diff --git a/InnerDetector/InDetValidation/InDetTruthVertexValidation/CMakeLists.txt b/InnerDetector/InDetValidation/InDetTruthVertexValidation/CMakeLists.txt
index 8d9c36b25eb9ee4a98b3a2879e58a503b7d2fcee..14eebba8b7d4c4a54b9b287a1aea11ff261d1954 100644
--- a/InnerDetector/InDetValidation/InDetTruthVertexValidation/CMakeLists.txt
+++ b/InnerDetector/InDetValidation/InDetTruthVertexValidation/CMakeLists.txt
@@ -33,8 +33,9 @@ find_package( ROOT COMPONENTS Core Geometry Tree MathCore Hist RIO pthread TBB )
 
 # Generate a CINT dictionary source file:
 atlas_add_root_dictionary( InDetTruthVertexValidationLib _cintDictSource
-                           ROOT_HEADERS Root/LinkDef.h
-                           EXTERNAL_PACKAGES ROOT )
+   ROOT_HEADERS InDetTruthVertexValidation/InDetVertexTruthMatchUtils.h
+   InDetTruthVertexValidation/InDetVertexTruthMatchTool.h Root/LinkDef.h
+   EXTERNAL_PACKAGES ROOT )
 
 # Component(s) in the package:
 atlas_add_library( InDetTruthVertexValidationLib
diff --git a/PhysicsAnalysis/TopPhys/TopPhysUtils/TopDataPreparation/CMakeLists.txt b/PhysicsAnalysis/TopPhys/TopPhysUtils/TopDataPreparation/CMakeLists.txt
index 006d0fda5b55af5a8e348294bfeb9419ac281c68..9d568ba0a74c2e88e9e25df5b91ca1753f3ac1fb 100644
--- a/PhysicsAnalysis/TopPhys/TopPhysUtils/TopDataPreparation/CMakeLists.txt
+++ b/PhysicsAnalysis/TopPhys/TopPhysUtils/TopDataPreparation/CMakeLists.txt
@@ -1,15 +1,15 @@
-# Auto-generated on: 2017-03-09 17:44:33.125987
 
 # Declare the name of this package:
-atlas_subdir( TopDataPreparation None )
+atlas_subdir( TopDataPreparation )
 
 # This package uses ROOT:
 find_package( ROOT REQUIRED COMPONENTS Core Gpad Tree Hist RIO MathCore Graf )
 
 # Generate a CINT dictionary source file:
 atlas_add_root_dictionary( TopDataPreparation _cintDictSource
-                           ROOT_HEADERS Root/LinkDef.h
-                           EXTERNAL_PACKAGES ROOT )
+   ROOT_HEADERS TopDataPreparation/SampleXsection.h
+   TopDataPreparation/SampleXsectionSvc.h Root/LinkDef.h
+   EXTERNAL_PACKAGES ROOT )
 
 # Build a library that other components can link against:
 atlas_add_library( TopDataPreparation Root/*.cxx Root/*.h Root/*.icc
diff --git a/PhysicsAnalysis/TopPhys/xAOD/TopAnalysis/CMakeLists.txt b/PhysicsAnalysis/TopPhys/xAOD/TopAnalysis/CMakeLists.txt
index 5369d691651856262f1ef83b0be93336640dfec1..61452def1bec7ab6ff6f7365f86a98851dd2ee47 100644
--- a/PhysicsAnalysis/TopPhys/xAOD/TopAnalysis/CMakeLists.txt
+++ b/PhysicsAnalysis/TopPhys/xAOD/TopAnalysis/CMakeLists.txt
@@ -1,7 +1,6 @@
-# Auto-generated on: 2017-03-08 14:47:33.629640
 
 # Declare the name of this package:
-atlas_subdir( TopAnalysis None )
+atlas_subdir( TopAnalysis )
 
 # This package depends on other packages:
 atlas_depends_on_subdirs( PUBLIC
@@ -31,13 +30,12 @@ atlas_depends_on_subdirs( PUBLIC
 # This package uses ROOT:
 find_package( ROOT REQUIRED COMPONENTS Core Gpad Tree Hist RIO MathCore Graf )
 
