index 78%
rename from src/generator/NEUTInputHandler.hxx
rename to src/generator/input/NEUTInputHandler.hxx
index 9426658..8216d9b 100644
--- a/src/generator/NEUTInputHandler.hxx
+++ b/src/generator/input/NEUTInputHandler.hxx
@@ -1,56 +1,54 @@
 // Copyright 2018 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/>.
  *******************************************************************************/
 
-#ifndef GENERATOR_NEUTINPUTHANDLER_HXX_SEEN
-#define GENERATOR_NEUTINPUTHANDLER_HXX_SEEN
+#ifndef GENERATOR_INPUT_NEUTINPUTHANDLER_HXX_SEEN
+#define GENERATOR_INPUT_NEUTINPUTHANDLER_HXX_SEEN
 
-#include "core/IInputHandler.hxx"
-#include "core/FullEvent.hxx"
+#include "event/FullEvent.hxx"
+
+#include "input/IInputHandler.hxx"
 
 #include <memory>
 
 namespace fhicl {
 class ParameterSet;
 }
 
 namespace nuis {
-namespace core {
-class MinimalEvent;
-} // namespace core
 namespace utility {
 class TreeFile;
 }
 } // namespace nuis
 
 class NEUTInputHandler : public IInputHandler {
   mutable std::unique_ptr<nuis::utility::TreeFile> fInputTree;
-  mutable nuis::core::FullEvent fReaderEvent;
+  mutable nuis::event::FullEvent fReaderEvent;
 
 public:
   NEUTInputHandler();
   NEUTInputHandler(NEUTInputHandler const &) = delete;
   NEUTInputHandler(NEUTInputHandler &&);
 
   void Initialize(fhicl::ParameterSet const &);
-  nuis::core::MinimalEvent const &GetMinimalEvent(ev_index_t idx) const;
-  nuis::core::FullEvent const &GetFullEvent(ev_index_t idx) const;
+  nuis::event::MinimalEvent const &GetMinimalEvent(ev_index_t idx) const;
+  nuis::event::FullEvent const &GetFullEvent(ev_index_t idx) const;
   size_t GetNEvents() const;
 };
 
 #endif
diff --git a/src/generator/NuWroInputHandler.cxx b/src/generator/input/NuWroInputHandler.cxx
similarity index 92%
rename from src/generator/NuWroInputHandler.cxx
rename to src/generator/input/NuWroInputHandler.cxx
index 9a951c6..8d40dd8 100644
--- a/src/generator/NuWroInputHandler.cxx
+++ b/src/generator/input/NuWroInputHandler.cxx
@@ -1,44 +1,42 @@
-#include "NuWroInputHandler.hxx"
-
-#include "core/FullEvent.hxx"
+#include "generator/input/NuWroInputHandler.hxx"
 
 #include "utility/ROOTUtility.hxx"
 
 #include "fhiclcpp/ParameterSet.h"
 
-using namespace nuis::core;
+using namespace nuis::event;
 using namespace nuis::utility;
 
 NuWroInputHandler::NuWroInputHandler() : fInputTree(nullptr) {}
 NuWroInputHandler::NuWroInputHandler(NuWroInputHandler &&other)
     : fInputTree(std::move(other.fInputTree)),
       fReaderEvent(std::move(other.fReaderEvent)) {}
 
 void NuWroInputHandler::Initialize(fhicl::ParameterSet const &ps) {
 
   fInputTree = CheckGetTTree(ps.get<std::string>("file"), "treeout");
 
   fReaderEvent.fNuWroEvent = nullptr;
   fInputTree->tree->SetBranchAddress("e", &fReaderEvent.fNuWroEvent);
 }
 MinimalEvent const &NuWroInputHandler::GetMinimalEvent(ev_index_t idx) const {
   if (idx >= GetNEvents()) {
     throw IInputHandler::invalid_entry()
         << "[ERROR]: Attempted to get entry " << idx
         << " from an InputHandler with only " << GetNEvents();
   }
   fInputTree->tree->GetEntry(idx);
   return fReaderEvent;
 }
 
 FullEvent const &NuWroInputHandler::GetFullEvent(ev_index_t idx) const {
   (void)GetMinimalEvent(idx);
   // Fill particle stack
   return fReaderEvent;
 }
 
 size_t NuWroInputHandler::GetNEvents() const {
   return fInputTree->tree->GetEntries();
 }
 
 DECLARE_PLUGIN(IInputHandler, NuWroInputHandler);
diff --git a/src/generator/NuWroInputHandler.hxx b/src/generator/input/NuWroInputHandler.hxx
similarity index 78%
rename from src/generator/NuWroInputHandler.hxx
rename to src/generator/input/NuWroInputHandler.hxx
index 750748a..a2567ac 100644
--- a/src/generator/NuWroInputHandler.hxx
+++ b/src/generator/input/NuWroInputHandler.hxx
@@ -1,56 +1,54 @@
 // Copyright 2018 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/>.
  *******************************************************************************/
 
-#ifndef GENERATOR_NUWROINPUTHANDLER_HXX_SEEN
-#define GENERATOR_NUWROINPUTHANDLER_HXX_SEEN
+#ifndef GENERATOR_INPUT_NUWROINPUTHANDLER_HXX_SEEN
+#define GENERATOR_INPUT_NUWROINPUTHANDLER_HXX_SEEN
 
-#include "core/IInputHandler.hxx"
-#include "core/FullEvent.hxx"
+#include "event/FullEvent.hxx"
+
+#include "input/IInputHandler.hxx"
 
 #include <memory>
 
 namespace fhicl {
 class ParameterSet;
 }
 
 namespace nuis {
-namespace core {
-class MinimalEvent;
-} // namespace core
 namespace utility {
 class TreeFile;
 }
 } // namespace nuis
 
 class NuWroInputHandler : public IInputHandler {
   mutable std::unique_ptr<nuis::utility::TreeFile> fInputTree;
-  mutable nuis::core::FullEvent fReaderEvent;
+  mutable nuis::event::FullEvent fReaderEvent;
 
 public:
   NuWroInputHandler();
   NuWroInputHandler(NuWroInputHandler const &) = delete;
   NuWroInputHandler(NuWroInputHandler &&);
 
   void Initialize(fhicl::ParameterSet const &);
-  nuis::core::MinimalEvent const &GetMinimalEvent(ev_index_t idx) const;
-  nuis::core::FullEvent const &GetFullEvent(ev_index_t idx) const;
+  nuis::event::MinimalEvent const &GetMinimalEvent(ev_index_t idx) const;
+  nuis::event::FullEvent const &GetFullEvent(ev_index_t idx) const;
   size_t GetNEvents() const;
 };
 
 #endif
diff --git a/src/generator/utility/CMakeLists.txt b/src/generator/utility/CMakeLists.txt
new file mode 100644
index 0000000..6075970
--- /dev/null
+++ b/src/generator/utility/CMakeLists.txt
@@ -0,0 +1,15 @@
+if(USE_NEUT)
+  LIST(APPEND GENERATOR_UTILS_IMPL NEUTUtility.cxx)
+  LIST(APPEND GENERATOR_UTILS_HDR NEUTUtility.hxx)
+endif(USE_NEUT)
+
+if(GENERATOR_UTILS_IMPL)
+  add_library(nuis_generator_utility SHARED ${GENERATOR_UTILS_IMPL})
+  target_link_libraries(nuis_generator_utility nuis_event)
+
+  install(TARGETS nuis_generator_utility DESTINATION lib)
+endif()
+
+if(GENERATOR_UTILS_HDR)
+  install(FILES ${GENERATOR_UTILS_HDR} DESTINATION include/generator/utility)
+endif()
diff --git a/src/generator/NEUTUtility.hxx b/src/generator/utility/NEUTUtility.cxx
similarity index 62%
rename from src/generator/NEUTUtility.hxx
rename to src/generator/utility/NEUTUtility.cxx
index 7d35c45..d3260ca 100644
--- a/src/generator/NEUTUtility.hxx
+++ b/src/generator/utility/NEUTUtility.cxx
@@ -1,81 +1,86 @@
-#ifndef GENERATOR_NEUTUTILITY_HXX_SEEN
-#define GENERATOR_NEUTUTILITY_HXX_SEEN
+#include "generator/utility/NEUTUtility.hxx"
 
-#include "core/Particle.hxx"
+#include "exception/exception.hxx"
 
-#include "utility/ChannelUtility.hxx"
+#include "utility/InteractionChannelUtility.hxx"
 #include "utility/PDGCodeUtility.hxx"
 
-#include "exception/exception.hxx"
-
 #include "neutpart.h"
-#include "neutvect.h"
+
+using namespace nuis::event;
+using namespace nuis::utility;
 
 NEW_NUIS_EXCEPT(unexpected_NEUT_particle_state);
 
-inline nuis::core::Particle::Status_t
-GetNeutParticleStatus(NeutPart const &part, nuis::core::Channel_t mode) {
+Particle::Status_t GetNeutParticleStatus(NeutPart const &part, Channel_t mode) {
+
+#ifdef DEBUG_NEUT_UTILITY
+  std::cout << "[DEBUG]: Mode: " << mode << ", Part: { Status: " << part.fStatus
+            << ", IsAlive: " << part.fIsAlive << ", PDG: " << part.fPID << " }."
+            << std::endl;
+#endif
+
   // Remove Pauli blocked events, probably just single pion events
   if (part.fStatus == 5) {
-    return nuis::core::Particle::Status_t::kBlocked;
+    return Particle::Status_t::kBlocked;
 
     // fStatus == -1 means initial  state
   } else if (part.fIsAlive == false && part.fStatus == -1) {
-    return nuis::core::Particle::Status_t::kPrimaryInitialState;
+    return Particle::Status_t::kPrimaryInitialState;
 
     // NEUT has a bit of a strange convention for fIsAlive and fStatus
     // combinations
     // for NC and neutrino particle isAlive true/false and status 2 means
     // final state particle
     // for other particles in NC status 2 means it's an FSI particle
     // for CC it means it was an FSI particle
   } else if (part.fStatus == 2) {
     // NC case is a little strange... The outgoing neutrino might be alive or
     // not alive. Remaining particles with status 2 are FSI particles that
     // reinteracted
-    if (nuis::utility::IsNC(mode) &&
-        nuis::utility::IsNeutralLepton(part.fPID)) {
-      return nuis::core::Particle::Status_t::kNuclearLeaving;
+    if (IsNC(mode) && IsNeutralLepton(part.fPID)) {
+      return Particle::Status_t::kNuclearLeaving;
       // The usual CC case
     } else if (part.fIsAlive == true) {
-      return nuis::core::Particle::Status_t::kIntermediate;
+      // return Particle::Status_t::kIntermediate;
+      throw unexpected_NEUT_particle_state()
+          << "[ERROR] Found unexpected NEUT particle in neutvect stack: Mode: "
+          << mode << ", Part: { Status: " << part.fStatus
+          << ", IsAlive: " << part.fIsAlive << ", PDG: " << part.fPID << " }.";
     }
 
   } else if ((part.fIsAlive == true) && (part.fStatus == 2) &&
-             nuis::utility::IsNeutralLepton(part.fPID)) {
-    return nuis::core::Particle::Status_t::kNuclearLeaving;
+             IsNeutralLepton(part.fPID)) {
+    return Particle::Status_t::kNuclearLeaving;
 
   } else if ((part.fIsAlive == true) && (part.fStatus == 0)) {
-    return nuis::core::Particle::Status_t::kNuclearLeaving;
+    return Particle::Status_t::kNuclearLeaving;
 
   } else if (!part.fIsAlive && ((part.fStatus == 1) || (part.fStatus == 3) ||
                                 (part.fStatus == 4) || (part.fStatus == 7) ||
                                 (part.fStatus == 8))) {
-    return nuis::core::Particle::Status_t::kIntermediate;
+    return Particle::Status_t::kIntermediate;
 
