diff --git a/alignment/CMakeLists.txt b/alignment/CMakeLists.txt
index 719d93c57b..e787549c22 100644
--- a/alignment/CMakeLists.txt
+++ b/alignment/CMakeLists.txt
@@ -1,5 +1,5 @@
 ################################################################################
-# Copyright (C) 2014-2022 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
+# Copyright (C) 2014-2023 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
 #                                                                              #
 #              This software is distributed under the terms of the             #
 #              GNU Lesser General Public Licence (LGPL) version 3,             #
@@ -20,8 +20,10 @@ fairroot_library_settings(${target})
 target_include_directories(${target} PUBLIC
   $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
   $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
+)
 
-  # TODO: DELETE ME ONCE USING root targets
+# TODO: DELETE ME ONCE USING root targets
+target_include_directories(${target} SYSTEM PUBLIC
   ${ROOT_INCLUDE_DIR}
 )
 
diff --git a/base/CMakeLists.txt b/base/CMakeLists.txt
index 8e77b1902d..6962f7e69b 100644
--- a/base/CMakeLists.txt
+++ b/base/CMakeLists.txt
@@ -1,5 +1,5 @@
  ################################################################################
- # Copyright (C) 2014-2022 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
+ # Copyright (C) 2014-2023 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
  #                                                                              #
  #              This software is distributed under the terms of the             #
  #              GNU Lesser General Public Licence (LGPL) version 3,             #
@@ -96,8 +96,10 @@ target_include_directories(${target} PUBLIC
   $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/source>
   $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/sink>
   $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
+)
 
-  # DELETE ME ONCE USING root targets
+# TODO: DELETE ME ONCE USING root targets
+target_include_directories(${target} SYSTEM PUBLIC
   ${ROOT_INCLUDE_DIR}
 )
 
diff --git a/base/sim/fastsim/CMakeLists.txt b/base/sim/fastsim/CMakeLists.txt
index 01274493d7..e29bcd69cd 100644
--- a/base/sim/fastsim/CMakeLists.txt
+++ b/base/sim/fastsim/CMakeLists.txt
@@ -1,5 +1,5 @@
 ################################################################################
-# Copyright (C) 2014-2022 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
+# Copyright (C) 2014-2023 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
 #                                                                              #
 #              This software is distributed under the terms of the             #
 #              GNU Lesser General Public Licence (LGPL) version 3,             #
@@ -25,8 +25,10 @@ set_target_properties(${target} PROPERTIES OUTPUT_NAME FairFastSim)
 target_include_directories(${target} PUBLIC
   $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
   $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
+)
 
-  # TODO: DELETE ME ONCE USING root targets
+# TODO: DELETE ME ONCE USING root targets
+target_include_directories(${target} SYSTEM PUBLIC
   ${ROOT_INCLUDE_DIR}
 )
 
diff --git a/basemq/CMakeLists.txt b/basemq/CMakeLists.txt
index ef8791f629..61e2b47e3c 100644
--- a/basemq/CMakeLists.txt
+++ b/basemq/CMakeLists.txt
@@ -1,5 +1,5 @@
 ################################################################################
-# Copyright (C) 2014-2022 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
+# Copyright (C) 2014-2023 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
 #                                                                              #
 #              This software is distributed under the terms of the             #
 #              GNU Lesser General Public Licence (LGPL) version 3,             #
@@ -52,8 +52,10 @@ target_include_directories(${target} PUBLIC
   $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/policies/Serialization>
   $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/policies/Storage>
   $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
+)
 
-  # TODO: DELETE ME ONCE USING root targets
+# TODO: DELETE ME ONCE USING root targets
+target_include_directories(${target} SYSTEM PUBLIC
   ${ROOT_INCLUDE_DIR} # TClonesArray, TMessage, etc
 )
 
diff --git a/datamatch/CMakeLists.txt b/datamatch/CMakeLists.txt
index 127602d2c3..081ed07dac 100644
--- a/datamatch/CMakeLists.txt
+++ b/datamatch/CMakeLists.txt
@@ -1,5 +1,5 @@
 ################################################################################
-# Copyright (C) 2014-2022 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
+# Copyright (C) 2014-2023 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
 #                                                                              #
 #              This software is distributed under the terms of the             #
 #              GNU Lesser General Public Licence (LGPL) version 3,             #
@@ -31,8 +31,10 @@ set_target_properties(${target} PROPERTIES OUTPUT_NAME FairDataMatch)
 target_include_directories(${target} PUBLIC
   $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
   $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
+)
 