-# Custom definitions needed for this package:
-add_definitions( -g )
-
 # Generate a CINT dictionary source file:
 atlas_add_root_dictionary( TopAnalysis _cintDictSource
-                           ROOT_HEADERS Root/LinkDef.h
-                           EXTERNAL_PACKAGES ROOT )
+   ROOT_HEADERS TopAnalysis/ObjectLoaderStandardCuts.h
+   TopAnalysis/EventSaverFlatNtuple.h TopAnalysis/EventSaverxAOD.h
+   TopAnalysis/EventSaverxAODNext.h Root/LinkDef.h
+   EXTERNAL_PACKAGES ROOT )
 
 # Build a library that other components can link against:
 atlas_add_library( TopAnalysis Root/*.cxx Root/*.h Root/*.icc
diff --git a/PhysicsAnalysis/TopPhys/xAOD/TopConfiguration/CMakeLists.txt b/PhysicsAnalysis/TopPhys/xAOD/TopConfiguration/CMakeLists.txt
index 40fc8c714216072ae14018e554fb08773b4fb5de..4f7b254566bd7319e75728b627dd987045181dcb 100644
--- a/PhysicsAnalysis/TopPhys/xAOD/TopConfiguration/CMakeLists.txt
+++ b/PhysicsAnalysis/TopPhys/xAOD/TopConfiguration/CMakeLists.txt
@@ -1,7 +1,6 @@
-# Auto-generated on: 2017-03-08 14:47:35.608258
 
 # Declare the name of this package:
-atlas_subdir( TopConfiguration None )
+atlas_subdir( TopConfiguration )
 
 # This package depends on other packages:
 atlas_depends_on_subdirs( PUBLIC
@@ -11,12 +10,10 @@ atlas_depends_on_subdirs( PUBLIC
 find_package( ROOT REQUIRED COMPONENTS Core Gpad Tree Hist RIO MathCore Graf )
 find_package( Boost REQUIRED COMPONENTS iostreams )
 
-message( STATUS "${Boost_LIBRARIES}" )
-
 # Generate a CINT dictionary source file:
 atlas_add_root_dictionary( TopConfiguration _cintDictSource
-                           ROOT_HEADERS Root/LinkDef.h
-                           EXTERNAL_PACKAGES ROOT )
+   ROOT_HEADERS TopConfiguration/TopPersistentSettings.h Root/LinkDef.h
+   EXTERNAL_PACKAGES ROOT )
 
 # Build a library that other components can link against:
 atlas_add_library( TopConfiguration Root/*.cxx Root/*.h Root/*.icc
diff --git a/PhysicsAnalysis/TopPhys/xAOD/TopEvent/CMakeLists.txt b/PhysicsAnalysis/TopPhys/xAOD/TopEvent/CMakeLists.txt
index 867e742c8c54e5d74640ced11785ace31ce8419e..ef2ff4ab1debfb6b4f2f9c78d2806048afa0c2b2 100644
--- a/PhysicsAnalysis/TopPhys/xAOD/TopEvent/CMakeLists.txt
+++ b/PhysicsAnalysis/TopPhys/xAOD/TopEvent/CMakeLists.txt
@@ -1,7 +1,6 @@
-# Auto-generated on: 2017-03-08 14:47:36.020351
 
 # Declare the name of this package:
-atlas_subdir( TopEvent None )
+atlas_subdir( TopEvent )
 
 # This package depends on other packages:
 atlas_depends_on_subdirs( PUBLIC
@@ -26,8 +25,9 @@ find_package( ROOT REQUIRED COMPONENTS Core Gpad Tree Hist RIO MathCore Graf )
 
 # Generate a CINT dictionary source file:
 atlas_add_root_dictionary( TopEvent _cintDictSource
-                           ROOT_HEADERS Root/LinkDef.h
-                           EXTERNAL_PACKAGES ROOT )
+   ROOT_HEADERS TopEvent/SystematicEvent.h TopEvent/KLFitterResult.h
+   TopEvent/PseudoTopResult.h Root/LinkDef.h
+   EXTERNAL_PACKAGES ROOT )
 
 # Build a library that other components can link against:
 atlas_add_library( TopEvent Root/*.cxx Root/*.h Root/*.icc
diff --git a/PhysicsAnalysis/TopPhys/xAOD/TopEventReconstructionTools/CMakeLists.txt b/PhysicsAnalysis/TopPhys/xAOD/TopEventReconstructionTools/CMakeLists.txt
index b5c4a637ac3a2aea92449d201de47d004774ba2e..c3017dfafd18d6d416f218ceb7866598f4c05b81 100644
--- a/PhysicsAnalysis/TopPhys/xAOD/TopEventReconstructionTools/CMakeLists.txt
+++ b/PhysicsAnalysis/TopPhys/xAOD/TopEventReconstructionTools/CMakeLists.txt
@@ -1,7 +1,6 @@
-# Auto-generated on: 2017-03-08 14:47:36.489231
 