     // There's one hyper weird case where fStatus = -3. This apparently
     // corresponds to a nucleon being ejected via pion FSI when there is "data
     // available"
   } else if (!part.fIsAlive && (part.fStatus == -3)) {
-    return nuis::core::Particle::Status_t::kUnknown;
+    return Particle::Status_t::kUnknown;
     // NC neutrino outgoing
   } else if (!part.fIsAlive && part.fStatus == 0 &&
-             (abs(part.fPID) == 16 || abs(part.fPID) == 14 ||
-              abs(part.fPID) == 12)) {
-    return nuis::core::Particle::Status_t::kNuclearLeaving;
+             IsNeutralLepton(part.fPID)) {
+    return Particle::Status_t::kNuclearLeaving;
 
     // Warn if we still find alive particles without classifying them
   } else if (part.fIsAlive == true) {
     throw unexpected_NEUT_particle_state()
         << "[ERROR]: Undefined NEUT state "
         << " Alive: " << part.fIsAlive << " Status: " << part.fStatus
         << " PDG: " << part.fPID;
   }
   // Warn if we find dead particles that we haven't classified
   throw unexpected_NEUT_particle_state()
       << "[ERROR]: Undefined NEUT state "
       << " Alive: " << part.fIsAlive << " Status: " << part.fStatus
       << " PDG: " << part.fPID;
 }
-
-#endif
diff --git a/src/generator/utility/NEUTUtility.hxx b/src/generator/utility/NEUTUtility.hxx
new file mode 100644
index 0000000..ea2b3ab
--- /dev/null
+++ b/src/generator/utility/NEUTUtility.hxx
@@ -0,0 +1,11 @@
+#ifndef GENERATOR_UTILITY_NEUTUTILITY_HXX_SEEN
+#define GENERATOR_UTILITY_NEUTUTILITY_HXX_SEEN
+
+#include "event/Particle.hxx"
+#include "event/types.hxx"
+
+class NeutPart;
+
+nuis::event::Particle::Status_t
+GetNeutParticleStatus(NeutPart const &, nuis::event::Channel_t);
+#endif
diff --git a/src/input/CMakeLists.txt b/src/input/CMakeLists.txt
new file mode 100644
index 0000000..5aad051
--- /dev/null
+++ b/src/input/CMakeLists.txt
@@ -0,0 +1,12 @@
+SET(input_implementation_files
+  InputManager.cxx)
+
+SET(input_header_files
+  InputManager.hxx
+  IInputHandler.hxx)
+
+add_library(nuis_input SHARED ${input_implementation_files})
+target_link_libraries(nuis_input)
+
+install(TARGETS nuis_input DESTINATION lib)
+install(FILES ${input_header_files} DESTINATION include/input)
diff --git a/src/core/IInputHandler.hxx b/src/input/IInputHandler.hxx
similarity index 82%
rename from src/core/IInputHandler.hxx
rename to src/input/IInputHandler.hxx
index 94aaebf..8be40d3 100644
--- a/src/core/IInputHandler.hxx
+++ b/src/input/IInputHandler.hxx
@@ -1,109 +1,111 @@
 // Copyright 2018 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/>.
  *******************************************************************************/
 
 #ifndef CORE_IINPUTHANDLER_HXX_SEEN
 #define CORE_IINPUTHANDLER_HXX_SEEN
 
 #include "plugins/traits.hxx"
 
 #include "exception/exception.hxx"
 
 #include <iterator>
 
 namespace fhicl {
 class ParameterSet;
 }
 
 namespace nuis {
-namespace core {
+namespace event {
 class MinimalEvent;
 class FullEvent;
 } // namespace core
 } // namespace nuis
 
 class IInputHandler {
 public:
   struct FullEvent_const_iterator
       : public std::iterator<
-            std::input_iterator_tag, nuis::core::FullEvent const, size_t,
-            nuis::core::FullEvent const *, nuis::core::FullEvent const &> {
+            std::input_iterator_tag, nuis::event::FullEvent const, size_t,
+            nuis::event::FullEvent const *, nuis::event::FullEvent const &> {
 
     FullEvent_const_iterator(size_t _idx, IInputHandler const *_ih) {
       idx = _idx;
       ih = _ih;
     }
     FullEvent_const_iterator(FullEvent_const_iterator const &other) {
       idx = other.idx;
       ih = other.ih;
     }
     FullEvent_const_iterator operator=(FullEvent_const_iterator const &other) {
       idx = other.idx;
       ih = other.ih;
       return (*this);
     }
 
     bool operator==(FullEvent_const_iterator const &other) {
       return (idx == other.idx);
     }
     bool operator!=(FullEvent_const_iterator const &other) {
       return !(*this == other);
     }
-    nuis::core::FullEvent const &operator*() { return ih->GetFullEvent(idx); }
-    nuis::core::FullEvent const *operator->() { return &ih->GetFullEvent(idx); }
+    nuis::event::FullEvent const &operator*() { return ih->GetFullEvent(idx); }
+    nuis::event::FullEvent const *operator->() { return &ih->GetFullEvent(idx); }
 
     FullEvent_const_iterator operator++() {
       idx++;
       return *this;
     }
     FullEvent_const_iterator operator++(int) {
       FullEvent_const_iterator tmp(*this);
       idx++;
       return tmp;
     }
 
   private:
     size_t idx;
     IInputHandler const *ih;
   };
 
   NEW_NUIS_EXCEPT(invalid_input_file);
   NEW_NUIS_EXCEPT(invalid_entry);
 
   typedef size_t ev_index_t;
 
   virtual void Initialize(fhicl::ParameterSet const &) = 0;
-  virtual nuis::core::MinimalEvent const &
+  virtual nuis::event::MinimalEvent const &
   GetMinimalEvent(ev_index_t idx) const = 0;
-  virtual nuis::core::FullEvent const &GetFullEvent(ev_index_t idx) const = 0;
+  virtual nuis::event::FullEvent const &GetFullEvent(ev_index_t idx) const = 0;
+  virtual void RecalculateEventWeights(){};
+  virtual double GetEventWeight(ev_index_t idx) const {};
 
   virtual size_t GetNEvents() const = 0;
 
   FullEvent_const_iterator begin() const {
     return FullEvent_const_iterator(0, this);
   }
   FullEvent_const_iterator end() const {
     return FullEvent_const_iterator(GetNEvents(), this);
   }
 
   virtual ~IInputHandler() {}
 };
 
 DECLARE_PLUGIN_INTERFACE(IInputHandler);
 
 #endif
diff --git a/src/core/InputManager.cxx b/src/input/InputManager.cxx
similarity index 95%
rename from src/core/InputManager.cxx
rename to src/input/InputManager.cxx
index 12cfce8..8928d84 100644
--- a/src/core/InputManager.cxx
+++ b/src/input/InputManager.cxx
@@ -1,65 +1,65 @@
-#include "core/InputManager.hxx"
+#include "input/InputManager.hxx"
 
 #include "plugins/Instantiate.hxx"
 
 #include "fhiclcpp/ParameterSet.h"
 
 #include <iomanip>
 
 namespace nuis {
-namespace core {
+namespace input {
 
 InputManager *InputManager::_global_inst = nullptr;
 
 InputManager::NamedInputHandler::NamedInputHandler(
     std::string const &file,
     plugins::plugin_traits<IInputHandler>::unique_ptr_t &&IH) {
   name = file;
   handler = std::move(IH);
 }
 
 InputManager::InputManager() : Inputs() {}
 
 InputManager &InputManager::Get() {
   if (!_global_inst) {
     _global_inst = new InputManager();
   }
   return *_global_inst;
 }
 
 InputManager::Input_id_t
 InputManager::EnsureInputLoaded(fhicl::ParameterSet const &ps) {
   std::string const &file_name = ps.get<std::string>("file");
   for (size_t i = 0; i < Inputs.size(); ++i) {
     if (Inputs[i].name == file_name) {
       return i;
     }
   }
 
   Inputs.emplace_back(file_name,
                       nuis::plugins::Instantiate<IInputHandler>(
                           ps.get<std::string>("input_type") + "InputHandler"));
   Inputs.back().handler->Initialize(ps);
   return (Inputs.size() - 1);
 }
 InputManager::Input_id_t
 InputManager::GetInputId(std::string const &file_name) const {
   for (size_t i = 0; i < Inputs.size(); ++i) {
     if (Inputs[i].name == file_name) {
       return i;
     }
   }
   throw unknown_input() << "[ERROR]: Input file " << std::quoted(file_name)
                         << " has not been loaded.";
 }
 IInputHandler const &
 InputManager::GetInputHandler(InputManager::Input_id_t id) const {
   if (id >= Inputs.size()) {
     throw unknown_input() << "[ERROR]: Attempted to get input with id " << id
                           << ", but only have " << Inputs.size()
                           << " loaded inputs.";
   }
   return *Inputs[id].handler.get();
 }
-} // namespace core
+} // namespace input
 } // namespace nuis
diff --git a/src/core/InputManager.hxx b/src/input/InputManager.hxx
similarity index 96%
rename from src/core/InputManager.hxx
rename to src/input/InputManager.hxx
index c30c9cc..0a119f5 100644
--- a/src/core/InputManager.hxx
+++ b/src/input/InputManager.hxx
@@ -1,64 +1,64 @@
 // Copyright 2018 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/>.
  *******************************************************************************/
 
 #ifndef CORE_INPUTMANAGER_HXX_SEEN
 #define CORE_INPUTMANAGER_HXX_SEEN
 
-#include "core/IInputHandler.hxx"
+#include "input/IInputHandler.hxx"
 
 #include "plugins/traits.hxx"
 
 #include "exception/exception.hxx"
 
 #include <string>
 #include <vector>
 
 namespace fhicl {
 class ParameterSet;
 }
 
 namespace nuis {
-namespace core {
+namespace input {
 class InputManager {
   struct NamedInputHandler {
     NamedInputHandler(std::string const &,
                       plugins::plugin_traits<IInputHandler>::unique_ptr_t &&);
     std::string name;
     plugins::plugin_traits<IInputHandler>::unique_ptr_t handler;
   };
   std::vector<NamedInputHandler> Inputs;
 
   InputManager();
 
   static InputManager *_global_inst;
 public:
 
   static InputManager &Get();
 
   NEW_NUIS_EXCEPT(unknown_input);
   typedef size_t Input_id_t;
 
   Input_id_t EnsureInputLoaded(fhicl::ParameterSet const &);
   Input_id_t GetInputId(std::string const &) const;
   IInputHandler const &GetInputHandler(Input_id_t) const;
 };
-} // namespace core
+} // namespace input
 } // namespace nuis
 