-  # TODO: DELETE ME ONCE USING root targets
+# TODO: DELETE ME ONCE USING root targets
+target_include_directories(${target} SYSTEM PUBLIC
   ${ROOT_INCLUDE_DIR}
 )
 
diff --git a/eventdisplay/CMakeLists.txt b/eventdisplay/CMakeLists.txt
index f5a6161fa0..d7fb6c3254 100644
--- a/eventdisplay/CMakeLists.txt
+++ b/eventdisplay/CMakeLists.txt
@@ -1,5 +1,5 @@
 ################################################################################
-# Copyright (C) 2014-2022 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
+# Copyright (C) 2014-2023 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
 #                                                                              #
 #              This software is distributed under the terms of the             #
 #              GNU Lesser General Public Licence (LGPL) version 3,             #
@@ -52,8 +52,10 @@ target_include_directories(${target} PUBLIC
   $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/gui>
   $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/datasource>
   $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
+)
 
-  # TODO: DELETE ME ONCE USING root targets
+# TODO: DELETE ME ONCE USING root targets
+target_include_directories(${target} SYSTEM PUBLIC
   ${ROOT_INCLUDE_DIR}
 )
 
diff --git a/examples/MQ/Lmd/CMakeLists.txt b/examples/MQ/Lmd/CMakeLists.txt
index 013b0131c2..d73259b174 100644
--- a/examples/MQ/Lmd/CMakeLists.txt
+++ b/examples/MQ/Lmd/CMakeLists.txt
@@ -1,5 +1,5 @@
 ################################################################################
-# Copyright (C) 2014-2022 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
+# Copyright (C) 2014-2023 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
 #                                                                              #
 #              This software is distributed under the terms of the             #
 #              GNU Lesser General Public Licence (LGPL) version 3,             #
@@ -23,8 +23,10 @@ set_target_properties(${target} PROPERTIES ${PROJECT_LIBRARY_PROPERTIES})
 target_include_directories(${target} PUBLIC
   $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
   $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
+)
 
-  # TODO: DELETE ME ONCE USING root targets
+# TODO: DELETE ME ONCE USING root targets
+target_include_directories(${target} SYSTEM PUBLIC
   ${ROOT_INCLUDE_DIR}
 )
 
diff --git a/examples/MQ/histogramServer/CMakeLists.txt b/examples/MQ/histogramServer/CMakeLists.txt
index fc88c9d4ec..7aa72454cc 100644
--- a/examples/MQ/histogramServer/CMakeLists.txt
+++ b/examples/MQ/histogramServer/CMakeLists.txt
@@ -1,5 +1,5 @@
 ################################################################################
-# Copyright (C) 2014-2022 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
+# Copyright (C) 2014-2023 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
 #                                                                              #
 #              This software is distributed under the terms of the             #
 #              GNU Lesser General Public Licence (LGPL) version 3,             #
@@ -24,8 +24,10 @@ set_target_properties(${target} PROPERTIES ${PROJECT_LIBRARY_PROPERTIES})
 target_include_directories(${target} PUBLIC
   $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
   $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
+)
 
-  # TODO: DELETE ME ONCE USING root targets
+# TODO: DELETE ME ONCE USING root targets
+target_include_directories(${target} SYSTEM PUBLIC
   ${ROOT_INCLUDE_DIR}
 )
 
diff --git a/examples/MQ/parameters/CMakeLists.txt b/examples/MQ/parameters/CMakeLists.txt
index adbd962cd8..42c0dcf10a 100644
--- a/examples/MQ/parameters/CMakeLists.txt
+++ b/examples/MQ/parameters/CMakeLists.txt
@@ -1,5 +1,5 @@
 ################################################################################
-# Copyright (C) 2014-2022 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
+# Copyright (C) 2014-2023 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
 #                                                                              #
 #              This software is distributed under the terms of the             #
 #              GNU Lesser General Public Licence (LGPL) version 3,             #
@@ -27,8 +27,10 @@ set_target_properties(${target} PROPERTIES ${PROJECT_LIBRARY_PROPERTIES})
 target_include_directories(${target} PUBLIC
   $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
   $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
+)
 