 # Declare the name of this package:
-atlas_subdir( TopEventReconstructionTools None )
+atlas_subdir( TopEventReconstructionTools )
 
 # This package depends on other packages:
 atlas_depends_on_subdirs( PUBLIC
@@ -21,8 +20,9 @@ find_package( KLFitter )
 
 # Generate a CINT dictionary source file:
 atlas_add_root_dictionary( TopEventReconstructionTools _cintDictSource
-                           ROOT_HEADERS Root/LinkDef.h
-                           EXTERNAL_PACKAGES ROOT )
+   ROOT_HEADERS TopEventReconstructionTools/TopEventReconstructionToolsLoader.h
+   Root/LinkDef.h
+   EXTERNAL_PACKAGES ROOT )
 
 # Build a library that other components can link against:
 atlas_add_library( TopEventReconstructionTools Root/*.cxx Root/*.h Root/*.icc
diff --git a/PhysicsAnalysis/TopPhys/xAOD/TopEventSelectionTools/CMakeLists.txt b/PhysicsAnalysis/TopPhys/xAOD/TopEventSelectionTools/CMakeLists.txt
index 7fb43493d7fba746a1ea1761ab31ee16a7e21fe7..3413593ed74b58b021ca87770a9512e41aca9207 100644
--- a/PhysicsAnalysis/TopPhys/xAOD/TopEventSelectionTools/CMakeLists.txt
+++ b/PhysicsAnalysis/TopPhys/xAOD/TopEventSelectionTools/CMakeLists.txt
@@ -1,7 +1,6 @@
-# Auto-generated on: 2017-03-08 14:47:36.708684
 
 # Declare the name of this package:
-atlas_subdir( TopEventSelectionTools None )
+atlas_subdir( TopEventSelectionTools )
 
 # This package depends on other packages:
 atlas_depends_on_subdirs( PUBLIC
@@ -16,13 +15,11 @@ atlas_depends_on_subdirs( PUBLIC
 # This package uses ROOT:
 find_package( ROOT REQUIRED COMPONENTS Core Gpad Tree Hist RIO MathCore Graf )
 
-# Custom definitions needed for this package:
-add_definitions( -g )
-
 # Generate a CINT dictionary source file:
 atlas_add_root_dictionary( TopEventSelectionTools _cintDictSource
-                           ROOT_HEADERS Root/LinkDef.h
-                           EXTERNAL_PACKAGES ROOT )
+   ROOT_HEADERS TopEventSelectionTools/ToolLoaderBase.h
+   TopEventSelectionTools/TopEventSelectionToolsLoader.h Root/LinkDef.h
+   EXTERNAL_PACKAGES ROOT )
 
 # Build a library that other components can link against:
 atlas_add_library( TopEventSelectionTools Root/*.cxx Root/*.h Root/*.icc
diff --git a/PhysicsAnalysis/TopPhys/xAOD/TopFakes/CMakeLists.txt b/PhysicsAnalysis/TopPhys/xAOD/TopFakes/CMakeLists.txt
index bf87cf3d7c5417042e15eb18f38040220f581ef4..18c2a2477a833ea557f1df47af41e1834ce1bb00 100644
--- a/PhysicsAnalysis/TopPhys/xAOD/TopFakes/CMakeLists.txt
+++ b/PhysicsAnalysis/TopPhys/xAOD/TopFakes/CMakeLists.txt
@@ -1,7 +1,6 @@
-# Auto-generated on: 2017-03-08 14:47:37.318937
 
 # Declare the name of this package:
-atlas_subdir( TopFakes None )
+atlas_subdir( TopFakes )
 
 # This package depends on other packages:
 atlas_depends_on_subdirs( PUBLIC
@@ -12,9 +11,14 @@ atlas_depends_on_subdirs( PUBLIC
 find_package( ROOT REQUIRED COMPONENTS Core Gpad Tree Hist RIO Math MathCore MathMore Graf Matrix )
 