 #endif
diff --git a/src/persistency/CMakeLists.txt b/src/persistency/CMakeLists.txt
new file mode 100644
index 0000000..ff430d5
--- /dev/null
+++ b/src/persistency/CMakeLists.txt
@@ -0,0 +1,11 @@
+set(persistency_implementation_files
+ROOTOutput.cxx)
+
+set(persistency_header_files
+ROOTOutput.hxx)
+
+add_library(nuis_persistency SHARED ${persistency_implementation_files})
+add_dependencies(nuis_persistency nuis_config fhiclcpp-simple)
+
+install(TARGETS nuis_persistency DESTINATION lib)
+install(FILES ${persistency_header_files} DESTINATION include/persistency)
diff --git a/src/persistency/ROOTOutput.cxx b/src/persistency/ROOTOutput.cxx
new file mode 100644
index 0000000..7d83df5
--- /dev/null
+++ b/src/persistency/ROOTOutput.cxx
@@ -0,0 +1,45 @@
+#include "persistency/ROOTOutput.hxx"
+
+#include "utility/ROOTUtility.hxx"
+
+#include "config/GlobalConfiguration.hxx"
+
+#include "fhiclcpp/ParameterSet.h"
+
+#include "TFile.h"
+
+namespace nuis {
+namespace persistency {
+
+struct NamedTFile {
+  std::string name;
+  std::shared_ptr<TFile> file;
+};
+static std::vector<NamedTFile> Files;
+
+std::shared_ptr<TFile> GetOutputFile(std::string const &name) {
+  for (NamedTFile &file : Files) {
+    if (file.name == name) {
+      return file.file;
+    }
+  }
+
+  fhicl::ParameterSet const &persistency =
+      config::GetDocument().get<fhicl::ParameterSet>("persistency");
+  std::string file_name = persistency.get<std::string>(name + ".output_file");
+  std::string open_opts =
+      persistency.get<std::string>(name + ".open_mode", "CREATE");
+
+  NamedTFile ntf;
+  ntf.name = name;
+  ntf.file = std::make_shared<TFile>(file_name.c_str(), open_opts.c_str());
+  if (!ntf.file || !ntf.file->IsOpen()) {
+    throw utility::failed_to_open_TFile()
+        << "[ERROR]: Failed to open output file: " << std::quoted(file_name)
+        << " in write mode with opts = " << std::quoted(open_opts);
+  }
+  Files.push_back(ntf);
+  return Files.back().file;
+}
+} // namespace persistency
+} // namespace nuis
diff --git a/src/persistency/ROOTOutput.hxx b/src/persistency/ROOTOutput.hxx
new file mode 100644
index 0000000..a10c7f5
--- /dev/null
+++ b/src/persistency/ROOTOutput.hxx
@@ -0,0 +1,36 @@
+#ifndef PERSITENCY_ROOTOUTPUT_HXX_SEEN
+#define PERSITENCY_ROOTOUTPUT_HXX_SEEN
+
+#include "TFile.h"
+
+#include <memory>
+#include <string>
+
+namespace nuis {
+namespace persistency {
+/// Will get/open a TFile that is described in the global config
+///
+/// The named streams will be used to configure the file name and open mode from
+/// the global config element persistency.<name>: {file: output.root opts:
+/// CREATE}
+std::shared_ptr<TFile> GetOutputFile(std::string const &name = "default");
+
+template <typename T>
+void WriteToOutputFile(T *object, std::string const &object_name,
+           std::string const &dir_name = "",
+           std::string const &file_name = "default") {
+  std::shared_ptr<TFile> f = GetOutputFile(file_name);
+
+  f->cd();
+  if (dir_name.length()) {
+    if (!f->cd(dir_name.c_str())) {
+      f->mkdir(dir_name.c_str())->cd();
+    }
+  }
+
+  object->Write(object_name.c_str(), TObject::kOverwrite);
+}
+} // namespace persistency
+} // namespace nuis
+
+#endif
diff --git a/src/plugins/Instantiate.hxx b/src/plugins/Instantiate.hxx
index ab60a2b..05c2bbd 100644
--- a/src/plugins/Instantiate.hxx
+++ b/src/plugins/Instantiate.hxx
@@ -1,242 +1,273 @@
 // Copyright 2018 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/>.
  *******************************************************************************/
 
 #ifndef PLUGINS_PLUGINMANAGER_HXX_SEEN
 #define PLUGINS_PLUGINMANAGER_HXX_SEEN
 
 #include "plugins/traits.hxx"
 
 #include "config/GlobalConfiguration.hxx"
 
 #include "utility/FileSystemUtility.hxx"
 
 #include "exception/exception.hxx"
 
 #include "fhiclcpp/ParameterSet.h"
 #include "string_parsers/to_string.hxx"
 
 // linux
 #include <dlfcn.h>
 
 #include <functional>
 #include <iomanip>
 #include <iostream>
 #include <memory>
 #include <string>
 #include <vector>
 
+// #define DEBUG_INSTANTIATE
+
 namespace nuis {
 namespace plugins {
 
 NEW_NUIS_EXCEPT(failed_to_find_instantiator);
 NEW_NUIS_EXCEPT(malformed_plugin_interface);
 NEW_NUIS_EXCEPT(failed_to_load_so);
 
 typedef void *(*inst_fcn)();
 typedef void (*dltr_fcn)(void *);
 
 template <typename T> struct PluginInstantiator {
 
   std::string FQ_so_path;
   std::string Base_classname;
   std::string Classname;
   void *dllib;
   inst_fcn Instantiator;
   dltr_fcn Deleter;
 
   PluginInstantiator()
       : FQ_so_path(""), Base_classname(""), Classname(""), dllib(nullptr),
         Instantiator(nullptr), Deleter(nullptr) {}
   PluginInstantiator(PluginInstantiator const &) = delete;
   PluginInstantiator(PluginInstantiator &&other) {
     FQ_so_path = std::move(other.FQ_so_path);
     Base_classname = std::move(other.Base_classname);
     Classname = std::move(other.Classname);
     dllib = other.dllib;
     Instantiator = other.Instantiator;
     Deleter = other.Deleter;
 
     other.FQ_so_path = "";
     other.Base_classname = "";
     other.Classname = "";
     other.dllib = nullptr;
     other.Instantiator = nullptr;
     other.Deleter = nullptr;
   }
 
   typename plugin_traits<T>::unique_ptr_t Instantiate() {
-    std::cout << (void *)Deleter << std::endl;
     T *inst = reinterpret_cast<T *>((*Instantiator)());
     dltr_fcn dltr = Deleter;
     std::string cln = Classname;
     std::function<void(T *)> deleter = [=](T *inst) {
+#ifdef DEBUG_INSTANTIATE
       std::cout << "[INFO]: Deleting instance of " << cln << " with "
                 << (void *)dltr << std::endl;
+#endif
       (*dltr)(inst);
     };
     return typename plugin_traits<T>::unique_ptr_t(inst, deleter);
   }
 };
 
 struct NamedSO {
   std::string name;
   void *dllib;
 
   NamedSO() : name(""), dllib(nullptr) {}
   NamedSO(NamedSO const &) = delete;
   NamedSO(NamedSO &&other) : name(std::move(other.name)), dllib(other.dllib) {
     other.dllib = nullptr;
   }
 
   ~NamedSO() {
     if (dllib) {
+#ifdef DEBUG_INSTANTIATE
       std::cout << "[INFO]: dlclose on shared object: " << std::quoted(name)
                 << std::endl;
+#endif
       dlclose(dllib);
     }
   }
 };
 
 NamedSO &GetSharedObject(std::string const &FQPath) {
   static std::vector<NamedSO> LoadedSharedObjects;
 
   for (NamedSO &so : LoadedSharedObjects) {
     if (so.name == FQPath) {
       return so;
     }
   }
 
   NamedSO so;
   so.name = FQPath;
   so.dllib = dlopen(FQPath.c_str(), RTLD_NOW | RTLD_GLOBAL);
 
   char const *dlerr_cstr = dlerror();
   std::string dlerr;
   if (dlerr_cstr) {
     dlerr = dlerr_cstr;
   }
 
   if (dlerr.length()) {
     throw failed_to_load_so()
         << "[INFO]: Failed to load shared object: " << FQPath
         << " with dlerror: " << dlerr;
   } else {
+#ifdef DEBUG_INSTANTIATE
     std::cout << "[INFO]: Loaded shared object " << FQPath << std::endl;
+#endif
   }
 
   LoadedSharedObjects.push_back(std::move(so));
   return LoadedSharedObjects.back();
 }
 
 template <typename T>
 typename plugin_traits<T>::unique_ptr_t
 Instantiate(std::string const &classname) {
 
   static std::vector<PluginInstantiator<T>> LoadedPlugins;
 
-  std::vector<std::string> plugin_search_dirs = config::GetDocument().get<std::vector<std::string>>("plugin_search_path");
+  fhicl::ParameterSet const &plugins =
+      config::GetDocument().get<fhicl::ParameterSet>("plugins");
+  fhicl::ParameterSet const &search_paths =
+      plugins.get<fhicl::ParameterSet>("search_paths");
+
+  std::vector<std::string> plugin_search_dirs;
+  // Look for plugin search paths in sequence elements of the
+  // plugins.search_paths table
+  for (std::string const &key : search_paths.get_names()) {
+    if (!search_paths.is_key_to_sequence(key)) {
+      continue;
+    }
+    for (std::string const &path :
+         search_paths.get<std::vector<std::string>>(key)) {
+      plugin_search_dirs.push_back(path);
+    }
+  }
 
   for (std::string path : plugin_search_dirs) {
     path = utility::EnsureTrailingSlash(path);
     for (std::string const &so_name :
          utility::GetMatchingFiles(path, ".*\\.so")) {
 
       for (PluginInstantiator<T> &plugin : LoadedPlugins) {
         if (plugin.FQ_so_path == (path + so_name) &&
             (plugin.Base_classname == plugin_traits<T>::interface_name()) &&
             (plugin.Classname == classname)) {
+#ifdef DEBUG_INSTANTIATE
           std::cout << "[INFO]: Using already loaded PluginInstantiator"
                     << std::endl;
+#endif
           return plugin.Instantiate();
         }
       }
 
       PluginInstantiator<T> plugin;
       plugin.FQ_so_path = path + so_name;
       plugin.Base_classname = plugin_traits<T>::interface_name();
       plugin.Classname = classname;
       plugin.dllib = GetSharedObject(plugin.FQ_so_path).dllib;
 
       char const *dlerr_cstr = nullptr;
       std::string dlerr("");
 
       plugin.Instantiator = reinterpret_cast<inst_fcn>(dlsym(
           plugin.dllib,
           plugin_traits<T>::instantiator_function_name(classname).c_str()));
 
       dlerr_cstr = dlerror();
       if (dlerr_cstr) {
         dlerr = dlerr_cstr;
       }
 
       if (dlerr_cstr) {
+#ifdef DEBUG_INSTANTIATE
         std::cout << "[INFO]: Failed to load appropriate instantiator method: "
                   << plugin_traits<T>::instantiator_function_name(classname)
                   << " from shared object " << plugin.FQ_so_path;
+#endif
         continue;
       } else {
+#ifdef DEBUG_INSTANTIATE
         std::cout << "[INFO]: Loaded instantiator method: "
                   << plugin_traits<T>::instantiator_function_name(classname)
                   << " from shared object " << plugin.FQ_so_path << std::endl;
+#endif
       }
 
       plugin.Deleter = reinterpret_cast<dltr_fcn>(
           dlsym(plugin.dllib,
                 plugin_traits<T>::deleter_function_name(classname).c_str()));
 
-      std::cout << (void *)plugin.Deleter << std::endl;
-
       dlerr_cstr = dlerror();
       if (dlerr_cstr) {
         dlerr = dlerr_cstr;
       }
 
       if (dlerr_cstr) {
         throw malformed_plugin_interface()
             << "[ERROR]: Failed to load appropriate deleter method: "
             << plugin_traits<T>::deleter_function_name(classname)
             << " from shared object " << plugin.FQ_so_path
             << " with error:  " << std::quoted(dlerr);
       } else {
+#ifdef DEBUG_INSTANTIATE
         std::cout << "[INFO]: Loaded deleter method: "
                   << plugin_traits<T>::deleter_function_name(classname)
                   << " from shared object " << plugin.FQ_so_path << std::endl;
+#endif
       }
 
+#ifdef DEBUG_INSTANTIATE
       std::cout << "[INFO]: Checking if shared object "
                 << std::quoted(plugin.FQ_so_path)
                 << " knows how to instantiate class " << std::quoted(classname)
                 << " via interface "
                 << std::quoted(plugin_traits<T>::interface_name()) << std::endl;
+#endif
 
