diff --git a/Tools/AthDataQuality/CMakeLists.txt b/Tools/AthDataQuality/CMakeLists.txt
index 867eda38130e13a355bcbf07a7b2214955c499b7..2ad01452d32819d9b797b5a74e6a8a08d6fe8c51 100644
--- a/Tools/AthDataQuality/CMakeLists.txt
+++ b/Tools/AthDataQuality/CMakeLists.txt
@@ -1,13 +1,8 @@
-################################################################################
-# Package: AthDataQuality
-################################################################################
+# Copyright (C) 2002-2020 CERN for the benefit of the ATLAS collaboration
 
 # Declare the package name:
 atlas_subdir( AthDataQuality )
 
-# Declare the package's dependencies:
-atlas_depends_on_subdirs( PRIVATE ART )
-
 # Install files from the package:
 atlas_install_python_modules( python/*.py )
 atlas_install_runtime( test/*.sh )
diff --git a/Tools/FilePeeker/CMakeLists.txt b/Tools/FilePeeker/CMakeLists.txt
index 55244d5d9ce24c9ad53e70533cb1fbe983763153..71227e12e947dee42e66a2b353f7206d437037ee 100644
--- a/Tools/FilePeeker/CMakeLists.txt
+++ b/Tools/FilePeeker/CMakeLists.txt
@@ -1,39 +1,22 @@
-################################################################################
-# Package: FilePeekers
-################################################################################
+# Copyright (C) 2002-2020 CERN for the benefit of the ATLAS collaboration
 
 # Declare the package name:
 atlas_subdir( FilePeeker )
 
 # Possible extra dependencies:
-set( extra_dep )
 set( extra_libs )
 if( NOT SIMULATIONBASE )
-  set( extra_dep Event/ByteStreamEventTPCnv )
   set( extra_libs ByteStreamEventTPCnv )
 endif()
 
-
-# Declare the package's dependencies:
-atlas_depends_on_subdirs( PUBLIC
-                          PRIVATE
-                          Event/EventTPCnv
-                          Database/IOVDbTPCnv
-                          ${extra_dep})
-
-
 # External dependencies:
+find_package( Boost )
 find_package( ROOT COMPONENTS Core Tree RIO)
 if( NOT SIMULATIONBASE )
-  find_package( tdaq-common COMPONENTS DataReader EventStorage ers )
+  find_package( tdaq-common COMPONENTS DataReader EventStorage )
 endif()
 
-find_package( Boost )
-
-# tag ROOTBasicLibs was not recognized in automatic conversion in cmt2cmake
-
 # Component(s) in the package:
-
 atlas_add_executable( PoolFilePeeker
                       src/PoolFilePeeker.cxx
                       src/FileMetaData.cxx
@@ -50,4 +33,4 @@ if( NOT SIMULATIONBASE )
 endif()
 
 # Install files from the package:
-atlas_install_python_modules( python/*.py )
+atlas_install_python_modules( python/*.py POST_BUILD_CMD ${ATLAS_FLAKE8} )
diff --git a/Tools/FilePeeker/python/FilePeeker.py b/Tools/FilePeeker/python/FilePeeker.py
index 45d4070b3816a9f18a06b1f0bd202ea6c2b7234c..1a5aa9d161f13385fd1ab164749d075c931807a2 100644
--- a/Tools/FilePeeker/python/FilePeeker.py
+++ b/Tools/FilePeeker/python/FilePeeker.py
@@ -1,8 +1,9 @@
-# Copyright (C) 2002-2019 CERN for the benefit of the ATLAS collaboration
+# Copyright (C) 2002-2020 CERN for the benefit of the ATLAS collaboration
 
 from __future__ import print_function
 
-import os,sys
+import os
+import sys
 from subprocess import check_output
 
 
@@ -31,9 +32,9 @@ def PeekFiles(inputfiles):
     fullResult=dict()
     for line in retval.split(os.linesep):
         linesplit=line.split(":")
-        if len(linesplit)!=2: continue;
-        k=linesplit[0].strip();
-        v=linesplit[1].strip();
+        if len(linesplit)!=2: continue
+        k=linesplit[0].strip()
+        v=linesplit[1].strip()
         if len(v)==0: continue
         if (k=="File"):
             result=dict()
diff --git a/Tools/FullChainTransforms/CMakeLists.txt b/Tools/FullChainTransforms/CMakeLists.txt
index ec92bf021352f81b895b0f34a759e45ea0824f28..ffd6f4efcc2bf79b49d06a042f9ac4d7d3ab1bac 100644
--- a/Tools/FullChainTransforms/CMakeLists.txt
+++ b/Tools/FullChainTransforms/CMakeLists.txt
@@ -1,19 +1,9 @@
-################################################################################
-# Package: FullChainTransforms
-################################################################################
+# Copyright (C) 2002-2020 CERN for the benefit of the ATLAS collaboration
 