-  # TODO: DELETE ME ONCE USING root targets
+# TODO: DELETE ME ONCE USING root targets
+target_include_directories(${target} SYSTEM PUBLIC
   ${ROOT_INCLUDE_DIR}
 )
 
diff --git a/examples/MQ/pixelAlternative/src/CMakeLists.txt b/examples/MQ/pixelAlternative/src/CMakeLists.txt
index 428de1e469..4b8927289a 100644
--- a/examples/MQ/pixelAlternative/src/CMakeLists.txt
+++ b/examples/MQ/pixelAlternative/src/CMakeLists.txt
@@ -1,5 +1,5 @@
 ################################################################################
-# Copyright (C) 2014-2022 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
+# Copyright (C) 2014-2023 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
 #                                                                              #
 #              This software is distributed under the terms of the             #
 #              GNU Lesser General Public Licence (LGPL) version 3,             #
@@ -34,8 +34,10 @@ target_include_directories(${target} PUBLIC
   $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
   $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/devices>
   $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
+)
 
-  # TODO: DELETE ME ONCE USING root targets
+# TODO: DELETE ME ONCE USING root targets
+target_include_directories(${target} SYSTEM PUBLIC
   ${ROOT_INCLUDE_DIR}
 )
 
diff --git a/examples/MQ/pixelDetector/src/CMakeLists.txt b/examples/MQ/pixelDetector/src/CMakeLists.txt
index 403de50b05..87f694f445 100644
--- a/examples/MQ/pixelDetector/src/CMakeLists.txt
+++ b/examples/MQ/pixelDetector/src/CMakeLists.txt
@@ -1,5 +1,5 @@
 ################################################################################
-# Copyright (C) 2014-2022 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
+# Copyright (C) 2014-2023 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
 #                                                                              #
 #              This software is distributed under the terms of the             #
 #              GNU Lesser General Public Licence (LGPL) version 3,             #
@@ -62,8 +62,10 @@ target_include_directories(${target} PUBLIC
   $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
   $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/devices>
   $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
+)
 
-  # TODO: DELETE ME ONCE USING root targets
+# TODO: DELETE ME ONCE USING root targets
+target_include_directories(${target} SYSTEM PUBLIC
   ${ROOT_INCLUDE_DIR}
 )
 
diff --git a/examples/MQ/pixelSimSplit/src/CMakeLists.txt b/examples/MQ/pixelSimSplit/src/CMakeLists.txt
index 428e0c0a1f..27da53320c 100644
--- a/examples/MQ/pixelSimSplit/src/CMakeLists.txt
+++ b/examples/MQ/pixelSimSplit/src/CMakeLists.txt
@@ -1,5 +1,5 @@
 ################################################################################
-# Copyright (C) 2014-2022 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
+# Copyright (C) 2014-2023 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
 #                                                                              #
 #              This software is distributed under the terms of the             #
 #              GNU Lesser General Public Licence (LGPL) version 3,             #
@@ -34,8 +34,10 @@ target_include_directories(${target} PUBLIC
   $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
   $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/devices>
   $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
+)
 
-  # TODO: DELETE ME ONCE USING root targets
+# TODO: DELETE ME ONCE USING root targets
+target_include_directories(${target} SYSTEM PUBLIC
   ${ROOT_INCLUDE_DIR}
 )
 
diff --git a/examples/MQ/serialization/CMakeLists.txt b/examples/MQ/serialization/CMakeLists.txt
index dd98970508..588c34fa8d 100644
--- a/examples/MQ/serialization/CMakeLists.txt
+++ b/examples/MQ/serialization/CMakeLists.txt
@@ -1,5 +1,5 @@
 ################################################################################
-# Copyright (C) 2014-2022 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
+# Copyright (C) 2014-2023 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
 #                                                                              #
 #              This software is distributed under the terms of the             #
 #              GNU Lesser General Public Licence (LGPL) version 3,             #
@@ -20,8 +20,10 @@ set_target_properties(${target} PROPERTIES ${PROJECT_LIBRARY_PROPERTIES})
 target_include_directories(${target} PUBLIC
   $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/data>
   $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
+)
 
