diff --git a/bindings/tpython/CMakeLists.txt b/bindings/tpython/CMakeLists.txt
index fafae367ef9f6..55e6aca6d999b 100644
--- a/bindings/tpython/CMakeLists.txt
+++ b/bindings/tpython/CMakeLists.txt
@@ -8,11 +8,16 @@
 # CMakeLists.txt file for building TPython
 ###########################################################
 
+set(TPYTHON_HEADERS
+  TPyArg.h
+  TPyClassGenerator.h
+  TPyReturn.h
+  TPython.h
+)
+
 ROOT_STANDARD_LIBRARY_PACKAGE(ROOTTPython
   HEADERS
-    TPyArg.h
-    TPyReturn.h
-    TPython.h
+    ${TPYTHON_HEADERS}
   SOURCES
     src/TPyArg.cxx
     src/TPyClassGenerator.cxx
@@ -30,6 +35,18 @@ ROOT_STANDARD_LIBRARY_PACKAGE(ROOTTPython
     Python3::Python
 )
 
+set(RELATIVE_INC_HEADERS ${TPYTHON_HEADERS})
+list(TRANSFORM RELATIVE_INC_HEADERS PREPEND inc/)
+target_sources(ROOTTPython
+PRIVATE
+  FILE_SET private_header_files
+  TYPE HEADERS
+  BASE_DIRS inc/
+  FILES
+    ${RELATIVE_INC_HEADERS}
+    inc/LinkDef.h
+)
+
 # On Windows we can't use the stable ABI yet: it requires linking against a
 # different libpython, so as long as we don't build all translation units in
 # the ROOT Pythonization library with the stable ABI we should not use it.
diff --git a/main/CMakeLists.txt b/main/CMakeLists.txt
index e7c447f54cd95..f25cd29f56dd6 100644
--- a/main/CMakeLists.txt
+++ b/main/CMakeLists.txt
@@ -142,20 +142,33 @@ endif()
 add_dependencies(genreflex rootcling)
 add_dependencies(rootcint rootcint)
 
+add_library(rootexecutableHelpers INTERFACE)
+target_sources(rootexecutableHelpers
+PUBLIC
+  FILE_SET HEADERS
+  TYPE HEADERS
+  BASE_DIRS src/
+  FILES
+    src/RootObjTree.hxx
+    src/RootObjTree.cxx
+    src/logging.hxx
+    src/wildcards.hpp
+)
+
 if (TARGET Gui)
-  ROOT_EXECUTABLE(rootbrowse src/rootbrowse.cxx LIBRARIES RIO Core Rint Gui)
+  ROOT_EXECUTABLE(rootbrowse src/rootbrowse.cxx LIBRARIES RIO Core Rint Gui rootexecutableHelpers)
   target_include_directories(rootbrowse PRIVATE ${CMAKE_SOURCE_DIR}/core/utils/inc)
 endif()
 
-ROOT_EXECUTABLE(rootcp src/rootcp.cxx LIBRARIES RIO Tree Core Rint)
+ROOT_EXECUTABLE(rootcp src/rootcp.cxx LIBRARIES RIO Tree Core Rint rootexecutableHelpers)
 target_include_directories(rootcp PRIVATE ${CMAKE_SOURCE_DIR}/core/utils/inc)
 
-ROOT_EXECUTABLE(rootls src/rootls.cxx LIBRARIES RIO Tree Core Rint ROOTNTuple)
+ROOT_EXECUTABLE(rootls src/rootls.cxx LIBRARIES RIO Tree Core Rint ROOTNTuple rootexecutableHelpers)
 target_include_directories(rootls PRIVATE ${CMAKE_SOURCE_DIR}/core/utils/inc)
 
-ROOT_EXECUTABLE(rootmkdir src/rootmkdir.cxx LIBRARIES RIO Core Rint)
+ROOT_EXECUTABLE(rootmkdir src/rootmkdir.cxx LIBRARIES RIO Core Rint rootexecutableHelpers)
 target_include_directories(rootmkdir PRIVATE ${CMAKE_SOURCE_DIR}/core/utils/inc)
 