 # Declare the package name:
 atlas_subdir( FullChainTransforms )
 
-# Declare the package's dependencies:
-atlas_depends_on_subdirs( PUBLIC
-                          PhysicsAnalysis/PATJobTransforms
-                          Reconstruction/RecJobTransforms
-                          Simulation/SimuJobTransforms
-                          Tools/PyJobTransforms )
-
 # Install files from the package:
-atlas_install_python_modules( python/*.py )
+atlas_install_python_modules( python/*.py POST_BUILD_CMD ${ATLAS_FLAKE8} )
+atlas_install_runtime( scripts/*.py POST_BUILD_CMD ${ATLAS_FLAKE8} )
 atlas_install_joboptions( share/*.py )
-atlas_install_runtime( scripts/*.py )
-
diff --git a/Tools/FullChainTransforms/python/FastChainWriteMetadata.py b/Tools/FullChainTransforms/python/FastChainWriteMetadata.py
index 9e71a8d21a467e3f2314646ad65ada2c5bc55aed..d222bc6dc08a2c35e7b097fddd8307e9b3753a37 100644
--- a/Tools/FullChainTransforms/python/FastChainWriteMetadata.py
+++ b/Tools/FullChainTransforms/python/FastChainWriteMetadata.py
@@ -1,4 +1,4 @@
-# Copyright (C) 2002-2018 CERN for the benefit of the ATLAS collaboration
+# Copyright (C) 2002-2020 CERN for the benefit of the ATLAS collaboration
 
 from AthenaCommon.Logging import logging
 logFastChainWriteMetadata = logging.getLogger( 'FastChainWriteMetadata' )
@@ -190,11 +190,11 @@ def writeDigitizationMetadata():
         attrname = det+"_on"
         checkfn = getattr(DetFlags.digitize, attrname, None)
         if checkfn is None:
-            logFastChainWriteMetadata.info("No attribute '%s' found on DetFlags.digitize" % attrname)
+            logFastChainWriteMetadata.info("No attribute '%s' found on DetFlags.digitize", attrname)
             continue
         if checkfn():
             digiDets.append(det)
-    logFastChainWriteMetadata.info("Setting 'DigitizedDetectors' = %s" % repr(digiDets))
+    logFastChainWriteMetadata.info("Setting 'DigitizedDetectors' = %s", repr(digiDets))
     dbFiller.addDigitParam('DigitizedDetectors', repr(digiDets))
 
     #-------------------------------------------------
@@ -230,7 +230,7 @@ def createSimulationParametersMetadata():
     dbFiller.genSimDb()
     folder = "/Simulation/Parameters"
     dbConnection = "sqlite://;schema=SimParams.db;dbname=SIMPARAM"
-    import IOVDbSvc.IOVDb
+    import IOVDbSvc.IOVDb  # noqa: F401
     from AthenaCommon.AppMgr import ServiceMgr
     ServiceMgr.IOVDbSvc.Folders += [ folder + "<dbConnection>" + dbConnection + "</dbConnection>" ]
     ServiceMgr.IOVDbSvc.FoldersToMetaData += [folder]
diff --git a/Tools/FullChainTransforms/scripts/FastChain_tf.py b/Tools/FullChainTransforms/scripts/FastChain_tf.py
index 6ac4ee33b3fd43257aed0077e9b35de9336a14e4..e8fc864c45fde63c8bf1c3ef5832c00c39fab204 100755
--- a/Tools/FullChainTransforms/scripts/FastChain_tf.py
+++ b/Tools/FullChainTransforms/scripts/FastChain_tf.py
@@ -1,6 +1,6 @@
 #! /usr/bin/env python
 
-# Copyright (C) 2002-2018 CERN for the benefit of the ATLAS collaboration
+# Copyright (C) 2002-2020 CERN for the benefit of the ATLAS collaboration
 
 #  FastChain_tf.py
 #  One step transform to run SIM+DIGI as one job, then reco
@@ -10,18 +10,16 @@
 import sys
 import time
 
-import logging
-
 # Setup core logging here
 from PyJobTransforms.trfLogger import msg
-msg.info('logging set in %s' % sys.argv[0])
+msg.info('logging set in %s', sys.argv[0])
 
 from PyJobTransforms.transform import transform
 from PyJobTransforms.trfExe import athenaExecutor
 from PyJobTransforms.trfArgs import addAthenaArguments, addDetectorArguments, addTriggerArguments
 from PyJobTransforms.trfDecorators import stdTrfExceptionHandler, sigUsrStackTrace
 from RecJobTransforms.recTransformUtils import addRecoSubsteps, addAllRecoArgs
-from SimuJobTransforms.simTrfArgs import addForwardDetTrfArgs, addCommonSimTrfArgs, addBasicDigiArgs, addCommonSimDigTrfArgs, addTrackRecordArgs, addSim_tfArgs, addPileUpTrfArgs
+from SimuJobTransforms.simTrfArgs import addCommonSimTrfArgs, addBasicDigiArgs, addCommonSimDigTrfArgs, addTrackRecordArgs, addSim_tfArgs, addPileUpTrfArgs
 from PATJobTransforms.PATTransformUtils import addPhysValidationFiles, addValidationArguments, appendPhysValidationSubstep
 
 from PyJobTransforms.trfArgClasses import argFactory, argList, argRDOFile
@@ -30,14 +28,14 @@ from PyJobTransforms.trfArgClasses import argFactory, argList, argRDOFile
 @sigUsrStackTrace
 def main():
 
-    msg.info('This is %s' % sys.argv[0])
+    msg.info('This is %s', sys.argv[0])
 
     trf = getTransform()
     trf.parseCmdLineArgs(sys.argv[1:])
     trf.execute()
     trf.generateReport()
 