-  # TODO: DELETE ME ONCE USING root targets
+# TODO: DELETE ME ONCE USING root targets
+target_include_directories(${target} SYSTEM PUBLIC
   ${ROOT_INCLUDE_DIR}
 )
 
diff --git a/examples/advanced/MbsTutorial/CMakeLists.txt b/examples/advanced/MbsTutorial/CMakeLists.txt
index 01ecb2053c..21594c83fc 100644
--- a/examples/advanced/MbsTutorial/CMakeLists.txt
+++ b/examples/advanced/MbsTutorial/CMakeLists.txt
@@ -1,5 +1,5 @@
 ################################################################################
-# Copyright (C) 2014-2022 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
+# Copyright (C) 2014-2023 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
 #                                                                              #
 #              This software is distributed under the terms of the             #
 #              GNU Lesser General Public Licence (LGPL) version 3,             #
@@ -25,8 +25,10 @@ set_target_properties(${target} PROPERTIES ${PROJECT_LIBRARY_PROPERTIES})
 target_include_directories(${target} PUBLIC
   $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
   $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
+)
 
-  # TODO: DELETE ME ONCE USING root targets
+# TODO: DELETE ME ONCE USING root targets
+target_include_directories(${target} SYSTEM PUBLIC
   ${ROOT_INCLUDE_DIR}
 )
 
diff --git a/examples/advanced/Tutorial3/CMakeLists.txt b/examples/advanced/Tutorial3/CMakeLists.txt
index de79437f94..dbb8b72993 100644
--- a/examples/advanced/Tutorial3/CMakeLists.txt
+++ b/examples/advanced/Tutorial3/CMakeLists.txt
@@ -1,5 +1,5 @@
 ################################################################################
-# Copyright (C) 2014-2022 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
+# Copyright (C) 2014-2023 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
 #                                                                              #
 #              This software is distributed under the terms of the             #
 #              GNU Lesser General Public Licence (LGPL) version 3,             #
@@ -110,8 +110,10 @@ target_include_directories(${target} PUBLIC
   $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/timeBasedSimulation>
   $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
   $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
+)
 
-  # TODO: DELETE ME ONCE USING root targets
+# TODO: DELETE ME ONCE USING root targets
+target_include_directories(${target} SYSTEM PUBLIC
   ${ROOT_INCLUDE_DIR}
 )
 
diff --git a/examples/advanced/propagator/src/CMakeLists.txt b/examples/advanced/propagator/src/CMakeLists.txt
index 240e1c76f1..0acfb8b6ab 100644
--- a/examples/advanced/propagator/src/CMakeLists.txt
+++ b/examples/advanced/propagator/src/CMakeLists.txt
@@ -1,5 +1,5 @@
  ################################################################################
- # Copyright (C) 2019-2022 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
+ # Copyright (C) 2019-2023 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
  #                                                                              #
  #              This software is distributed under the terms of the             #
  #              GNU Lesser General Public Licence (LGPL) version 3,             #
@@ -37,8 +37,10 @@ target_include_directories(${target} PUBLIC
   $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
   
   $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
+)
 
-  # TODO: DELETE ME ONCE USING root targets
+# TODO: DELETE ME ONCE USING root targets
+target_include_directories(${target} SYSTEM PUBLIC
   ${ROOT_INCLUDE_DIR}
 )
 