       LoadedPlugins.push_back(std::move(plugin));
       return LoadedPlugins.back().Instantiate();
     }
   }
   throw failed_to_find_instantiator()
       << "[ERROR]: Failed to find instantiator for classname: "
       << std::quoted(classname) << " using interface "
       << std::quoted(plugin_traits<T>::interface_name())
       << " from configured search paths: "
       << fhicl::string_parsers::T2Str<std::vector<std::string>>(
              plugin_search_dirs);
 }
 } // namespace plugins
 } // namespace nuis
 #endif
diff --git a/src/samples/CMakeLists.txt b/src/samples/CMakeLists.txt
index 98771ed..89b8852 100644
--- a/src/samples/CMakeLists.txt
+++ b/src/samples/CMakeLists.txt
@@ -1,6 +1,17 @@
 set(samples_header_files
 ISample.hxx)
 
 install(FILES ${samples_header_files} DESTINATION include/samples)
 
 add_subdirectory(MCTools)
+
+add_subdirectory(nuA)
+
+cmessage(DEBUG "INuADataComparisons: ${INuADataComparisons}")
+
+SET(INuADataComparisons_List)
+if(NOT IDataComparisons STREQUAL "")
+  string(REPLACE ";" "," INuADataComparisons_List ${INuADataComparisons})
+endif()
+
+SET(INuADataComparisons_List ${INuADataComparisons_List} PARENT_SCOPE)
diff --git a/src/samples/IDataComparison.hxx b/src/samples/IDataComparison.hxx
index f73db5b..ef9e78d 100644
--- a/src/samples/IDataComparison.hxx
+++ b/src/samples/IDataComparison.hxx
@@ -1,32 +1,72 @@
 // Copyright 2018 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/>.
  *******************************************************************************/
 
 #ifndef SAMPLES_IDATACOMPARISON_HXX_SEEN
 #define SAMPLES_IDATACOMPARISON_HXX_SEEN
 
 #include "samples/ISample.hxx"
 
+#include "fhiclcpp/ParameterSet.h"
+
+#include <iomanip>
+#include <sstream>
+
 class IDataComparison : public ISample {
+public:
+  virtual double GetGOF() = 0;
+
+  virtual std::string GetJournalReference() {
+    std::stringstream ss("");
+    ss << "Unknown Journal Ref. for IDataComparison: " << std::quoted(Name());
+    return ss.str();
+  }
+
+  virtual std::string GetTargetMaterial() {
+    std::stringstream ss("");
+    ss << "Unknown Target material for IDataComparison: " << std::quoted(Name());
+    return ss.str();
+  }
+
+  virtual std::string GetFluxDescription() {
+    std::stringstream ss("");
+    ss << "Unknown Flux description for IDataComparison: " << std::quoted(Name());
+    return ss.str();
+  }
+
+  virtual std::string GetSignalDescription() {
+    std::stringstream ss("");
+    ss << "Unknown Signal description for IDataComparison: " << std::quoted(
+        Name());
+    return ss.str();
+  }
+
+  virtual std::string GetDocumentation() {
+    std::stringstream ss("");
+    ss << "No documentation provided for IDataComparison: " << std::quoted(Name());
+    return ss.str();
+  }
 
-  double GetGOF() = 0;
+  virtual fhicl::ParameterSet GetExampleConfiguration() {
+    return fhicl::ParameterSet();
+  }
 };
 
 DECLARE_PLUGIN_INTERFACE(IDataComparison);
 
 #endif
diff --git a/src/samples/ISample.hxx b/src/samples/ISample.hxx
index 23df06a..a45b135 100644
--- a/src/samples/ISample.hxx
+++ b/src/samples/ISample.hxx
@@ -1,65 +1,68 @@
 // Copyright 2018 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/>.
  *******************************************************************************/
 
 #ifndef SAMPLES_ISAMPLE_HXX_SEEN
 #define SAMPLES_ISAMPLE_HXX_SEEN
 
 #include "plugins/traits.hxx"
 
 #include "exception/exception.hxx"
 
 #include <string>
 #include <limits>
 
 namespace fhicl {
 class ParameterSet;
 }
 
 namespace nuis {
-namespace core {
+namespace event {
 class FullEvent;
 class MinimalEvent;
 } // namespace core
 } // namespace nuis
 
 class ISample {
 public:
   NEW_NUIS_EXCEPT(uninitialized_ISample);
   NEW_NUIS_EXCEPT(unimplemented_ISample_optional_method);
 
   virtual void Initialize(fhicl::ParameterSet const &) = 0;
 
-  virtual void ProcessEvent(nuis::core::FullEvent const &) {
+  //Interface for processing a single, external event
+  //
+  // ISamples are not required to implement processing events from 'outside'.
+  virtual void ProcessEvent(nuis::event::FullEvent const &) {
     throw unimplemented_ISample_optional_method()
         << "[ERROR]: ISample " << Name() << " does not implement ProcessEvent.";
   }
 
   virtual void
   ProcessSample(size_t nmax = std::numeric_limits<size_t>::max()) = 0;
 
   virtual void Write() = 0;
 
   virtual std::string Name() = 0;
 
   virtual ~ISample() {}
 };
 
 DECLARE_PLUGIN_INTERFACE(ISample);
 
 #endif
diff --git a/src/samples/MCTools/CMakeLists.txt b/src/samples/MCTools/CMakeLists.txt
index cff9823..86f316d 100644
--- a/src/samples/MCTools/CMakeLists.txt
+++ b/src/samples/MCTools/CMakeLists.txt
@@ -1,10 +1,10 @@
 if(USE_NuWro)
   LIST(APPEND MC_TOOL_IMPL NuisToNuWro.cxx)
 endif(USE_NuWro)
 
 LIST(APPEND MC_TOOL_IMPL VerboseEventSummary.cxx)
 
 add_library(MCTools SHARED ${MC_TOOL_IMPL})
-target_link_libraries(MCTools nuis_core nuis_config)
+target_link_libraries(MCTools nuis_event nuis_input nuis_config)
 
 install(TARGETS MCTools DESTINATION plugins)
diff --git a/src/samples/MCTools/NuisToNuWro.cxx b/src/samples/MCTools/NuisToNuWro.cxx
index eef38c0..ebba240 100644
--- a/src/samples/MCTools/NuisToNuWro.cxx
+++ b/src/samples/MCTools/NuisToNuWro.cxx
@@ -1,45 +1,86 @@
 #include "samples/ISample.hxx"
 
-#include "core/FullEvent.hxx"
-#include "core/InputManager.hxx"
+#include "event/FullEvent.hxx"
+
+#include "input/InputManager.hxx"
+
+#include "utility/FullEventUtility.hxx"
+#include "utility/ROOTUtility.hxx"
+
+#include "fhiclcpp/ParameterSet.h"
 
 #include <iostream>
 #include <limits>
 
-using namespace nuis::core;
+using namespace nuis::event;
+using namespace nuis::input;
+using namespace nuis::utility;
 
 class NuisToNuWro : public ISample {
 public:
   InputManager::Input_id_t fIH_id;
 
+  std::unique_ptr<TreeFile> fOutputTree;
+
+  event *fOutputEvent;
+
   NuisToNuWro()
-      : fIH_id(std::numeric_limits<InputManager::Input_id_t>::max()) {}
+      : fIH_id(std::numeric_limits<InputManager::Input_id_t>::max()),
+        fOutputTree(nullptr), fOutputEvent(nullptr) {}
 
   void Initialize(fhicl::ParameterSet const &ps) {
     fIH_id = InputManager::Get().EnsureInputLoaded(ps);
+
+    fOutputTree =
+        MakeNewTTree(ps.get<std::string>("output_file"), "treeout", "RECREATE");
+    fOutputTree->tree->Branch("e", &fOutputEvent);
   }
 
   void ProcessEvent(FullEvent const &ps) {
-    std::cout << ps.fNuWroEvent->dyn << std::endl;
+    fOutputEvent->in.clear();
+    fOutputEvent->out.clear();
+    fOutputEvent->post.clear();
+
+    for (Particle const &part : GetISParticles(ps)) {
+      particle nuwro_part(part.pdg, part.P4.M());
+      nuwro_part.set_momentum(vect(part.P4.X(), part.P4.Y(), part.P4.Z()));
+      fOutputEvent->in.push_back(nuwro_part);
+    }
+
+    for (Particle const &part : GetPrimaryFSParticles(ps)) {
+      particle nuwro_part(part.pdg, part.P4.M());
+      nuwro_part.set_momentum(vect(part.P4.X(), part.P4.Y(), part.P4.Z()));
+      fOutputEvent->out.push_back(nuwro_part);
+    }
+
+    for (Particle const &part : GetNuclearLeavingParticles(ps)) {
+      particle nuwro_part(part.pdg, part.P4.M());
+      nuwro_part.set_momentum(vect(part.P4.X(), part.P4.Y(), part.P4.Z()));
+      fOutputEvent->post.push_back(nuwro_part);
+    }
+
+    fOutputTree->tree->Fill();
   }
 
   void ProcessSample(size_t nmax) {
     if (fIH_id == std::numeric_limits<InputManager::Input_id_t>::max()) {
       throw uninitialized_ISample();
     }
 
     IInputHandler const &IH = InputManager::Get().GetInputHandler(fIH_id);
     size_t n = 0;
     for (auto const &fe : IH) {
       if (++n > nmax) {
         break;
       }
       ProcessEvent(fe);
     }
   }
 
-  void Write() {}
+  void Write() {
+    fOutputTree->file->Write();
+  }
   std::string Name() { return "NuisToNuWro"; }
 };
 
 DECLARE_PLUGIN(ISample, NuisToNuWro);
diff --git a/src/samples/MCTools/VerboseEventSummary.cxx b/src/samples/MCTools/VerboseEventSummary.cxx
index 73470ce..f56c7ee 100644
--- a/src/samples/MCTools/VerboseEventSummary.cxx
+++ b/src/samples/MCTools/VerboseEventSummary.cxx
@@ -1,58 +1,60 @@
 #include "samples/ISample.hxx"
 
-#include "core/FullEvent.hxx"
-#include "core/InputManager.hxx"
+#include "event/FullEvent.hxx"
+
+#include "input/InputManager.hxx"
 
 #include <iostream>
 #include <limits>
 
-using namespace nuis::core;
+using namespace nuis::event;
+using namespace nuis::input;
 
 class VerboseEventSummary : public ISample {
 public:
   InputManager::Input_id_t fIH_id;
 
   VerboseEventSummary()
       : fIH_id(std::numeric_limits<InputManager::Input_id_t>::max()) {}
 
   void Initialize(fhicl::ParameterSet const &ps) {
     fIH_id = InputManager::Get().EnsureInputLoaded(ps);
   }
 
   void ProcessEvent(FullEvent const &ps) {
     std::cout << "Event: Interaction mode = " << ps.mode
               << ", probe: { PDG: " << ps.probe_pdg
-              << ", Energy: " << ps.probe_E << "}." << std::endl;
+              << ", Energy: " << ps.probe_E << " MeV }." << std::endl;
     for (auto &status_stack : ps.ParticleStack) {
       std::cout << "\t[" << status_stack.status << "]" << std::endl;
 
-      for (nuis::core::Particle const &part : status_stack.particles) {
+      for (Particle const &part : status_stack.particles) {
         std::cout << "\t\t{ PDG: " << part.pdg << ", P3: [ " << part.P4[0]
                   << ", " << part.P4[1] << ", " << part.P4[2]
                   << "], E: " << part.P4[3] << ", M: " << part.P4.M()
-                  << std::endl
-                  << std::endl;
+                  << " }" << std::endl;
       }
     }
+      std::cout << std::endl;
   }
 
   void ProcessSample(size_t nmax) {
     if (fIH_id == std::numeric_limits<InputManager::Input_id_t>::max()) {
       throw uninitialized_ISample();
     }
 
     IInputHandler const &IH = InputManager::Get().GetInputHandler(fIH_id);
     size_t n = 0;
     for (auto const &fe : IH) {
       if (++n > nmax) {
         break;
       }
       ProcessEvent(fe);
     }
   }
 
   void Write() {}
   std::string Name() { return "VerboseEventSummary"; }
 };
 