-    msg.info("%s stopped at %s, trf exit code %d" % (sys.argv[0], time.asctime(), trf.exitCode))
+    msg.info("%s stopped at %s, trf exit code %d", sys.argv[0], time.asctime(), trf.exitCode)
     sys.exit(trf.exitCode)
 
 def getTransform():
@@ -51,7 +49,7 @@ def getTransform():
                                    inData=['NULL','EVNT'],
                                    outData=['RDO','NULL'] ))
     # Overlay
-    from EventOverlayJobTransforms.overlayTransformUtils import addOverlay_PoolSubstep, addOverlay_PoolArguments
+    from EventOverlayJobTransforms.overlayTransformUtils import addOverlay_PoolArguments
     executorSet.add(athenaExecutor(name = 'OverlayPool', skeletonFile = 'EventOverlayJobTransforms/skeleton.OverlayPool_tf.py',
                                    substep = 'overlayPOOL', tryDropAndReload = False, perfMonFile = 'ntuple.pmon.gz',
                                    inData = [('HITS', 'RDO_BKG')], outData = ['RDO', 'RDO_SGNL']))
diff --git a/Tools/FullChainTransforms/scripts/FullChain_tf.py b/Tools/FullChainTransforms/scripts/FullChain_tf.py
index be0f01bc5c3b6be89f2a0db50c0da647e65260b7..c90303d8b6ffa1ebfbc7cef861d4a2e00ec0d619 100755
--- a/Tools/FullChainTransforms/scripts/FullChain_tf.py
+++ b/Tools/FullChainTransforms/scripts/FullChain_tf.py
@@ -1,45 +1,40 @@
 #! /usr/bin/env python
 
-# Copyright (C) 2002-2017 CERN for the benefit of the ATLAS collaboration
+# Copyright (C) 2002-2020 CERN for the benefit of the ATLAS collaboration
 
 ## FullChain_tf.py 
 #  One step transform that will start from EVNT and run ISF right through 
 #  to AOD output
-#  @version $Id: FullChain_tf.py 592310 2014-04-10 09:51:28Z graemes $ 
 
 import sys
 import time
 
-import logging
-
 # Setup core logging here
 from PyJobTransforms.trfLogger import msg
-msg.info('logging set in %s' % sys.argv[0])
+msg.info('logging set in %s', sys.argv[0])
 
 from PyJobTransforms.transform import transform
 from PyJobTransforms.trfExe import athenaExecutor
 from PyJobTransforms.trfArgs import addAthenaArguments, addDetectorArguments, addTriggerArguments
 from PyJobTransforms.trfDecorators import stdTrfExceptionHandler, sigUsrStackTrace
 from RecJobTransforms.recTransformUtils import addRecoSubsteps, addAllRecoArgs
-from SimuJobTransforms.simTrfArgs import addForwardDetTrfArgs, addCosmicsTrfArgs, addForwardDetTrfArgs, addCommonSimTrfArgs, addBasicDigiArgs, addPileUpTrfArgs, addCommonSimDigTrfArgs, addTrackRecordArgs, addSim_tfArgs
+from SimuJobTransforms.simTrfArgs import addCosmicsTrfArgs, addForwardDetTrfArgs, addCommonSimTrfArgs, addBasicDigiArgs, addPileUpTrfArgs, addCommonSimDigTrfArgs, addTrackRecordArgs, addSim_tfArgs
 from SimuJobTransforms.SimTransformUtils import addDigitizationSubstep
 