diff --git a/examples/common/eventdisplay/CMakeLists.txt b/examples/common/eventdisplay/CMakeLists.txt
index 0e58076f24..55d09ff90a 100644
--- a/examples/common/eventdisplay/CMakeLists.txt
+++ b/examples/common/eventdisplay/CMakeLists.txt
@@ -1,5 +1,5 @@
 ################################################################################
-# Copyright (C) 2014-2022 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
+# Copyright (C) 2014-2023 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
 #                                                                              #
 #              This software is distributed under the terms of the             #
 #              GNU Lesser General Public Licence (LGPL) version 3,             #
@@ -23,7 +23,10 @@ set_target_properties(${target} PROPERTIES ${PROJECT_LIBRARY_PROPERTIES})
 target_include_directories(${target} PUBLIC
   $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
   $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
-  # TODO: DELETE ME ONCE USING root targets
+)
+
+# TODO: DELETE ME ONCE USING root targets
+target_include_directories(${target} SYSTEM PUBLIC
   ${ROOT_INCLUDE_DIR}
 )
 
diff --git a/examples/common/gconfig/CMakeLists.txt b/examples/common/gconfig/CMakeLists.txt
index 27886b9ea5..a77319baa6 100644
--- a/examples/common/gconfig/CMakeLists.txt
+++ b/examples/common/gconfig/CMakeLists.txt
@@ -1,5 +1,5 @@
 ################################################################################
-# Copyright (C) 2014-2022 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
+# Copyright (C) 2014-2023 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
 #                                                                              #
 #              This software is distributed under the terms of the             #
 #              GNU Lesser General Public Licence (LGPL) version 3,             #
@@ -22,8 +22,10 @@ target_include_directories(${target} PUBLIC
   $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
   $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}/examples/common/mcstack>
   $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
+)
 
-  # TODO: DELETE ME ONCE USING root targets
+# TODO: DELETE ME ONCE USING root targets
+target_include_directories(${target} SYSTEM PUBLIC
   ${ROOT_INCLUDE_DIR}
 )
 
diff --git a/examples/common/mcstack/CMakeLists.txt b/examples/common/mcstack/CMakeLists.txt
index a98d10f903..14c2527c2d 100644
--- a/examples/common/mcstack/CMakeLists.txt
+++ b/examples/common/mcstack/CMakeLists.txt
@@ -1,5 +1,5 @@
 ################################################################################
-# Copyright (C) 2014-2022 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
+# Copyright (C) 2014-2023 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
 #                                                                              #
 #              This software is distributed under the terms of the             #
 #              GNU Lesser General Public Licence (LGPL) version 3,             #
@@ -26,8 +26,10 @@ set_target_properties(${target} PROPERTIES ${PROJECT_LIBRARY_PROPERTIES})
 target_include_directories(${target} PUBLIC
   $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
   $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
+)
 
-  # TODO: DELETE ME ONCE USING root targets
+# TODO: DELETE ME ONCE USING root targets
+target_include_directories(${target} SYSTEM PUBLIC
   ${ROOT_INCLUDE_DIR}
 )
 
diff --git a/examples/common/passive/CMakeLists.txt b/examples/common/passive/CMakeLists.txt
index 85e878f0d9..8483e51ae5 100644
--- a/examples/common/passive/CMakeLists.txt
+++ b/examples/common/passive/CMakeLists.txt
@@ -1,5 +1,5 @@
 ################################################################################
-# Copyright (C) 2014-2019 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
+# Copyright (C) 2014-2023 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
 #                                                                              #
 #              This software is distributed under the terms of the             #
 #              GNU Lesser General Public Licence (LGPL) version 3,             #
@@ -30,8 +30,10 @@ set_target_properties(${target} PROPERTIES ${PROJECT_LIBRARY_PROPERTIES})
 target_include_directories(${target} PUBLIC
   $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
   $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
+)
 
-  # TODO: DELETE ME ONCE USING root targets
+# TODO: DELETE ME ONCE USING root targets
+target_include_directories(${target} SYSTEM PUBLIC
   ${ROOT_INCLUDE_DIR}
 )
 
diff --git a/examples/simulation/Tutorial1/src/CMakeLists.txt b/examples/simulation/Tutorial1/src/CMakeLists.txt
index 4ad7cfffef..4c562c3d8a 100644
--- a/examples/simulation/Tutorial1/src/CMakeLists.txt
+++ b/examples/simulation/Tutorial1/src/CMakeLists.txt
@@ -1,5 +1,5 @@
 ################################################################################
-# Copyright (C) 2014-2022 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
+# Copyright (C) 2014-2023 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
 #                                                                              #
 #              This software is distributed under the terms of the             #
 #              GNU Lesser General Public Licence (LGPL) version 3,             #
@@ -28,8 +28,10 @@ set_target_properties(${target} PROPERTIES ${PROJECT_LIBRARY_PROPERTIES})
 target_include_directories(${target} PUBLIC
   $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
   $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
+)
 