 # Generate a CINT dictionary source file:
+set( _extraHeader )
+if( XAOD_STANDALONE )
+   set( _extraHeader TopFakes/TopFakesMMWeightCalculator.h )
+endif()
 atlas_add_root_dictionary( TopFakes _cintDictSource
-                           ROOT_HEADERS Root/LinkDef.h
-                           EXTERNAL_PACKAGES ROOT )
+   ROOT_HEADERS ${_extraHeader} TopFakes/FakesWeights.h TopFakes/MMEffSet.h
+   TopFakes/MMEfficiency.h TopFakes/MatrixUtils.h Root/LinkDef.h
+   EXTERNAL_PACKAGES ROOT )
 
 # Build a library that other components can link against:
 atlas_add_library( TopFakes Root/*.cxx Root/*.h Root/*.icc
diff --git a/PhysicsAnalysis/TopPhys/xAOD/TopObjectSelectionTools/CMakeLists.txt b/PhysicsAnalysis/TopPhys/xAOD/TopObjectSelectionTools/CMakeLists.txt
index 444d0abb932443cb6c8485273f1de870b40fe275..421048d9bed4a809e74359fd5e77c4154d8fbf36 100644
--- a/PhysicsAnalysis/TopPhys/xAOD/TopObjectSelectionTools/CMakeLists.txt
+++ b/PhysicsAnalysis/TopPhys/xAOD/TopObjectSelectionTools/CMakeLists.txt
@@ -1,7 +1,6 @@
-# Auto-generated on: 2017-03-08 14:47:37.990954
 
 # Declare the name of this package:
-atlas_subdir( TopObjectSelectionTools None )
+atlas_subdir( TopObjectSelectionTools )
 
 # This package depends on other packages:
 atlas_depends_on_subdirs( PUBLIC
@@ -31,13 +30,10 @@ atlas_depends_on_subdirs( PUBLIC
 # This package uses ROOT:
 find_package( ROOT REQUIRED COMPONENTS Core Gpad Tree Hist RIO MathCore Graf )
 
-# Custom definitions needed for this package:
-add_definitions( -g )
-
 # Generate a CINT dictionary source file:
 atlas_add_root_dictionary( TopObjectSelectionTools _cintDictSource
-                           ROOT_HEADERS Root/LinkDef.h
-                           EXTERNAL_PACKAGES ROOT )
+   ROOT_HEADERS TopObjectSelectionTools/RCJetMC15.h Root/LinkDef.h
+   EXTERNAL_PACKAGES ROOT )
 
 # Build a library that other components can link against:
 atlas_add_library( TopObjectSelectionTools Root/*.cxx Root/*.h Root/*.icc
diff --git a/PhysicsAnalysis/TopPhys/xAOD/TopPartons/CMakeLists.txt b/PhysicsAnalysis/TopPhys/xAOD/TopPartons/CMakeLists.txt
index 6ca87a65978478f07d23628e63367244600cdc62..e39ada9b15a41f896215f4c8c6cd9e3d783c23cf 100644
--- a/PhysicsAnalysis/TopPhys/xAOD/TopPartons/CMakeLists.txt
+++ b/PhysicsAnalysis/TopPhys/xAOD/TopPartons/CMakeLists.txt
@@ -1,7 +1,6 @@
-# Auto-generated on: 2017-03-08 14:47:38.930377
 
 # Declare the name of this package:
-atlas_subdir( TopPartons None )
+atlas_subdir( TopPartons )
 
 # This package depends on other packages:
 atlas_depends_on_subdirs( PUBLIC
@@ -15,13 +14,10 @@ atlas_depends_on_subdirs( PUBLIC
 # This package uses ROOT:
 find_package( ROOT REQUIRED COMPONENTS Core Gpad Tree Hist RIO MathCore TMVA Graf )
 
-# Custom definitions needed for this package:
-add_definitions( -g )
-
 # Generate a CINT dictionary source file:
 atlas_add_root_dictionary( TopPartons _cintDictSource
-                           ROOT_HEADERS Root/LinkDef.h
-                           EXTERNAL_PACKAGES ROOT )
+   ROOT_HEADERS TopPartons/PartonHistory.h Root/LinkDef.h
+   EXTERNAL_PACKAGES ROOT )
 
 # Build a library that other components can link against:
 atlas_add_library( TopPartons Root/*.cxx Root/*.h Root/*.icc