-import PyJobTransforms.trfArgClasses as trfArgClasses
-
 ListOfDefaultPositionalKeys=['--AFPOn', '--ALFAOn', '--AMIConfig', '--AMITag', '--AddCaloDigi', '--CosmicFilterVolume', '--CosmicFilterVolume2', '--CosmicPtSlice', '--DBRelease', '--DataRunNumber', '--FwdRegionOn', '--LucidOn', '--ZDCOn', '--asetup', '--athena', '--athenaopts', '--autoConfiguration', '--beamType', '--bunchSpacing', '--checkEventCount', '--command', '--conditionsTag', '--digiRndmSvc', '--digiSeedOffset1', '--digiSeedOffset2', '--doAllNoise', '--enableLooperKiller', '--env', '--eventAcceptanceEfficiency', '--execOnly', '--firstEvent', '--geometryVersion', '--ignoreErrors', '--ignoreFiles', '--ignorePatterns', '--imf', '--inputAODFile', '--inputBSFile', '--inputBeamGasHitsFile', '--inputBeamHaloHitsFile', '--inputCavernHitsFile', '--inputESDFile', '--inputEVNTFile', '--inputEVNT_TRFile', '--inputHITSFile', '--inputHighPtMinbiasHitsFile', '--inputLowPtMinbiasHitsFile', '--inputNTUP_COMMONFile', '--inputRDOFile', '--jobNumber', '--maxEvents', '--numberOfBeamGas', '--numberOfBeamHalo', '--numberOfCavernBkg', '--numberOfHighPtMinBias', '--numberOfLowPtMinBias', '--orphanKiller', '--outputAODFile', '--outputAOD_SKIMFile', '--outputD2AODM_WMUNUFile', '--outputD2AODM_ZEEFile', '--outputD2AODM_ZMUMUFile', '--outputD2AOD_DIONIAFile', '--outputD2AOD_DIPHOFile', '--outputD2AOD_H4LFile', '--outputD2AOD_WENUFile', '--outputD2AOD_ZEEFile', '--outputD2ESDM_TRKJETFile', '--outputD2ESD_DIPHOFile', '--outputD2ESD_JPSIUPSMMFile', '--outputD2ESD_WENUFile', '--outputD2ESD_WMUNUFile', '--outputD2ESD_ZMMFile', '--outputDAODFile', '--outputDAODM_HIGHMJJFile', '--outputDAODM_HSG1File', '--outputDAODM_SGLEMFile', '--outputDAODM_SGLMUFile', '--outputDAODM_SGLPHFile', '--outputDAODM_SGLTAUFile', '--outputDAOD_2EMFile', '--outputDAOD_2L2QHSG2File', '--outputDAOD_2LHSG2File', '--outputDAOD_2MUFile', '--outputDAOD_2PHFile', '--outputDAOD_4LHSG2File', '--outputDAOD_EGLOOSEFile', '--outputDAOD_ELLOOSE18File', '--outputDAOD_ELLOOSEFile', '--outputDAOD_EMJETFile', '--outputDAOD_EMMETFile', '--outputDAOD_EMMUFile', '--outputDAOD_EMTAUFile', '--outputDAOD_H4LBREMRECFile', '--outputDAOD_HIGHMDIJETFile', '--outputDAOD_HSG2File', '--outputDAOD_JETMETFile', '--outputDAOD_JPSIMUMUFile', '--outputDAOD_MUFile', '--outputDAOD_MUJETFile', '--outputDAOD_MUMETFile', '--outputDAOD_MUTAUFile', '--outputDAOD_ONIAMUMUFile', '--outputDAOD_PHLOOSEFile', '--outputDAOD_RNDMFile', '--outputDAOD_SKIMELFile', '--outputDAOD_SUSYEGAMMAFile', '--outputDAOD_SUSYJETSFile', '--outputDAOD_SUSYMUONSFile', '--outputDAOD_TAUJETFile', '--outputDAOD_TESTFile', '--outputDAOD_UPSIMUMUFile', '--outputDAOD_ZEEGAMMAFile', '--outputDAOD_ZMUMUGAMMAFile', '--outputDESDM_EOVERPFile', '--outputDESDM_ALLCELLSFile', '--outputDESDM_BEAMSPOTFile', '--outputDESDM_EGAMMAFile', '--outputDESDM_METFile', '--outputDESDM_MUONFile', '--outputDESDM_RPVLLCCFile', '--outputDESDM_RPVLLFile', '--outputDESDM_TRACKFile', '--outputDESD_CALJETFile', '--outputDESD_CALOCOMMFile', '--outputDESD_COLLCANDFile', '--outputDESD_CTLFWJETFile', '--outputDESD_EGTAUCOMMFile', '--outputDESD_EMCLUSCOMMFile', '--outputDESD_FWJETFile', '--outputDESD_HIRAREFile', '--outputDESD_IDCOMMFile', '--outputDESD_IDPROJCOMMFile', '--outputDESD_MBIASFile', '--outputDESD_MUONCOMMFile', '--outputDESD_ONIAMUMUHIFile', '--outputDESD_PHOJETFile', '--outputDESD_PIXELCOMMFile', '--outputDESD_PRESCALEDFile', '--outputDESD_RANDOMCOMMFile', '--outputDESD_RPCCOMMFile', '--outputDESD_SCTCOMMFile', '--outputDESD_SGLELFile', '--outputDESD_SGLMUFile', '--outputDESD_SKIMELFile', '--outputDESD_TGCCOMMFile', '--outputDESD_TILECOMMFile', '--outputDNTUPFile', '--outputDRAW_IDPROJCOMMFile', '--outputDRAW_WENUFile', '--outputDRAW_WMUNUFile', '--outputDRAW_ZEEFile', '--outputDRAW_ZMUMUFile', '--outputESDFile', '--outputEVNT_TRFile', '--outputHISTFile', '--outputHIST_AODFile', '--outputHITSFile', '--outputNTUP_2L2QHSG2File', '--outputNTUP_2LHSG2File', '--outputNTUP_4LHSG2File', '--outputNTUP_BKGDFile', '--outputNTUP_BTAGD3PDFile', '--outputNTUP_BTAGEFFFile', '--outputNTUP_BTAGFULLFile', '--outputNTUP_BTAGGHOSTFile', '--outputNTUP_BTAGSLIMFile', '--outputNTUP_CLUSTERCORRECTIONFile', '--outputNTUP_COMMONFile', '--outputNTUP_EGAMMAFile', '--outputNTUP_ENHBIASFile', '--outputNTUP_FASTMONFile', '--outputNTUP_HECNOISEFile', '--outputNTUP_HIFile', '--outputNTUP_HIGHMULTFile', '--outputNTUP_HSG2File', '--outputNTUP_HSG5GAMHFile', '--outputNTUP_HSG5GAMZFile', '--outputNTUP_HSG5WHFile', '--outputNTUP_HSG5WHQFile', '--outputNTUP_HSG5WHUFile', '--outputNTUP_HSG5ZBBFile', '--outputNTUP_HSG5ZHLLFile', '--outputNTUP_HSG5ZHLLUFile', '--outputNTUP_HSG5ZHMETFile', '--outputNTUP_HSG5ZHMETUFile', '--outputNTUP_IDVTXFile', '--outputNTUP_IDVTXLUMIFile', '--outputNTUP_JETMETEMCLFile', '--outputNTUP_JETMETFULLFile', '--outputNTUP_JETMETFile', '--outputNTUP_JETMETWZFile', '--outputNTUP_L1CALOFile', '--outputNTUP_L1CALOPROBFile', '--outputNTUP_L1TGCFile', '--outputNTUP_LARNOISEFile', '--outputNTUP_MCPFile', '--outputNTUP_MINBIASFile', '--outputNTUP_MUFASTFile', '--outputNTUP_MUONCALIBFile', '--outputNTUP_MUONFile', '--outputNTUP_PHOTONFile', '--outputNTUP_PHYSICSFile', '--outputNTUP_PROMPTPHOTFile', '--outputNTUP_SCTFile', '--outputNTUP_SMBKGEFile', '--outputNTUP_SMBKGMUFile', '--outputNTUP_SMDILEPFile', '--outputNTUP_SMDYEEFile', '--outputNTUP_SMDYMUMUFile', '--outputNTUP_SMLIGHTFile', '--outputNTUP_SMQCDFile', '--outputNTUP_SMTRILEPFile', '--outputNTUP_SMWENUFile', '--outputNTUP_SMWENUJJFile', '--outputNTUP_SMWMUNUFile', '--outputNTUP_SMWMUNUJJFile', '--outputNTUP_SMWZFile', '--outputNTUP_SMWZSOFTFile', '--outputNTUP_SMZEEFile', '--outputNTUP_SMZMUMUFile', '--outputNTUP_SUSY01LEPFile', '--outputNTUP_SUSY23LEPFile', '--outputNTUP_SUSY34LEPFile', '--outputNTUP_SUSYBOOSTFile', '--outputNTUP_SUSYFile', '--outputNTUP_SUSYLEPTAUFile', '--outputNTUP_SUSYLLPFile', '--outputNTUP_SUSYRAZORFile', '--outputNTUP_SUSYSKIMFile', '--outputNTUP_SUSYTAGFile', '--outputNTUP_SUSYTRUTHFile', '--outputNTUP_TAUFULLFile', '--outputNTUP_TAUFile', '--outputNTUP_TAUMEDIUMFile', '--outputNTUP_TAUSMALLFile', '--outputNTUP_TOPBOOSTFile', '--outputNTUP_TOPEJETFile', '--outputNTUP_TOPELFile', '--outputNTUP_TOPFile', '--outputNTUP_TOPJETFile', '--outputNTUP_TOPMUFile', '--outputNTUP_TPHSG2File', '--outputNTUP_TRIGBJETFile', '--outputNTUP_TRIGFile', '--outputNTUP_TRIGMUFile', '--outputNTUP_TRKVALIDFile', '--outputNTUP_TRTFile', '--outputNTUP_TRUTHFile', '--outputNTUP_WPRIMEENFile', '--outputNTUP_WPRIMEMNFile', '--outputNTUP_WZFile', '--outputNTUP_ZPRIMEEEFile', '--outputNTUP_ZPRIMEMMFile', '--outputRDOFile', '--outputTAGFile', '--physicsList', '--pileupFinalBunch', '--pileupInitialBunch', '--postExec', '--postInclude', '--preExec', '--preInclude', '--randomSeed', '--reductionConf', '--reportName', '--reportType', '--runNumber', '--samplingFractionDbTag', '--showGraph', '--showPath', '--showSteps', '--simulator', '--skipEvents', '--skipFileValidation', '--skipInputFileValidation', '--skipOutputFileValidation', '--tcmalloc', '--testPileUpConfig', '--tmpRDO', '--trigFilterList', '--triggerConfig', '--useISF']
 