-  # TODO: DELETE ME ONCE USING root targets
+# TODO: DELETE ME ONCE USING root targets
+target_include_directories(${target} SYSTEM PUBLIC
   ${ROOT_INCLUDE_DIR}
 )
 
diff --git a/examples/simulation/Tutorial2/src/CMakeLists.txt b/examples/simulation/Tutorial2/src/CMakeLists.txt
index 8595887774..202a004abc 100644
--- a/examples/simulation/Tutorial2/src/CMakeLists.txt
+++ b/examples/simulation/Tutorial2/src/CMakeLists.txt
@@ -1,5 +1,5 @@
 ################################################################################
-# Copyright (C) 2014-2022 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
+# Copyright (C) 2014-2023 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
 #                                                                              #
 #              This software is distributed under the terms of the             #
 #              GNU Lesser General Public Licence (LGPL) version 3,             #
@@ -28,8 +28,10 @@ set_target_properties(${target} PROPERTIES ${PROJECT_LIBRARY_PROPERTIES})
 target_include_directories(${target} PUBLIC
   $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
   $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
+)
 
-  # TODO: DELETE ME ONCE USING root targets
+# TODO: DELETE ME ONCE USING root targets
+target_include_directories(${target} SYSTEM PUBLIC
   ${ROOT_INCLUDE_DIR}
 )
 
diff --git a/examples/simulation/Tutorial4/src/CMakeLists.txt b/examples/simulation/Tutorial4/src/CMakeLists.txt
index fa8363ebd6..53d1014d29 100644
--- a/examples/simulation/Tutorial4/src/CMakeLists.txt
+++ b/examples/simulation/Tutorial4/src/CMakeLists.txt
@@ -1,5 +1,5 @@
 ################################################################################
-# Copyright (C) 2014-2022 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
+# Copyright (C) 2014-2023 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
 #                                                                              #
 #              This software is distributed under the terms of the             #
 #              GNU Lesser General Public Licence (LGPL) version 3,             #
@@ -47,8 +47,10 @@ target_include_directories(${target} PUBLIC
   $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/reco>
   $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/tools>
   $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
+)
 
-  # TODO: DELETE ME ONCE USING root targets
+# TODO: DELETE ME ONCE USING root targets
+target_include_directories(${target} SYSTEM PUBLIC
   ${ROOT_INCLUDE_DIR}
 )
 
diff --git a/examples/simulation/rutherford/src/CMakeLists.txt b/examples/simulation/rutherford/src/CMakeLists.txt
index 2dd99bf614..fc483390e0 100644
--- a/examples/simulation/rutherford/src/CMakeLists.txt
+++ b/examples/simulation/rutherford/src/CMakeLists.txt
@@ -1,5 +1,5 @@
 ################################################################################
-# Copyright (C) 2014-2022 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
+# Copyright (C) 2014-2023 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
 #                                                                              #
 #              This software is distributed under the terms of the             #
 #              GNU Lesser General Public Licence (LGPL) version 3,             #
@@ -25,8 +25,10 @@ set_target_properties(${target} PROPERTIES ${PROJECT_LIBRARY_PROPERTIES})
 target_include_directories(${target} PUBLIC
   $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
   $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
+)
 
-  # TODO: DELETE ME ONCE USING root targets
+# TODO: DELETE ME ONCE USING root targets
+target_include_directories(${target} SYSTEM PUBLIC
   ${ROOT_INCLUDE_DIR}
 )
 
diff --git a/fairtools/CMakeLists.txt b/fairtools/CMakeLists.txt
index 4442161335..440f406ff4 100644
--- a/fairtools/CMakeLists.txt
+++ b/fairtools/CMakeLists.txt
@@ -1,5 +1,5 @@
 ################################################################################
-# Copyright (C) 2014-2022 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
+# Copyright (C) 2014-2023 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
 #                                                                              #
 #              This software is distributed under the terms of the             #
 #              GNU Lesser General Public Licence (LGPL) version 3,             #
@@ -30,8 +30,10 @@ set_target_properties(${target} PROPERTIES OUTPUT_NAME FairTools)
 target_include_directories(${target} PUBLIC
   $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
   $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
+)
 