 DECLARE_PLUGIN(ISample, VerboseEventSummary);
diff --git a/src/samples/nuA/BubbleChamber/ANL/ANL_CCQE_Evt_1DQ2_nu.cxx b/src/samples/nuA/BubbleChamber/ANL/ANL_CCQE_Evt_1DQ2_nu.cxx
new file mode 100644
index 0000000..07504b1
--- /dev/null
+++ b/src/samples/nuA/BubbleChamber/ANL/ANL_CCQE_Evt_1DQ2_nu.cxx
@@ -0,0 +1,236 @@
+// Copyright 2018 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/>.
+ *******************************************************************************/
+
+//********************************************************************
+
+#include "samples/IDataComparison.hxx"
+
+#include "event/FullEvent.hxx"
+
+#include "input/InputManager.hxx"
+
+#include "persistency/ROOTOutput.hxx"
+
+#include "utility/FileSystemUtility.hxx"
+#include "utility/FullEventUtility.hxx"
+#include "utility/KinematicUtility.hxx"
+#include "utility/PDGCodeUtility.hxx"
+#include "utility/ROOTUtility.hxx"
+
+#include "TH1D.h"
+
+using namespace nuis::event;
+using namespace nuis::input;
+using namespace nuis::utility;
+using namespace nuis::persistency;
+
+class ANL_CCQE_Evt_1DQ2_nu : public IDataComparison {
+
+public:
+  NEW_NUIS_EXCEPT(invalid_publication_specifier);
+
+  enum Publication { kPRL31, kPRD16, kPRD26 };
+  Publication Pub;
+  std::string Pub_str;
+  bool UseD2Corr;
+
+  InputManager::Input_id_t fIH_id;
+  std::string write_directory;
+
+  std::unique_ptr<TH1D> fData;
+  std::unique_ptr<TH1D> fPrediction;
+
+  std::pair<double, double> EnuRange;
+
+  ANL_CCQE_Evt_1DQ2_nu()
+      : Pub(kPRD26), Pub_str(""), UseD2Corr(false),
+        fIH_id(std::numeric_limits<InputManager::Input_id_t>::max()),
+        write_directory("ANL_CCQE_Evt_1DQ2_nu"), fData(nullptr),
+        fPrediction(nullptr) {}
+
+  std::string GetJournalReference() {
+    return "PRL 31 844 / PRD 16 3103 / PRD 26 537";
+  }
+  std::string GetTargetMaterial() { return "D2"; }
+  std::string GetFluxDescription() { return "ANL Muon Neutrino"; }
+  std::string GetSignalDescription() { return "True CCQE"; }
+  std::string GetDocumentation() {
+    return "Can specify \"publication: <PUB>\", where <PUB> is one of [ PRL31, "
+           "PRD16, PRD26 ] to clarify a publication for comparison. Defaults "
+           "to PRD26.\n"
+           "Can enable deuterium Q2 correction by specifying "
+           "\"use_D2_correction: true\"";
+  }
+  fhicl::ParameterSet GetExampleConfiguration() {
+    fhicl::ParameterSet exps;
+
+    exps.put<std::string>("name", "ANL_CCQE_Evt_1DQ2_nu");
+    exps.put<std::string>("input_type", "Generator");
+    exps.put<std::string>("file", "ANL_Events.root");
+    exps.put<std::string>("write_directory", "ANL_CCQE_Evt_1DQ2_nu_Generator");
+    exps.put<std::string>("publication", "PRD26");
+    exps.put<bool>("use_D2_correction", true);
+
+    fhicl::ParameterSet fd;
+    fd.put<std::string>("file", "ANL_fake_data.root");
+    fd.put<std::string>("histogram_name", "fake_data");
+
+    exps.put("fake_data", fd);
+
+    return exps;
+  }
+
+  void Initialize(fhicl::ParameterSet const &ps) {
+
+    if (!ps.has_key("publication")) {
+      std::string publication = ps.get<std::string>("publication");
+      if (publication == "PRL31") {
+        Pub = kPRL31;
+      } else if (publication == "PRD16") {
+        Pub = kPRD16;
+      } else if (publication == "PRD26") {
+        Pub = kPRD26;
+      } else {
+        throw invalid_publication_specifier()
+            << "[ERROR]: Found unexpected publication specifier "
+            << std::quoted(publication)
+            << ". Expected one of [ PRL31, PRD16, PRD26 ]";
+      }
+    }
+
+    switch (Pub) {
+    case kPRL31: {
+      Pub_str = "PRL31_844";
+      EnuRange = std::pair<double, double>{0.0, 3.0};
+      break;
+    }
+    case kPRD16: {
+      Pub_str = "PRD16_3103";
+      EnuRange = std::pair<double, double>{0.0, 6.0};
+      break;
+    }
+    case kPRD26: {
+      Pub_str = "PRD26_537";
+      EnuRange = std::pair<double, double>{0.0, 6.0};
+      break;
+    }
+    }
+
+    if (ps.has_key("use_D2_correction")) {
+      UseD2Corr = ps.get<bool>("use_D2_correction");
+    }
+
+    if (ps.has_key("use_D2_correction")) {
+      UseD2Corr = ps.get<bool>("use_D2_correction");
+    }
+
+    if (ps.has_key("write_directory")) {
+      write_directory = ps.get<std::string>("write_directory");
+    }
+
+    fIH_id = InputManager::Get().EnsureInputLoaded(ps);
+
+    if (ps.has_key("fake_data")) {
+      fhicl::ParameterSet const &fd = ps.get<fhicl::ParameterSet>("fake_data");
+      fData = GetHistogramFromROOTFile<TH1D>(
+          fd.get<std::string>("file"), fd.get<std::string>("histogram_name"));
+    } else {
+      fData = GetHistogramFromROOTFile<TH1D>(
+          GetDataDir() + "nuA/BubbleChamber/ANL/ANL_CCQE_Data_" + Pub_str +
+              ".root",
+          "ANL_1DQ2_Data");
+    }
+    fPrediction = CloneHistogram(fData, true);
+  }
+
+  std::vector<bool> fIsSignal;
+  std::vector<double> fQ2;
+
+  void ProcessEvent(FullEvent const &fev) {
+    fQ2.push_back(GetNeutrinoQ2QERec(fev));
+  }
+
+  bool IsSignal(FullEvent const &fev) {
+
+    if (fev.mode != Channel_t::kCCQE) {
+      return false;
+    }
+
+    Particle ISNumu = GetISNeutralLepton(fev);
+
+    if (!ISNumu) {
+      return false;
+    }
+
+    if (ISNumu.pdg != pdgcodes::kNuMu) {
+      return false;
+    }
+
+    if ((ISNumu.P4.E() < EnuRange.first) || (ISNumu.P4.E() > EnuRange.second)) {
+      return false;
+    }
+
+    double Q2 = GetNeutrinoQ2QERec(fev);
+    if (Q2 <= 0) {
+      return false;
+    }
+
+    return true;
+  }
+
+  void ProcessSample(size_t nmax) {
+    if (fIH_id == std::numeric_limits<InputManager::Input_id_t>::max()) {
+      throw uninitialized_ISample();
+    }
+    IInputHandler const &IH = InputManager::Get().GetInputHandler(fIH_id);
+
+    size_t NEvsToProcess = std::min(nmax, IH.GetNEvents());
+    IInputHandler::ev_index_t ev_idx = 0;
+    size_t NSigEvents = 0;
+
+    bool DetermineSignalEvents = !fIsSignal.size();
+
+    while (ev_idx < NEvsToProcess) {
+      if (DetermineSignalEvents) {
+        FullEvent const &fev = IH.GetFullEvent(ev_idx);
+        bool is_sig = IsSignal(fev);
+        fIsSignal.push_back(is_sig);
+        if (is_sig) {
+          ProcessEvent(fev);
+        }
+      }
+
+      if (fIsSignal[ev_idx]) {
+        fPrediction->Fill(fQ2[NSigEvents++], IH.GetEventWeight(ev_idx));
+      }
+
+      ev_idx++;
+    }
+  }
+  void Write() {
+
+    WriteToOutputFile<TH1D>(fData.get(), "Data", write_directory);
+    WriteToOutputFile<TH1D>(fPrediction.get(), "Prediction", write_directory);
+  }
+  std::string Name() { return "ANL_CCQE_Evt_1DQ2_nu"; }
+
+  double GetGOF() { return 0; /*CalcChi2(fData, fPrediction);*/ }
+};
+
+DECLARE_PLUGIN(IDataComparison, ANL_CCQE_Evt_1DQ2_nu);
diff --git a/src/samples/nuA/BubbleChamber/ANL/CMakeLists.txt b/src/samples/nuA/BubbleChamber/ANL/CMakeLists.txt
new file mode 100644
index 0000000..0aa6e75
--- /dev/null
+++ b/src/samples/nuA/BubbleChamber/ANL/CMakeLists.txt
@@ -0,0 +1,14 @@
+SET(SAMPLES ANL_CCQE_Evt_1DQ2_nu)
+
+LIST(APPEND INuADataComparisons ANL_CCQE_Evt_1DQ2_nu)
+
+foreach(S ${SAMPLES})
+  LIST(APPEND SAMPLES_src ${S}.cxx)
+endforeach()
+
+add_library(ANLDataComparisons SHARED ${SAMPLES_src})
+target_link_libraries(ANLDataComparisons nuis_event nuis_input nuis_config nuis_persistency)
+
+install(TARGETS ANLDataComparisons DESTINATION plugins)
+
+SET(INuADataComparisons ${INuADataComparisons} PARENT_SCOPE)
diff --git a/src/samples/nuA/BubbleChamber/CMakeLists.txt b/src/samples/nuA/BubbleChamber/CMakeLists.txt
new file mode 100644
index 0000000..0c841fc
--- /dev/null
+++ b/src/samples/nuA/BubbleChamber/CMakeLists.txt
@@ -0,0 +1,3 @@
+add_subdirectory(ANL)
+
+SET(INuADataComparisons ${INuADataComparisons} PARENT_SCOPE)
diff --git a/src/samples/nuA/CMakeLists.txt b/src/samples/nuA/CMakeLists.txt
new file mode 100644
index 0000000..836e6d7
--- /dev/null
+++ b/src/samples/nuA/CMakeLists.txt
@@ -0,0 +1,3 @@
+add_subdirectory(BubbleChamber)
+
+SET(INuADataComparisons ${INuADataComparisons} PARENT_SCOPE)
diff --git a/src/utility/CMakeLists.txt b/src/utility/CMakeLists.txt
index bc7e978..88ddaf6 100644
--- a/src/utility/CMakeLists.txt
+++ b/src/utility/CMakeLists.txt
@@ -1,6 +1,19 @@
+set(utility_implementation_files
+  FileSystemUtility.cxx
+  FullEventUtility.cxx
+  KinematicUtility.cxx)
+
 set(utility_header_files
-FileSystemUtility.hxx
-FullEventUtility.hxx
-PDGCodeUtility.hxx)
+  FileSystemUtility.hxx
+  FullEventUtility.hxx
+  InteractionChannelUtility.hxx
+  KinematicUtility.hxx
+  PDGCodeUtility.hxx
+  ROOTUtility.hxx)
+
+add_library(nuis_utility SHARED ${utility_implementation_files})
+target_link_libraries(nuis_utility)
+
+install(TARGETS nuis_utility DESTINATION lib)
 
 install(FILES ${utility_header_files} DESTINATION include/utility)
diff --git a/src/utility/FileSystemUtility.cxx b/src/utility/FileSystemUtility.cxx
new file mode 100644
index 0000000..a9acbb4
--- /dev/null
+++ b/src/utility/FileSystemUtility.cxx
@@ -0,0 +1,53 @@
+#include "utility/FileSystemUtility.hxx"
+
+#include "exception/exception.hxx"
+
+#include "config/GlobalConfiguration.hxx"
+
+#include "fhiclcpp/ParameterSet.h"
+
+#include <dirent.h>
+
+#include <regex>
+
+namespace nuis {
+namespace utility {
+
+NEW_NUIS_EXCEPT(unexpected_empty_string);
+
+std::string EnsureTrailingSlash(std::string str) {
+  if (!str.size()) {
+    throw unexpected_empty_string();
+  }
+  if (str.back() != '/') {
+    return str + '/';
+  }
+  return str;
+}
+
+std::vector<std::string> GetMatchingFiles(std::string directory, std::string const &pattern) {
+  directory = EnsureTrailingSlash(directory);
+  std::regex rpattern(pattern);
+
+  std::vector<std::string> matches;
+
+  DIR *dir;
+  struct dirent *ent;
+  dir = opendir(directory.c_str());
+  if (dir != NULL) {
+    while ((ent = readdir(dir)) != NULL) {
+      if (std::regex_match(ent->d_name, rpattern)) {
+        matches.push_back(ent->d_name);
+      }
+    }
+  }
+  return matches;
+}
+
+std::string GetDataDir() {
+  return EnsureTrailingSlash(
+      config::GetDocument().get<std::string>("data_dir"));
+}
+
+} // namespace utility
+} // namespace nuis
diff --git a/src/utility/FileSystemUtility.hxx b/src/utility/FileSystemUtility.hxx
index 92cfb79..eb7f7a0 100644
--- a/src/utility/FileSystemUtility.hxx
+++ b/src/utility/FileSystemUtility.hxx
@@ -1,67 +1,37 @@
 // Copyright 2018 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/>.
  *******************************************************************************/
 