 @stdTrfExceptionHandler
 @sigUsrStackTrace
 def main():
     
-    msg.info('This is %s' % sys.argv[0])
+    msg.info('This is %s', sys.argv[0])
 
     trf = getTransform()
     trf.parseCmdLineArgs(sys.argv[1:])
     trf.execute()
     trf.generateReport()
 
-    msg.info("%s stopped at %s, trf exit code %d" % (sys.argv[0], time.asctime(), trf.exitCode))
+    msg.info("%s stopped at %s, trf exit code %d", sys.argv[0], time.asctime(), trf.exitCode)
     sys.exit(trf.exitCode)
 
 def getTransform():
diff --git a/Tools/LWHists/CMakeLists.txt b/Tools/LWHists/CMakeLists.txt
index 1abe6a8eba07cb1722c57db53f20c3e46f92192e..0c29cddcdb1d9cd6f781eba808ad5acde544f368 100644
--- a/Tools/LWHists/CMakeLists.txt
+++ b/Tools/LWHists/CMakeLists.txt
@@ -1,13 +1,8 @@
-# $Id: CMakeLists.txt 763045 2016-07-19 20:30:19Z ssnyder $
-################################################################################
-# Package: LWHists
-################################################################################
+# Copyright (C) 2002-2020 CERN for the benefit of the ATLAS collaboration
 
 # Declare the package name:
 atlas_subdir( LWHists )
 
-atlas_depends_on_subdirs( PUBLIC Control/CxxUtils )
-
 # External dependencies:
 find_package( ROOT COMPONENTS Hist RIO Core MathCore )
 
diff --git a/Tools/PathResolver/CMakeLists.txt b/Tools/PathResolver/CMakeLists.txt
index f4bb5b712e3fc70a3be5dc66b76a03e94d7aec1c..74c0d795f4b50d9a06885f5bd030fedc06730696 100644
--- a/Tools/PathResolver/CMakeLists.txt
+++ b/Tools/PathResolver/CMakeLists.txt
@@ -1,25 +1,13 @@
-# $Id: CMakeLists.txt 744427 2016-05-03 11:50:05Z krasznaa $
-#
-# CMake configuration file for the PathResolver package.
-#
+# Copyright (C) 2002-2020 CERN for the benefit of the ATLAS collaboration
 
 # Declare the package name:
 atlas_subdir( PathResolver )
 
 # Extra dependencies based on which environment we are in:
 if( NOT XAOD_STANDALONE )
-   set( extra_deps GaudiKernel )
    set( extra_libs GaudiKernel )
 endif()
 