-ROOT_EXECUTABLE(rootrm src/rootrm.cxx LIBRARIES RIO Core Rint)
+ROOT_EXECUTABLE(rootrm src/rootrm.cxx LIBRARIES RIO Core Rint rootexecutableHelpers)
 target_include_directories(rootrm PRIVATE ${CMAKE_SOURCE_DIR}/core/utils/inc)
 
diff --git a/misc/rmkdepend/CMakeLists.txt b/misc/rmkdepend/CMakeLists.txt
index 2f0c9ccf4fee7..89640337e7108 100644
--- a/misc/rmkdepend/CMakeLists.txt
+++ b/misc/rmkdepend/CMakeLists.txt
@@ -15,3 +15,15 @@ ROOT_EXECUTABLE(rmkdepend
   parse.c
   pr.c
 )
+
+target_sources(rmkdepend
+PRIVATE
+  FILE_SET private_header_files
+  TYPE HEADERS
+  BASE_DIRS ./
+  FILES
+    def.h
+    ifparser.h
+    imakemdep.h
+)
+
diff --git a/montecarlo/eg/CMakeLists.txt b/montecarlo/eg/CMakeLists.txt
index f7854638d40e5..81fe9143d95f0 100644
--- a/montecarlo/eg/CMakeLists.txt
+++ b/montecarlo/eg/CMakeLists.txt
@@ -9,18 +9,22 @@
 # @author Pere Mato, CERN
 ############################################################################
 
+set(EG_HEADERS
+  TAttParticle.h
+  TDatabasePDG.h
+  TDecayChannel.h
+  TGenerator.h
+  TPDGCode.h
+  TParticleClassPDG.h
+  TParticle.h
+  TParticlePDG.h
+  TPrimary.h
+  TVirtualMCDecayer.h
+)
+
 ROOT_STANDARD_LIBRARY_PACKAGE(EG
   HEADERS
-    TAttParticle.h
-    TDatabasePDG.h
-    TDecayChannel.h
-    TGenerator.h
-    TPDGCode.h
-    TParticleClassPDG.h
-    TParticle.h
-    TParticlePDG.h
-    TPrimary.h
-    TVirtualMCDecayer.h
+    ${EG_HEADERS}
   SOURCES
     src/TAttParticle.cxx
     src/TDatabasePDG.cxx
@@ -41,4 +45,18 @@ ROOT_STANDARD_LIBRARY_PACKAGE(EG
     ROOTX3dViewer
 )
 
+set(RELATIVE_INC_HEADERS ${EG_HEADERS})
+list(TRANSFORM RELATIVE_INC_HEADERS PREPEND inc/)
+target_sources(EG
+PRIVATE
+  FILE_SET private_header_files
+  TYPE HEADERS
+  BASE_DIRS inc/
+  FILES
+    ${RELATIVE_INC_HEADERS}
+    inc/LinkDef.h
+    inc/Hepevt.h
+    inc/cfortran.h
+)
+
 ROOT_ADD_TEST_SUBDIRECTORY(test)
diff --git a/montecarlo/pythia8/CMakeLists.txt b/montecarlo/pythia8/CMakeLists.txt
index cb922369293d1..6c4f838eafcda 100644
--- a/montecarlo/pythia8/CMakeLists.txt
+++ b/montecarlo/pythia8/CMakeLists.txt
@@ -12,10 +12,14 @@
 # required also for cling
 include_directories(${PYTHIA8_INCLUDE_DIR})
 
+set(EGPYTHIA8_HEADERS
+  TPythia8.h
+  TPythia8Decayer.h
+)
+
 ROOT_STANDARD_LIBRARY_PACKAGE(EGPythia8
   HEADERS
-    TPythia8.h
-    TPythia8Decayer.h
+    ${EGPYTHIA8_HEADERS}
   SOURCES
     src/TPythia8.cxx
     src/TPythia8Decayer.cxx
@@ -26,6 +30,18 @@ ROOT_STANDARD_LIBRARY_PACKAGE(EGPythia8
     Physics
 )
 
+set(RELATIVE_INC_HEADERS ${EGPYTHIA8_HEADERS})
+list(TRANSFORM RELATIVE_INC_HEADERS PREPEND inc/)
+target_sources(EGPythia8
+PRIVATE
+  FILE_SET private_header_files
+  TYPE HEADERS
+  BASE_DIRS inc/
+  FILES
+    ${RELATIVE_INC_HEADERS}
+    inc/LinkDef.h
+)
+
 ROOT_ADD_CXX_FLAG(_EGPythia8_FLAGS -Wno-delete-non-virtual-dtor)
 ROOT_ADD_CXX_FLAG(_EGPythia8_FLAGS -Wno-misleading-indentation)
 ROOT_ADD_CXX_FLAG(_EGPythia8_FLAGS -Wno-overloaded-virtual)