 #ifndef UTILITY_FILESYSTEMUTILITY_HXX_SEEN
 #define UTILITY_FILESYSTEMUTILITY_HXX_SEEN
 
-#include "exception/exception.hxx"
-
-#include <dirent.h>
-
-#include <regex>
 #include <string>
 #include <vector>
 
 namespace nuis {
 namespace utility {
 
-NEW_NUIS_EXCEPT(unexpected_empty_string);
-
-inline std::string EnsureTrailingSlash(std::string str) {
-  if (!str.size()) {
-    throw unexpected_empty_string();
-  }
-  if (str.back() != '/') {
-    return str + '/';
-  }
-  return str;
-}
+std::string EnsureTrailingSlash(std::string);
 
-inline std::vector<std::string> GetMatchingFiles(std::string directory,
-                                                 std::string const &pattern) {
-  directory = EnsureTrailingSlash(directory);
-  std::regex rpattern(pattern);
+std::vector<std::string> GetMatchingFiles(std::string, std::string const &);
 
-  std::vector<std::string> matches;
+std::string GetDataDir();
 
-  DIR *dir;
-  struct dirent *ent;
-  dir = opendir(directory.c_str());
-  if (dir != NULL) {
-    while ((ent = readdir(dir)) != NULL) {
-      if (std::regex_match(ent->d_name, rpattern)) {
-        matches.push_back(ent->d_name);
-      }
-    }
-  }
-  return matches;
-}
 } // namespace utility
 } // namespace nuis
 #endif
diff --git a/src/utility/FullEventUtility.hxx b/src/utility/FullEventUtility.cxx
similarity index 66%
copy from src/utility/FullEventUtility.hxx
copy to src/utility/FullEventUtility.cxx
index ede12fc..a6be49a 100644
--- a/src/utility/FullEventUtility.hxx
+++ b/src/utility/FullEventUtility.cxx
@@ -1,149 +1,147 @@
-// Copyright 2018 L. Pickering, P Stowell, R. Terri, C. Wilkinson, C. Wret
+#include "utility/FullEventUtility.hxx"
 
-/*******************************************************************************
- *    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/>.
- *******************************************************************************/
+#include "event/FullEvent.hxx"
 
-#ifndef UTILITY_FULLEVENTUTILITY_HXX_SEEN
-#define UTILITY_FULLEVENTUTILITY_HXX_SEEN
+#include "utility/PDGCodeUtility.hxx"
+
+using namespace nuis::event;
 
 namespace nuis {
 namespace utility {
 
-template <size_t N>
-std::vector<Particle>
-GetParticles(FullEvent const &ev, std::vector<PDG_t> const &pdgs,
-             Particle::Status_t status = Particle::Status_t::kNuclearLeaving,
-             bool include_matching_pdg = true) {
+std::vector<Particle> GetParticles(FullEvent const &ev,
+                                   std::vector<PDG_t> const &pdgs,
+                                   Particle::Status_t status,
+                                   bool include_matching_pdg) {
   std::vector<Particle> selected_particles;
-  for (StatusParticles const &parts : ev.ParticleStack) {
+  for (auto const &parts : ev.ParticleStack) {
     if (parts.status != status) {
       continue;
     }
     for (Particle const &part : parts.particles) {
       bool matched_pdg = false;
-      for (pdg : pdgs) {
+      for (PDG_t pdg : pdgs) {
         matched_pdg = matched_pdg || (part.pdg == pdg);
       }
       bool keep = ((include_matching_pdg && matched_pdg) ||
                    (!include_matching_pdg && !matched_pdg));
-      if (!matched_pdg) {
+      if (!keep) {
         continue;
       }
       selected_particles.push_back(part);
     }
   }
   return selected_particles;
 }
 
-template <size_t N>
-Particle
-GetHMParticle(FullEvent const &ev, std::vector<PDG_t> const &pdgs,
-              Particle::Status_t status = Particle::Status_t::kNuclearLeaving,
-              bool include_matching_pdg = true) {
+std::vector<Particle> const &GetISParticles(FullEvent const &ev) {
+  return ev
+      .ParticleStack[static_cast<size_t>(
+          Particle::Status_t::kPrimaryInitialState)]
+      .particles;
+}
+std::vector<Particle> const &GetPrimaryFSParticles(FullEvent const &ev) {
+  return ev
+      .ParticleStack[static_cast<size_t>(
+          Particle::Status_t::kPrimaryFinalState)]
+      .particles;
+}
+std::vector<Particle> const &GetNuclearLeavingParticles(FullEvent const &ev) {
+  return ev
+      .ParticleStack[static_cast<size_t>(Particle::Status_t::kNuclearLeaving)]
+      .particles;
+}
+
+Particle GetHMParticle(FullEvent const &ev, std::vector<PDG_t> const &pdgs,
+                       Particle::Status_t status, bool include_matching_pdg) {
   Particle HMParticle;
-  for (StatusParticles const &parts : ev.ParticleStack) {
+  for (auto const &parts : ev.ParticleStack) {
     if (parts.status != status) {
       continue;
     }
     for (Particle const &part : parts.particles) {
       bool matched_pdg = false;
-      for (pdg : pdgs) {
+      for (PDG_t pdg : pdgs) {
         matched_pdg = matched_pdg || (part.pdg == pdg);
       }
       bool keep = ((include_matching_pdg && matched_pdg) ||
                    (!include_matching_pdg && !matched_pdg));
-      if (!matched_pdg) {
+      if (!keep) {
         continue;
       }
       if (part.P4.Vect().Mag() > HMParticle.P4.Vect().Mag()) {
         HMParticle = part;
       }
     }
   }
   return HMParticle;
 }
 
 std::vector<Particle> GetFSChargedLeptons(FullEvent const &ev) {
   return GetParticles(ev, pdgcodes::ChargedLeptons);
 }
 std::vector<Particle> GetFSNeutralLeptons(FullEvent const &ev) {
   return GetParticles(ev, pdgcodes::NeutralLeptons);
 }
 std::vector<Particle> GetISNeutralLeptons(FullEvent const &ev) {
   return GetParticles(ev, pdgcodes::NeutralLeptons,
                       Particle::Status_t::kPrimaryInitialState);
 }
 std::vector<Particle> GetFSChargedPions(FullEvent const &ev) {
   return GetParticles(ev, pdgcodes::ChargedPions);
 }
 std::vector<Particle> GetFSNeutralPions(FullEvent const &ev) {
   return GetParticles(ev, pdgcodes::NeutralPions);
 }
 std::vector<Particle> GetFSPions(FullEvent const &ev) {
   return GetParticles(ev, pdgcodes::Pions);
 }
 std::vector<Particle> GetFSProtons(FullEvent const &ev) {
   return GetParticles(ev, pdgcodes::Protons);
 }
 std::vector<Particle> GetFSNeutrons(FullEvent const &ev) {
   return GetParticles(ev, pdgcodes::Neutron);
 }
 std::vector<Particle> GetFSNucleons(FullEvent const &ev) {
   return GetParticles(ev, pdgcodes::Nucleons);
 }
 std::vector<Particle> GetFSOthers(FullEvent const &ev) {
   return GetParticles(ev, pdgcodes::CommonParticles,
                       Particle::Status_t::kNuclearLeaving, false);
 }
 
 Particle GetFSChargedLepton(FullEvent const &ev) {
   return GetHMParticle(ev, pdgcodes::ChargedLeptons);
 }
 Particle GetFSNeutralLepton(FullEvent const &ev) {
   return GetHMParticle(ev, pdgcodes::NeutralLeptons);
 }
 Particle GetISNeutralLepton(FullEvent const &ev) {
   return GetHMParticle(ev, pdgcodes::NeutralLeptons,
                        Particle::Status_t::kPrimaryInitialState);
 }
 Particle GetFSChargedPion(FullEvent const &ev) {
   return GetHMParticle(ev, pdgcodes::ChargedPions);
 }
 Particle GetFSNeutralPion(FullEvent const &ev) {
   return GetHMParticle(ev, pdgcodes::NeutralPions);
 }
 Particle GetFSPion(FullEvent const &ev) {
   return GetHMParticle(ev, pdgcodes::Pions);
 }
 Particle GetFSProton(FullEvent const &ev) {
   return GetHMParticle(ev, pdgcodes::Protons);
 }
 Particle GetFSNeutron(FullEvent const &ev) {
   return GetHMParticle(ev, pdgcodes::Neutron);
 }
 Particle GetFSNucleon(FullEvent const &ev) {
   return GetHMParticle(ev, pdgcodes::Nucleons);
 }
 Particle GetFSOther(FullEvent const &ev) {
   return GetHMParticle(ev, pdgcodes::CommonParticles,
                        Particle::Status_t::kNuclearLeaving, false);
 }
 
 } // namespace utility
 } // namespace nuis
-
-#endif
diff --git a/src/utility/FullEventUtility.hxx b/src/utility/FullEventUtility.hxx
index ede12fc..f497ea4 100644
--- a/src/utility/FullEventUtility.hxx
+++ b/src/utility/FullEventUtility.hxx
@@ -1,149 +1,80 @@
 // Copyright 2018 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/>.
  *******************************************************************************/
 
 #ifndef UTILITY_FULLEVENTUTILITY_HXX_SEEN
 #define UTILITY_FULLEVENTUTILITY_HXX_SEEN
 
+#include "event/types.hxx"
+#include "event/Particle.hxx"
+
+#include <vector>
+
+namespace nuis {
+namespace event {
+class FullEvent;
+} // namespace event
+} // namespace nuis
+
 namespace nuis {
 namespace utility {
 
-template <size_t N>
-std::vector<Particle>
-GetParticles(FullEvent const &ev, std::vector<PDG_t> const &pdgs,
-             Particle::Status_t status = Particle::Status_t::kNuclearLeaving,
-             bool include_matching_pdg = true) {
-  std::vector<Particle> selected_particles;
-  for (StatusParticles const &parts : ev.ParticleStack) {
-    if (parts.status != status) {
-      continue;
-    }
-    for (Particle const &part : parts.particles) {
-      bool matched_pdg = false;
-      for (pdg : pdgs) {
-        matched_pdg = matched_pdg || (part.pdg == pdg);
-      }
-      bool keep = ((include_matching_pdg && matched_pdg) ||
-                   (!include_matching_pdg && !matched_pdg));
-      if (!matched_pdg) {
-        continue;
-      }
-      selected_particles.push_back(part);
-    }
-  }
-  return selected_particles;
-}
+std::vector<event::Particle>
+GetParticles(event::FullEvent const &, std::vector<event::PDG_t> const &,
+             event::Particle::Status_t status =
+                 event::Particle::Status_t::kNuclearLeaving,
+             bool include_matching_pdg = true);
+
+std::vector<event::Particle> const &GetISParticles(event::FullEvent const &);
+std::vector<event::Particle> const &
+GetPrimaryFSParticles(event::FullEvent const &);
+std::vector<event::Particle> const &
+GetNuclearLeavingParticles(event::FullEvent const &);
 