-# Declare the package's dependencies:
-atlas_depends_on_subdirs(
-   PUBLIC
-   Control/AthToolSupport/AsgTools
-   Control/CxxUtils
-   PRIVATE
-   ${extra_deps} )
-
 # External dependencies:
 find_package( Boost COMPONENTS filesystem )
 find_package( ROOT COMPONENTS RIO Core )
diff --git a/Tools/PyUtils/test/test_genklass.sh b/Tools/PyUtils/test/test_genklass.sh
index 686ed2d6fa1e4b27bea0c2996360244c67cf061b..223fab32dd3579745707228bacb59a66da2af8e9 100755
--- a/Tools/PyUtils/test/test_genklass.sh
+++ b/Tools/PyUtils/test/test_genklass.sh
@@ -16,7 +16,6 @@ mkdir -p ${srcdir}/MyPkg/src/components
 if [ ! -f ${srcdir}/MyPkg/CMakeLists.txt ]; then
     cat <<EOF > ${srcdir}/MyPkg/CMakeLists.txt
 atlas_subdir( MyPkg )
-atlas_depends_on_subdirs( PRIVATE Control/AthenaBaseComps )
 atlas_add_component( MyPkg
                      src/components/*.cxx src/*.cxx
                      LINK_LIBRARIES AthenaBaseComps
diff --git a/Tools/XMLCoreParser/CMakeLists.txt b/Tools/XMLCoreParser/CMakeLists.txt
index 52807c6ec24259b51f0d4deb11f088899682be7f..ce2269e7865ee6d1b5b7be7ff8018e7441c64ba7 100644
--- a/Tools/XMLCoreParser/CMakeLists.txt
+++ b/Tools/XMLCoreParser/CMakeLists.txt
@@ -1,16 +1,8 @@
-################################################################################
-# Package: XMLCoreParser
-################################################################################
+# Copyright (C) 2002-2020 CERN for the benefit of the ATLAS collaboration
 
 # Declare the package name:
 atlas_subdir( XMLCoreParser )
 
-# Declare the package's dependencies:
-atlas_depends_on_subdirs( PUBLIC
-                          Control/CxxUtils
-                          PRIVATE
-                          AtlasTest/TestTools )
-
 # External dependencies:
 find_package( EXPAT )
 
@@ -21,31 +13,25 @@ atlas_add_library( XMLCoreParser
                    src/ExpatCoreParser.cxx
                    PUBLIC_HEADERS XMLCoreParser
                    PRIVATE_INCLUDE_DIRS ${EXPAT_INCLUDE_DIRS}
-                   PRIVATE_LINK_LIBRARIES ${EXPAT_LIBRARIES} TestTools CxxUtils )
+                   PRIVATE_LINK_LIBRARIES ${EXPAT_LIBRARIES} CxxUtils )
 
 atlas_add_test( example1_test
                 SOURCES
                 test/example1_test.cxx
                 INCLUDE_DIRS ${EXPAT_INCLUDE_DIRS}
-                LINK_LIBRARIES ${EXPAT_LIBRARIES} TestTools XMLCoreParser
+                LINK_LIBRARIES ${EXPAT_LIBRARIES} XMLCoreParser
                 ENVIRONMENT "XMLCOREPARSER_DATA=${CMAKE_CURRENT_SOURCE_DIR}/data" )
 
 atlas_add_test( example2_test
                 SOURCES
                 test/example2_test.cxx
                 INCLUDE_DIRS ${EXPAT_INCLUDE_DIRS}
-                LINK_LIBRARIES ${EXPAT_LIBRARIES} TestTools XMLCoreParser
+                LINK_LIBRARIES ${EXPAT_LIBRARIES} XMLCoreParser
                 ENVIRONMENT "XMLCOREPARSER_DATA=${CMAKE_CURRENT_SOURCE_DIR}/data" )
 