-  # TODO: DELETE ME ONCE USING root targets
+# TODO: DELETE ME ONCE USING root targets
+target_include_directories(${target} SYSTEM PUBLIC
   ${ROOT_INCLUDE_DIR}
 )
 
diff --git a/fairtools/MCConfigurator/CMakeLists.txt b/fairtools/MCConfigurator/CMakeLists.txt
index c4630675e2..46d60475a1 100644
--- a/fairtools/MCConfigurator/CMakeLists.txt
+++ b/fairtools/MCConfigurator/CMakeLists.txt
@@ -1,5 +1,5 @@
 ################################################################################
-# Copyright (C) 2014-2022 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
+# Copyright (C) 2014-2023 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
 #                                                                              #
 #              This software is distributed under the terms of the             #
 #              GNU Lesser General Public Licence (LGPL) version 3,             #
@@ -20,8 +20,10 @@ fairroot_library_settings(${target})
 target_include_directories(${target} PUBLIC
   $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
   $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
+)
 
-  # TODO: DELETE ME ONCE USING root targets
+# TODO: DELETE ME ONCE USING root targets
+target_include_directories(${target} SYSTEM PUBLIC
   ${ROOT_INCLUDE_DIR}
 )
 
diff --git a/fairtools/MCStepLogger/CMakeLists.txt b/fairtools/MCStepLogger/CMakeLists.txt
index a75265cb1e..a06fd43795 100644
--- a/fairtools/MCStepLogger/CMakeLists.txt
+++ b/fairtools/MCStepLogger/CMakeLists.txt
@@ -1,5 +1,5 @@
 ################################################################################
-#    Copyright (C) 2022 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH    #
+#    Copyright (C) 2023 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH    #
 #                                                                              #
 #              This software is distributed under the terms of the             #
 #              GNU Lesser General Public Licence (LGPL) version 3,             #
@@ -23,8 +23,10 @@ set_target_properties(${target} PROPERTIES OUTPUT_NAME FairMCStepLogger)
 target_include_directories(${target} PUBLIC
   $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
   $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
+)
 
-  # TODO: DELETE ME ONCE USING root targets
+# TODO: DELETE ME ONCE USING root targets
+target_include_directories(${target} SYSTEM PUBLIC
   ${ROOT_INCLUDE_DIR}
 )
 
diff --git a/geane/CMakeLists.txt b/geane/CMakeLists.txt
index 8606061414..cc359fb418 100644
--- a/geane/CMakeLists.txt
+++ b/geane/CMakeLists.txt
@@ -1,5 +1,5 @@
 ################################################################################
-# Copyright (C) 2014-2022 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
+# Copyright (C) 2014-2023 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
 #                                                                              #
 #              This software is distributed under the terms of the             #
 #              GNU Lesser General Public Licence (LGPL) version 3,             #
@@ -21,8 +21,10 @@ fairroot_library_settings(${target})
 target_include_directories(${target} PUBLIC
   $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
   $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
+)
 
-  # TODO: DELETE ME ONCE USING root targets
+# TODO: DELETE ME ONCE USING root targets
+target_include_directories(${target} SYSTEM PUBLIC
   ${ROOT_INCLUDE_DIR}
 )
 
diff --git a/generators/CMakeLists.txt b/generators/CMakeLists.txt
index 498410bf8c..a26a662edd 100644
--- a/generators/CMakeLists.txt
+++ b/generators/CMakeLists.txt
@@ -1,5 +1,5 @@
 ################################################################################
-# Copyright (C) 2014-2022 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
+# Copyright (C) 2014-2023 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
 #                                                                              #
 #              This software is distributed under the terms of the             #
 #              GNU Lesser General Public Licence (LGPL) version 3,             #
@@ -30,8 +30,10 @@ set_target_properties(${target} PROPERTIES OUTPUT_NAME Gen)
 target_include_directories(${target} PUBLIC
   $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
   $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
+)
 