-template <size_t N>
-Particle
-GetHMParticle(FullEvent const &ev, std::vector<PDG_t> const &pdgs,
-              Particle::Status_t status = Particle::Status_t::kNuclearLeaving,
-              bool include_matching_pdg = true) {
-  Particle HMParticle;
-  for (StatusParticles const &parts : ev.ParticleStack) {
-    if (parts.status != status) {
-      continue;
-    }
-    for (Particle const &part : parts.particles) {
-      bool matched_pdg = false;
-      for (pdg : pdgs) {
-        matched_pdg = matched_pdg || (part.pdg == pdg);
-      }
-      bool keep = ((include_matching_pdg && matched_pdg) ||
-                   (!include_matching_pdg && !matched_pdg));
-      if (!matched_pdg) {
-        continue;
-      }
-      if (part.P4.Vect().Mag() > HMParticle.P4.Vect().Mag()) {
-        HMParticle = part;
-      }
-    }
-  }
-  return HMParticle;
-}
+event::Particle GetHMParticle(event::FullEvent const &,
+                              std::vector<event::PDG_t> const &,
+                              event::Particle::Status_t status =
+                                  event::Particle::Status_t::kNuclearLeaving,
+                              bool include_matching_pdg = true);
 
-std::vector<Particle> GetFSChargedLeptons(FullEvent const &ev) {
-  return GetParticles(ev, pdgcodes::ChargedLeptons);
-}
-std::vector<Particle> GetFSNeutralLeptons(FullEvent const &ev) {
-  return GetParticles(ev, pdgcodes::NeutralLeptons);
-}
-std::vector<Particle> GetISNeutralLeptons(FullEvent const &ev) {
-  return GetParticles(ev, pdgcodes::NeutralLeptons,
-                      Particle::Status_t::kPrimaryInitialState);
-}
-std::vector<Particle> GetFSChargedPions(FullEvent const &ev) {
-  return GetParticles(ev, pdgcodes::ChargedPions);
-}
-std::vector<Particle> GetFSNeutralPions(FullEvent const &ev) {
-  return GetParticles(ev, pdgcodes::NeutralPions);
-}
-std::vector<Particle> GetFSPions(FullEvent const &ev) {
-  return GetParticles(ev, pdgcodes::Pions);
-}
-std::vector<Particle> GetFSProtons(FullEvent const &ev) {
-  return GetParticles(ev, pdgcodes::Protons);
-}
-std::vector<Particle> GetFSNeutrons(FullEvent const &ev) {
-  return GetParticles(ev, pdgcodes::Neutron);
-}
-std::vector<Particle> GetFSNucleons(FullEvent const &ev) {
-  return GetParticles(ev, pdgcodes::Nucleons);
-}
-std::vector<Particle> GetFSOthers(FullEvent const &ev) {
-  return GetParticles(ev, pdgcodes::CommonParticles,
-                      Particle::Status_t::kNuclearLeaving, false);
-}
+std::vector<event::Particle> GetFSChargedLeptons(event::FullEvent const &);
+std::vector<event::Particle> GetFSNeutralLeptons(event::FullEvent const &);
+std::vector<event::Particle> GetISNeutralLeptons(event::FullEvent const &);
+std::vector<event::Particle> GetFSChargedPions(event::FullEvent const &);
+std::vector<event::Particle> GetFSNeutralPions(event::FullEvent const &);
+std::vector<event::Particle> GetFSPions(event::FullEvent const &);
+std::vector<event::Particle> GetFSProtons(event::FullEvent const &);
+std::vector<event::Particle> GetFSNeutrons(event::FullEvent const &);
+std::vector<event::Particle> GetFSNucleons(event::FullEvent const &);
+std::vector<event::Particle> GetFSOthers(event::FullEvent const &);
 
-Particle GetFSChargedLepton(FullEvent const &ev) {
-  return GetHMParticle(ev, pdgcodes::ChargedLeptons);
-}
-Particle GetFSNeutralLepton(FullEvent const &ev) {
-  return GetHMParticle(ev, pdgcodes::NeutralLeptons);
-}
-Particle GetISNeutralLepton(FullEvent const &ev) {
-  return GetHMParticle(ev, pdgcodes::NeutralLeptons,
-                       Particle::Status_t::kPrimaryInitialState);
-}
-Particle GetFSChargedPion(FullEvent const &ev) {
-  return GetHMParticle(ev, pdgcodes::ChargedPions);
-}
-Particle GetFSNeutralPion(FullEvent const &ev) {
-  return GetHMParticle(ev, pdgcodes::NeutralPions);
-}
-Particle GetFSPion(FullEvent const &ev) {
-  return GetHMParticle(ev, pdgcodes::Pions);
-}
-Particle GetFSProton(FullEvent const &ev) {
-  return GetHMParticle(ev, pdgcodes::Protons);
-}
-Particle GetFSNeutron(FullEvent const &ev) {
-  return GetHMParticle(ev, pdgcodes::Neutron);
-}
-Particle GetFSNucleon(FullEvent const &ev) {
-  return GetHMParticle(ev, pdgcodes::Nucleons);
-}
-Particle GetFSOther(FullEvent const &ev) {
-  return GetHMParticle(ev, pdgcodes::CommonParticles,
-                       Particle::Status_t::kNuclearLeaving, false);
-}
+event::Particle GetFSChargedLepton(event::FullEvent const &);
+event::Particle GetFSNeutralLepton(event::FullEvent const &);
+event::Particle GetISNeutralLepton(event::FullEvent const &);
+event::Particle GetFSChargedPion(event::FullEvent const &);
+event::Particle GetFSNeutralPion(event::FullEvent const &);
+event::Particle GetFSPion(event::FullEvent const &);
+event::Particle GetFSProton(event::FullEvent const &);
+event::Particle GetFSNeutron(event::FullEvent const &);
+event::Particle GetFSNucleon(event::FullEvent const &);
+event::Particle GetFSOther(event::FullEvent const &);
 
 } // namespace utility
 } // namespace nuis
 
 #endif
diff --git a/src/utility/ChannelUtility.hxx b/src/utility/InteractionChannelUtility.hxx
similarity index 51%
rename from src/utility/ChannelUtility.hxx
rename to src/utility/InteractionChannelUtility.hxx
index 9aaa523..340c565 100644
--- a/src/utility/ChannelUtility.hxx
+++ b/src/utility/InteractionChannelUtility.hxx
@@ -1,58 +1,64 @@
 #ifndef UTILITY_CHANNELUTILITY_HXX_SEEN
 #define UTILITY_CHANNELUTILITY_HXX_SEEN
 
-#include "core/types.hxx"
+#include "event/types.hxx"
 
 #include "exception/exception.hxx"
 
 #include <iostream>
 
 namespace nuis {
 
 namespace utility {
 NEW_NUIS_EXCEPT(invalid_channel_conversion);
 
 #define X(A, B)                                                                \
   case B: {                                                                    \
-    return nuis::core::Channel_t::A;                                           \
+    return nuis::event::Channel_t::A;                                           \
   }
 
-inline core::Channel_t IntToChannel(int mode) {
+inline event::Channel_t IntToChannel(int mode) {
   switch (mode) {
     NUIS_INTERACTION_CHANNEL_LIST
   default: {
     throw invalid_channel_conversion()
         << "[ERROR]: Failed to parse mode integer " << mode
-        << " as a nuis::core::Channel_t.";
+        << " as a nuis::event::Channel_t.";
   }
   }
 }
 
 #undef X
 
 #define X(A, B)                                                                \
-  case core::Channel_t::A: {                                                   \
+  case event::Channel_t::A: {                                                   \
     return B;                                                                  \
   }
 
-inline int ChannelToInt(core::Channel_t mode) {
+inline int ChannelToInt(event::Channel_t mode) {
   switch (mode) {
     NUIS_INTERACTION_CHANNEL_LIST
   default: {
     throw invalid_channel_conversion()
         << "[ERROR]: Attempting to convert "
-           "undefined nuis::core::Channel_t to an "
+           "undefined nuis::event::Channel_t to an "
            "integer.";
   }
   }
 }
 
-inline bool IsNC(core::Channel_t mode) { return abs(ChannelToInt(mode) > 30); }
-inline bool IsCC(core::Channel_t mode) { return !IsNC(mode); }
-inline bool IsNu(core::Channel_t mode) { return ChannelToInt(mode) > 0; }
-inline bool IsNub(core::Channel_t mode) { return !IsNu(mode); }
+inline bool IsNC(event::Channel_t mode) { return abs(ChannelToInt(mode) > 30); }
+inline bool IsCC(event::Channel_t mode) { return !IsNC(mode); }
+inline bool IsNu(event::Channel_t mode) { return ChannelToInt(mode) > 0; }
+inline bool IsNub(event::Channel_t mode) { return !IsNu(mode); }
+inline bool IsCoh(event::Channel_t mode) {
+  return ((mode == event::Channel_t::kCCCohPi) ||
+          (mode == event::Channel_t::kNCCohPi) ||
+          (mode == event::Channel_t::kCCCohPi_nub) ||
+          (mode == event::Channel_t::kNCCohPi_nub));
+}
 
 } // namespace utility
 } // namespace nuis
 
 #endif
diff --git a/src/utility/KinematicUtility.cxx b/src/utility/KinematicUtility.cxx
new file mode 100644
index 0000000..711c65c
--- /dev/null
+++ b/src/utility/KinematicUtility.cxx
@@ -0,0 +1,11 @@
+#include "utility/KinematicUtility.hxx"
+
+namespace nuis {
+namespace utility {
+
+double GetNeutrinoQ2QERec(event::FullEvent const &fev){
+  return 0;
+}
+
+} // namespace utility
+} // namespace nuis
diff --git a/src/samples/IDataComparison.hxx b/src/utility/KinematicUtility.hxx
similarity index 77%
copy from src/samples/IDataComparison.hxx
copy to src/utility/KinematicUtility.hxx
index f73db5b..5b3bc73 100644
--- a/src/samples/IDataComparison.hxx
+++ b/src/utility/KinematicUtility.hxx
@@ -1,32 +1,34 @@
 // Copyright 2018 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/>.
  *******************************************************************************/
 
-#ifndef SAMPLES_IDATACOMPARISON_HXX_SEEN
-#define SAMPLES_IDATACOMPARISON_HXX_SEEN
+#ifndef UTILITY_KINEMATICUTILITY_HXX_SEEN
+#define UTILITY_KINEMATICUTILITY_HXX_SEEN
 
-#include "samples/ISample.hxx"
+#include "event/FullEvent.hxx"
+#include "event/Particle.hxx"
 
-class IDataComparison : public ISample {
+namespace nuis {
+namespace utility {
 
-  double GetGOF() = 0;
-};
+double GetNeutrinoQ2QERec(event::FullEvent const &fev);
 
-DECLARE_PLUGIN_INTERFACE(IDataComparison);
+} // namespace utility
+} // namespace nuis
 
 #endif
diff --git a/src/utility/PDGCodeUtility.hxx b/src/utility/PDGCodeUtility.hxx
index f62044c..711f575 100644
--- a/src/utility/PDGCodeUtility.hxx
+++ b/src/utility/PDGCodeUtility.hxx
@@ -1,116 +1,135 @@
 // Copyright 2018 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/>.
  *******************************************************************************/
 
 #ifndef UTILITY_PDGCODEUTILITY_HXX_SEEN
 #define UTILITY_PDGCODEUTILITY_HXX_SEEN
 
 #include "core/types.hxx"
 
 namespace nuis {
 namespace utility {
 namespace pdgcodes {
 
 enum MatterType { kMatter = 1, kMatterAntimatter = 0, kAntimatter = -1 };
+static core::PDG_t const kNuMu = 14;
+static core::PDG_t const kNuMuBar = -14;
 