-atlas_add_executable( example4
-                      doc/example4.cxx
-                      INCLUDE_DIRS ${EXPAT_INCLUDE_DIRS}
-                      LINK_LIBRARIES ${EXPAT_LIBRARIES} TestTools XMLCoreParser )
-
 atlas_add_executable( texpat
                       src/texpat.cxx
                       src/DOMNode.cxx
                       src/ExpatCoreParser.cxx
                       INCLUDE_DIRS ${EXPAT_INCLUDE_DIRS}
-                      LINK_LIBRARIES ${EXPAT_LIBRARIES} TestTools XMLCoreParser  CxxUtils )
-
+                      LINK_LIBRARIES ${EXPAT_LIBRARIES} XMLCoreParser CxxUtils )
diff --git a/Tools/XMLCoreParser/doc/Doxyfile b/Tools/XMLCoreParser/doc/Doxyfile
deleted file mode 100755
index f8a46019a8fb1dca75d4c4befe585958e012857a..0000000000000000000000000000000000000000
--- a/Tools/XMLCoreParser/doc/Doxyfile
+++ /dev/null
@@ -1,164 +0,0 @@
-# Doxyfile 1.2.10
-
-#---------------------------------------------------------------------------
-# General configuration options
-#---------------------------------------------------------------------------
-PROJECT_NAME           = XMLCoreParser
-PROJECT_NUMBER         = XMLCoreParser-00-00-09
-OUTPUT_DIRECTORY       = /afs/cern.ch/atlas/maxidisk/d86/fix/InstallArea/doc/XMLCoreParser
-OUTPUT_LANGUAGE        = English
-EXTRACT_ALL            = YES
-EXTRACT_PRIVATE        = YES
-EXTRACT_STATIC         = YES
-HIDE_UNDOC_MEMBERS     = NO
-HIDE_UNDOC_CLASSES     = NO
-BRIEF_MEMBER_DESC      = YES
-REPEAT_BRIEF           = YES
-ALWAYS_DETAILED_SEC    = NO
-FULL_PATH_NAMES        = NO
-STRIP_FROM_PATH        = 
-INTERNAL_DOCS          = NO
-CLASS_DIAGRAMS         = YES
-SOURCE_BROWSER         = YES
-INLINE_SOURCES         = YES
-STRIP_CODE_COMMENTS    = YES
-CASE_SENSE_NAMES       = YES
-SHORT_NAMES            = NO
-HIDE_SCOPE_NAMES       = NO
-VERBATIM_HEADERS       = YES
-SHOW_INCLUDE_FILES     = YES
-JAVADOC_AUTOBRIEF      = YES
-INHERIT_DOCS           = YES
-INLINE_INFO            = YES
-SORT_MEMBER_DOCS       = NO
-DISTRIBUTE_GROUP_DOC   = NO
-TAB_SIZE               = 8
-GENERATE_TODOLIST      = YES
-GENERATE_TESTLIST      = YES
-GENERATE_BUGLIST       = YES
-ALIASES                = 
-ENABLED_SECTIONS       = 
-MAX_INITIALIZER_LINES  = 30
-OPTIMIZE_OUTPUT_FOR_C  = NO
-SHOW_USED_FILES        = YES
-#---------------------------------------------------------------------------
-# configuration options related to warning and progress messages
-#---------------------------------------------------------------------------
-QUIET                  = NO
-WARNINGS               = YES
-WARN_IF_UNDOCUMENTED   = YES
-WARN_FORMAT            = 
-WARN_LOGFILE           = 
-#---------------------------------------------------------------------------
-# configuration options related to the input files
-#---------------------------------------------------------------------------
-INPUT =  ../src ../XMLCoreParser ../doc
-FILE_PATTERNS          = *.cxx *.h
-RECURSIVE              = YES
-EXCLUDE                = 
-EXCLUDE_PATTERNS       = 
-EXAMPLE_PATH           = ../doc ../cmt
-EXAMPLE_PATTERNS       = *.cxx *.html requirements
-IMAGE_PATH             = 
-INPUT_FILTER           = 
-FILTER_SOURCE_FILES    = NO
-#---------------------------------------------------------------------------
-# configuration options related to the alphabetical class index
-#---------------------------------------------------------------------------
-ALPHABETICAL_INDEX     = NO
-COLS_IN_ALPHA_INDEX    = 5
-IGNORE_PREFIX          = 
-#---------------------------------------------------------------------------
-# configuration options related to the HTML output
-#---------------------------------------------------------------------------
-GENERATE_HTML          = YES
-HTML_OUTPUT            = html
-HTML_HEADER            = 
-HTML_FOOTER            = 
-HTML_STYLESHEET        = 
-HTML_ALIGN_MEMBERS     = YES
-GENERATE_HTMLHELP      = NO
-GENERATE_CHI           = NO
-BINARY_TOC             = NO
-TOC_EXPAND             = NO
-DISABLE_INDEX          = NO
-ENUM_VALUES_PER_LINE   = 4
-GENERATE_TREEVIEW      = NO
-TREEVIEW_WIDTH         = 250
-#---------------------------------------------------------------------------
-# configuration options related to the LaTeX output
-#---------------------------------------------------------------------------
-GENERATE_LATEX         = NO
-LATEX_OUTPUT           = 
-COMPACT_LATEX          = NO
-PAPER_TYPE             = a4wide
-EXTRA_PACKAGES         = 
-LATEX_HEADER           = 
-PDF_HYPERLINKS         = NO
-USE_PDFLATEX           = NO
-LATEX_BATCHMODE        = NO
-#---------------------------------------------------------------------------
-# configuration options related to the RTF output
-#---------------------------------------------------------------------------
-GENERATE_RTF           = NO
-RTF_OUTPUT             = 
-COMPACT_RTF            = NO
-RTF_HYPERLINKS         = NO
-RTF_STYLESHEET_FILE    = 
-RTF_EXTENSIONS_FILE    = 
-#---------------------------------------------------------------------------
-# configuration options related to the man page output
-#---------------------------------------------------------------------------
-GENERATE_MAN           = NO
-MAN_OUTPUT             = 
-MAN_EXTENSION          = 
-MAN_LINKS              = NO
-#---------------------------------------------------------------------------
-# configuration options related to the XML output
-#---------------------------------------------------------------------------
-GENERATE_XML           = NO
-#---------------------------------------------------------------------------
-# Configuration options related to the preprocessor   
-#---------------------------------------------------------------------------
-ENABLE_PREPROCESSING   = YES
-MACRO_EXPANSION        = NO
-EXPAND_ONLY_PREDEF     = NO
-SEARCH_INCLUDES        = YES
-INCLUDE_PATH           = 
-INCLUDE_FILE_PATTERNS  = 
-PREDEFINED             = 
-EXPAND_AS_DEFINED      = 
-#---------------------------------------------------------------------------
-# Configuration::addtions related to external references   
-#---------------------------------------------------------------------------
-TAGFILES = 