-  # TODO: DELETE ME ONCE USING root targets
+# TODO: DELETE ME ONCE USING root targets
+target_include_directories(${target} SYSTEM PUBLIC
   ${ROOT_INCLUDE_DIR}
 )
 
diff --git a/geobase/CMakeLists.txt b/geobase/CMakeLists.txt
index 122e14316d..fd2cdae2f2 100644
--- a/geobase/CMakeLists.txt
+++ b/geobase/CMakeLists.txt
@@ -1,5 +1,5 @@
 ################################################################################
-# Copyright (C) 2014-2022 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
+# Copyright (C) 2014-2023 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
 #                                                                              #
 #              This software is distributed under the terms of the             #
 #              GNU Lesser General Public Licence (LGPL) version 3,             #
@@ -51,8 +51,10 @@ fairroot_library_settings(${target})
 target_include_directories(${target} PUBLIC
   $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
   $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
+)
 
-  # TODO: DELETE ME ONCE USING root targets
+# TODO: DELETE ME ONCE USING root targets
+target_include_directories(${target} SYSTEM PUBLIC
   ${ROOT_INCLUDE_DIR}
 )
 
diff --git a/parbase/CMakeLists.txt b/parbase/CMakeLists.txt
index 46242f46a1..1ff3afcc71 100644
--- a/parbase/CMakeLists.txt
+++ b/parbase/CMakeLists.txt
@@ -1,5 +1,5 @@
 ################################################################################
-# Copyright (C) 2014-2022 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
+# Copyright (C) 2014-2023 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
 #                                                                              #
 #              This software is distributed under the terms of the             #
 #              GNU Lesser General Public Licence (LGPL) version 3,             #
@@ -33,8 +33,10 @@ fairroot_library_settings(${target})
 target_include_directories(${target} PUBLIC
   $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
   $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
+)
 
-  # TODO: DELETE ME ONCE USING root targets
+# TODO: DELETE ME ONCE USING root targets
+target_include_directories(${target} SYSTEM PUBLIC
   ${ROOT_INCLUDE_DIR}
 )
 
diff --git a/parmq/CMakeLists.txt b/parmq/CMakeLists.txt
index 49461705b4..4854f62f6c 100644
--- a/parmq/CMakeLists.txt
+++ b/parmq/CMakeLists.txt
@@ -1,5 +1,5 @@
 ################################################################################
-# Copyright (C) 2014-2022 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
+# Copyright (C) 2014-2023 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
 #                                                                              #
 #              This software is distributed under the terms of the             #
 #              GNU Lesser General Public Licence (LGPL) version 3,             #
@@ -20,8 +20,10 @@ fairroot_library_settings(${target})
 target_include_directories(${target} PUBLIC
   $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
   $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
+)
 
-  # TODO: DELETE ME ONCE USING root targets
+# TODO: DELETE ME ONCE USING root targets
+target_include_directories(${target} SYSTEM PUBLIC
   ${ROOT_INCLUDE_DIR}
 )
 
diff --git a/trackbase/CMakeLists.txt b/trackbase/CMakeLists.txt
index 40246fcb7e..30baafb84c 100644
--- a/trackbase/CMakeLists.txt
+++ b/trackbase/CMakeLists.txt
@@ -1,5 +1,5 @@
 ################################################################################
-# Copyright (C) 2014-2022 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
+# Copyright (C) 2014-2023 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH  #
 #                                                                              #
 #              This software is distributed under the terms of the             #
 #              GNU Lesser General Public Licence (LGPL) version 3,             #
@@ -28,8 +28,10 @@ set_target_properties(${target} PROPERTIES OUTPUT_NAME TrkBase)
 target_include_directories(${target} PUBLIC
   $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
   $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
+)
 
-  # TODO: DELETE ME ONCE USING root targets
+# TODO: DELETE ME ONCE USING root targets
+target_include_directories(${target} SYSTEM PUBLIC
   ${ROOT_INCLUDE_DIR}
 )