-static std::vector<core::PDG_t> const ChargedLeptons{11, 13, 15, -11, -13, -15};
-static std::vector<core::PDG_t> const ChargedLeptons_matter{11, 13, 15};
-static std::vector<core::PDG_t> const ChargedLeptons_antimatter{-11, -13, -15};
+static core::PDG_t const kMu = 13;
+static core::PDG_t const kMuPlus = -13;
 
-static std::vector<core::PDG_t> const NeutralLeptons{12, 14, 16, -12, -14, -16};
-static std::vector<core::PDG_t> const NeutralLeptons_matter{12, 14, 16};
-static std::vector<core::PDG_t> const NeutralLeptons_antimatter{-12, -14, -16};
+static core::PDG_t const kNue = 12;
+static core::PDG_t const kNueBar = 12;
 
-static std::vector<core::PDG_t> const ChargedPions{211, -211};
-static std::vector<core::PDG_t> const NeutralPions{111};
-static std::vector<core::PDG_t> const Pions{211, -211, 111};
+static core::PDG_t const kPiPlus = 211;
+static core::PDG_t const kPiMinus = -211;
+static core::PDG_t const kPi0 = 111;
+
+static core::PDG_t const kProton = 2212;
+static core::PDG_t const kNeutron = 2112;
+
+static std::vector<core::PDG_t> const ChargedLeptons{11,  kMu,     15,
+                                                     -11, kMuPlus, -15};
+static std::vector<core::PDG_t> const ChargedLeptons_matter{11, kMu, 15};
+static std::vector<core::PDG_t> const ChargedLeptons_antimatter{-11, kMuPlus,
+                                                                -15};
+
+static std::vector<core::PDG_t> const NeutralLeptons{kNue,    kNuMu,    16,
+                                                     kNueBar, kNuMuBar, -16};
+static std::vector<core::PDG_t> const NeutralLeptons_matter{kNue, kNuMu, 16};
+static std::vector<core::PDG_t> const NeutralLeptons_antimatter{kNueBar,
+                                                                kNuMuBar, -16};
+
+static std::vector<core::PDG_t> const ChargedPions{kPiPlus, kPiMinus};
+static std::vector<core::PDG_t> const NeutralPions{kPi0};
+static std::vector<core::PDG_t> const Pions{kPiPlus, kPiMinus, kPi0};
 static std::vector<core::PDG_t> const Protons{2212, -2122};
 static std::vector<core::PDG_t> const Proton_matter{2212};
 static std::vector<core::PDG_t> const Proton_antimatter{-2212};
-static std::vector<core::PDG_t> const Neutron{2112};
-static std::vector<core::PDG_t> const Nucleons{2212, 2112, -2212};
-static std::vector<core::PDG_t> const Nucleons_matter{2212, 2112};
-static std::vector<core::PDG_t> const Nucleons_antimatter{-2212};
+static std::vector<core::PDG_t> const Neutron{kNeutron};
+static std::vector<core::PDG_t> const Nucleons{kProton, 2112, -2212};
+static std::vector<core::PDG_t> const Nucleons_matter{kProton, kNeutron};
+static std::vector<core::PDG_t> const Nucleons_antimatter{-2212, 2112};
 
 static std::vector<core::PDG_t> const CommonParticles{
-    11,  13,  15,  -11, -13,  -15, 12,   14,  16,
-    -12, -14, -16, 211, -211, 111, 2212, 2112};
+    11,      kMu,      15,  -11,     kMuPlus,  -15,  kNue,    kNuMu,   16,
+    kNueBar, kNuMuBar, -16, kPiPlus, kPiMinus, kPi0, kProton, kNeutron};
 } // namespace pdgcodes
 
 inline bool
 IsInPDGList(core::PDG_t pdg, std::vector<core::PDG_t> const &MatterList,
             std::vector<core::PDG_t> const &AntiMatterList,
             pdgcodes::MatterType type = pdgcodes::kMatterAntimatter) {
   switch (type) {
   case pdgcodes::kMatter: {
     return std::count(MatterList.begin(), MatterList.end(), pdg);
   }
   case pdgcodes::kMatterAntimatter: {
     return std::count(MatterList.begin(), MatterList.end(), pdg) ||
            std::count(AntiMatterList.begin(), AntiMatterList.end(), pdg);
   }
   case pdgcodes::kAntimatter: {
     return std::count(AntiMatterList.begin(), AntiMatterList.end(), pdg);
   }
   }
 }
 inline bool
 IsNeutralLepton(core::PDG_t pdg,
                 pdgcodes::MatterType type = pdgcodes::kMatterAntimatter) {
   return IsInPDGList(pdg, pdgcodes::NeutralLeptons_matter,
                      pdgcodes::NeutralLeptons_antimatter, type);
 }
 inline bool
 IsChargedLepton(core::PDG_t pdg,
                 pdgcodes::MatterType type = pdgcodes::kMatterAntimatter) {
   return IsInPDGList(pdg, pdgcodes::ChargedLeptons_matter,
                      pdgcodes::ChargedLeptons_antimatter, type);
 }
 inline bool IsProton(core::PDG_t pdg,
                      pdgcodes::MatterType type = pdgcodes::kMatterAntimatter) {
   return IsInPDGList(pdg, pdgcodes::Proton_matter, pdgcodes::Proton_antimatter,
                      type);
 }
 inline bool IsNeutron(core::PDG_t pdg) { return pdg == pdgcodes::Neutron[0]; }
 inline bool IsChargedPion(core::PDG_t pdg) {
   return std::count(pdgcodes::ChargedPions.begin(),
                     pdgcodes::ChargedPions.end(), pdg);
 }
 inline bool IsNeutralPion(core::PDG_t pdg) {
   return std::count(pdgcodes::NeutralPions.begin(),
                     pdgcodes::NeutralPions.end(), pdg);
 }
 inline bool IsPion(core::PDG_t pdg) {
   return std::count(pdgcodes::Pions.begin(), pdgcodes::Pions.end(), pdg);
 }
 inline bool IsOther(core::PDG_t pdg) {
   return !std::count(pdgcodes::CommonParticles.begin(),
                      pdgcodes::CommonParticles.end(), pdg);
 }
 
-core::PDG_t MakeNuclearPDG(size_t A, size_t Z) {
+inline core::PDG_t MakeNuclearPDG(size_t A, size_t Z) {
   return 1000 * Z + 10 * A + 1000000000;
 }
 
-size_t GetA(core::PDG_t pdg) { return ((pdg / 10) % 1000); }
-size_t GetZ(core::PDG_t pdg) { return ((pdg / 1000) % 1000); }
+inline size_t GetA(core::PDG_t pdg) { return ((pdg / 10) % 1000); }
+inline size_t GetZ(core::PDG_t pdg) { return ((pdg / 1000) % 1000); }
 
 } // namespace utility
 } // namespace nuis
 
 #endif
diff --git a/src/utility/ROOTUtility.hxx b/src/utility/ROOTUtility.hxx
index a4e1511..f738c7d 100644
--- a/src/utility/ROOTUtility.hxx
+++ b/src/utility/ROOTUtility.hxx
@@ -1,88 +1,166 @@
 // Copyright 2018 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/>.
  *******************************************************************************/
 
 #ifndef UTILITY_ROOTUTILITY_HXX_SEEN
 #define UTILITY_ROOTUTILITY_HXX_SEEN
 
 #include "TFile.h"
 #include "TTree.h"
 
 #include "exception/exception.hxx"
 
 #include <iomanip>
 #include <iostream>
 #include <memory>
 #include <string>
 
+class TH1;
+class TH1D;
+class TH1F;
+class TH2;
+class TH2D;
+class TH2F;
+
 namespace nuis {
 namespace utility {
 
 NEW_NUIS_EXCEPT(failed_to_open_TFile);
 NEW_NUIS_EXCEPT(failed_to_get_TTree);
+NEW_NUIS_EXCEPT(invalid_histogram_name);
+NEW_NUIS_EXCEPT(failed_to_clone);
 
-inline TFile *CheckOpenTFile(std::string const &fname, char const *opts="") {
+inline TFile *CheckOpenTFile(std::string const &fname, char const *opts = "") {
 
   TDirectory *ogDir = gDirectory;
 
   TFile *inpF = new TFile(fname.c_str(), opts);
   if (!inpF || !inpF->IsOpen()) {
     throw failed_to_open_TFile()
         << "[ERROR]: Couldn't open input file: " << std::quoted(fname);
   }
 
   if (ogDir) {
     ogDir->cd();
   }
 
   return inpF;
 }
 
 struct TreeFile {
   TFile *file;
   TTree *tree;
   TreeFile() : file(nullptr), tree(nullptr) {}
   TreeFile(TreeFile const &other) = delete;
   TreeFile(TreeFile &&other) : file(other.file), tree(other.tree) {
     other.file = nullptr;
     other.tree = nullptr;
   }
   ~TreeFile() {
     if (file) {
       file->Close();
     }
   }
 };
 
 inline std::unique_ptr<TreeFile> CheckGetTTree(std::string const &fname,
-                                               std::string const &tname) {
+                                               std::string const &tname,
+                                               char const *opts = "") {
   TreeFile tf;
-  tf.file = CheckOpenTFile(fname);
+  tf.file = CheckOpenTFile(fname, opts);
   tf.tree = dynamic_cast<TTree *>(tf.file->Get(tname.c_str()));
   if (!tf.tree) {
     throw failed_to_get_TTree()
         << "[ERROR]: Failed to get TTree named: " << std::quoted(tname)
         << " from TFile: " << std::quoted(fname);
   }
   return std::make_unique<TreeFile>(std::move(tf));
 }
 
+inline std::unique_ptr<TreeFile> MakeNewTTree(std::string const &fname,
+                                              std::string const &tname,
+                                              char const *opts = "") {
+  TreeFile tf;
+  tf.file = CheckOpenTFile(fname, opts);
+  tf.tree = new TTree(tname.c_str(), "");
+  tf.tree->SetDirectory(tf.file);
+  return std::make_unique<TreeFile>(std::move(tf));
+}
+
+template <typename HT> struct TH_traits {};
+
+template <> struct TH_traits<TH1> {
+  static std::string name() { return "TH1"; }
+};
+template <> struct TH_traits<TH1D> {
+  static std::string name() { return "TH1D"; }
+};
+template <> struct TH_traits<TH1F> {
+  static std::string name() { return "TH1F"; }
+};
+template <> struct TH_traits<TH2> {
+  static std::string name() { return "TH2"; }
+};
+template <> struct TH_traits<TH2D> {
+  static std::string name() { return "TH2D"; }
+};
+template <> struct TH_traits<TH2F> {
+  static std::string name() { return "TH2F"; }
+};
+
+template <typename HT>
+inline std::unique_ptr<HT> GetHistogramFromROOTFile(std::string const &fname,
+                                                    std::string const &hname) {
+  TFile *f = CheckOpenTFile(fname, "READ");
+  HT *h = dynamic_cast<HT *>(f->Get(hname.c_str()));
+  if (!h) {
+    throw invalid_histogram_name()
+        << "[ERROR]: Failed to get " << TH_traits<HT>::name() << " named "
+        << std::quoted(hname) << " from input file " << std::quoted(fname);
+  }
+  std::unique_ptr<HT> clone(dynamic_cast<HT *>(h->Clone()));
+  clone->SetDirectory(nullptr);
+
+  f->Close();
+  delete f;
+
+  return clone;
+}
+
+template <typename HT>
+inline std::unique_ptr<HT> CloneHistogram(std::unique_ptr<HT> const &source,
+                                          bool clear = false) {
+  std::unique_ptr<HT> target(dynamic_cast<HT *>(source->Clone()));
+  if (!target) {
+    throw failed_to_clone()
+        << "[ERROR]: Failed to clone a " << TH_traits<HT>::name()
+        << ", source = " << source.get();
+  }
+  target->SetDirectory(nullptr);
+
+  if (clear) {
+    target->Clear();
+  }
+
+  return target;
+}
+
 } // namespace utility
 } // namespace nuis
 
 #endif