-GENERATE_TAGFILE = /afs/cern.ch/atlas/maxidisk/d86/fix/InstallArea/doc/XMLCoreParser.tag
-ALLEXTERNALS           = NO
-PERL_PATH              = 
-#---------------------------------------------------------------------------
-# Configuration options related to the dot tool   
-#---------------------------------------------------------------------------
-HAVE_DOT               = YES
-CLASS_GRAPH            = YES
-COLLABORATION_GRAPH    = YES
-TEMPLATE_RELATIONS     = YES
-INCLUDE_GRAPH          = YES
-INCLUDED_BY_GRAPH      = YES
-GRAPHICAL_HIERARCHY    = YES
-DOT_PATH               = 
-DOTFILE_DIRS           = 
-MAX_DOT_GRAPH_WIDTH    = 1024
-MAX_DOT_GRAPH_HEIGHT   = 1024
-GENERATE_LEGEND        = YES
-DOT_CLEANUP            = YES
-DOT_IMAGE_FORMAT       = gif
-#---------------------------------------------------------------------------
-# Configuration::addtions related to the search engine   
-#---------------------------------------------------------------------------
-SEARCHENGINE           = NO
-CGI_NAME               = 
-CGI_URL                = 
-DOC_URL                = 
-DOC_ABSPATH            = 
-BIN_ABSPATH            = 
-EXT_DOC_PATHS          = 
diff --git a/Tools/XMLCoreParser/doc/example3.cxx b/Tools/XMLCoreParser/doc/example3.cxx
deleted file mode 100755
index 6bbf309ced981c538f006040d808ccc12537af3c..0000000000000000000000000000000000000000
--- a/Tools/XMLCoreParser/doc/example3.cxx
+++ /dev/null
@@ -1,105 +0,0 @@
-/*
-  Copyright (C) 2002-2017 CERN for the benefit of the ATLAS collaboration
-*/
-
-#include "XMLCoreParser/XMLCoreParser.h" 
-#include <iostream>
-#include <xercesc/util/XMLString.hpp> 
-
-class Printer : public XMLCoreFactory
-{
-public:
-
-  void do_start (XMLCoreParser& /*parser*/, const XMLCoreNode& node)
-      {
-        const XMLCh* nodeName = ((const DOMNode&) node).getNodeName();
-
-        char* temp = XMLString::transcode (nodeName);
-        std::cout << "<" << temp;
-        delete [] temp;
-        
-          // Output any attributes on this element
-        DOMNamedNodeMap* attributes = ((const DOMNode&) node).getAttributes();
-        int attrCount = attributes->getLength();
-        for (int i = 0; i < attrCount; i++)
-          {
-            DOMNode* attribute = attributes->item(i);
-            
-            temp = XMLString::transcode (attribute->getNodeName());
-            std::cout << " " << temp << "=\"";
-            delete [] temp;
-            
-            temp = XMLString::transcode (attribute->getNodeValue());
-            std::cout << temp << "\"";
-            delete [] temp;
-          }
-        
-          //
-          //  Test for the presence of children, which includes both
-          //  text content and nested elements.
-          //
-        DOMNode* child = ((const DOMNode&) node).getFirstChild();
-        if (child != 0)
-          {
-              // There are children. Close start-tag, and output children.
-              // No escapes are legal here
-            
-            std::cout << ">" << std::endl;
-          }
-      }
-
-  void do_end (XMLCoreParser& /*parser*/, const XMLCoreNode& node)
-      {
-        const XMLCh* nodeName = ((const DOMNode&) node).getNodeName();
-
-        char* temp = XMLString::transcode (nodeName);
-
-          //
-          //  Test for the presence of children, which includes both
-          //  text content and nested elements.
-          //
-        DOMNode* child = ((const DOMNode&) node).getFirstChild();
-        if (child != 0)
-          {
-              //
-              // Done with children.  Output the end tag.
-              //
-            
-            std::cout << "</" << temp << ">" << std::endl;
-          }
-        else
-          {
-            //
-            //  There were no children. Output the short form close of
-            //  the element start tag, making it an empty-element tag.
-            //
-            
-            std::cout << "/>" << std::endl;
-          }
-        if (temp != 0) delete [] temp;
-      }
-
-  void do_comment (XMLCoreParser& /*parser*/, const std::string& comment)
-      {
-        std::cout << "<!--" << comment << "-->" << std::endl;
-      }
-};
- 
-int main (int argc, char* argv[]) 
-{ 
-  XMLCoreParser p;
-  Printer printer;
- 
-  p.register_default_factory (&printer);
-
-  if (argc > 1) 
-    { 
-      const char* file = argv[1]; 
- 
-      p.visit (file); 
-    }
-
-  return (0); 
-} 
- 
- 
diff --git a/Tools/XMLCoreParser/doc/example4.cxx b/Tools/XMLCoreParser/doc/example4.cxx
deleted file mode 100755
index be1ebe3afb2aa1453c86ed5b1f913ad65da71750..0000000000000000000000000000000000000000
--- a/Tools/XMLCoreParser/doc/example4.cxx
+++ /dev/null
@@ -1,23 +0,0 @@
-/*
-  Copyright (C) 2002-2017 CERN for the benefit of the ATLAS collaboration
-*/
-
-
-
-#include "XMLCoreParser/XMLCoreParser.h"
-
-int main (int argc, char* argv[])
-{
-  XMLCoreParser parser;
-
-  parser.register_text_entity ("ABCD", "<abcd/>");
-
-  if (argc > 1)
-    {
-      const char* file = argv[1]; 
-
-      parser.parse (file);
-    }
-
-  return (0);
-}
diff --git a/Tools/XMLCoreParser/doc/packagedoc.h b/Tools/XMLCoreParser/doc/packagedoc.h
index 82a0b509e3b48d0e3078147ad8e28175b2bd6e95..5def1e44247c7a58dfa6e45d417be40bee270949 100644
--- a/Tools/XMLCoreParser/doc/packagedoc.h
+++ b/Tools/XMLCoreParser/doc/packagedoc.h
@@ -1,5 +1,5 @@
 /*
-  Copyright (C) 2002-2017 CERN for the benefit of the ATLAS collaboration
+  Copyright (C) 2002-2020 CERN for the benefit of the ATLAS collaboration
 */
 
 
@@ -107,43 +107,3 @@ It supports declaration of keyed callbacks associated with element names.
      </ul>
 
 */
-
-
-/**
-   
-   @example example1.cxx
-
-   Minimal use of the generic parser. 
-   
- */
-
-
-/**
-   
-   @example example2.cxx
-
-   Constructing a default factory class for simple pretty printing. 
-
-   Helper functions are used in this example. 
-*/
-
-
-/**
-   
-   @example example3.cxx
-
-   Constructing a default factory class for simple pretty printing. 
-
-   Direct manipulation of the DOM tree is used in this example 
-
-
- */
-
-/**
-   
-   @example example4.cxx
-
-   Example of how to register a text entity (to be run against example4.xml)
-
-
- */