diff --git a/Calorimeter/CaloExample/CaloRecEx/share/CaloRecEx_RTT_physics_0087851_BPTX.py b/Calorimeter/CaloExample/CaloRecEx/share/CaloRecEx_RTT_physics_0087851_BPTX.py
index 4ecfba70b14fb0891b35759aa4e9a2d95557be35..8c2f043fb7e7369766e16f44da29f0adbad32c63 100644
--- a/Calorimeter/CaloExample/CaloRecEx/share/CaloRecEx_RTT_physics_0087851_BPTX.py
+++ b/Calorimeter/CaloExample/CaloRecEx/share/CaloRecEx_RTT_physics_0087851_BPTX.py
@@ -40,7 +40,7 @@ runArgs.trigStream = 'IDCosmic'
 runArgs.preExec = ['from RecExConfig.RecFlags  import rec','rec.doMonitoring=False','rec.doInDet=False','rec.doMuon=False','rec.doMuonCombined=False','rec.doEgamma=False','rec.doTau=False','rec.doTrigger=False','from LArROD.LArRODFlags import larRODFlags','larRODFlags.readDigits.set_Value_and_Lock(False)','doTopoClusterCBNT=True']
 
 # Configuration fragment for DPD.
-runArgs.preInclude = ['RecExCommon/RecoUsefulFlags.py', 'RecExCommission/RecExCommissionRepro.py', 'RecExCommission/MinimalCommissioningSetup.py', 'RecJobTransforms/UseOracle.py']
+runArgs.preInclude = ['RecExCommon/RecoUsefulFlags.py', 'RecExCommission/RecExCommissionRepro.py', 'RecExCond/MinimalCommissioningSetup.py', 'RecJobTransforms/UseOracle.py']
 
 runArgs.postExec = ['from CaloRec.CaloRecConf import CBNTAA_CaloCluster','theCBNT_CaloClusterTopo=CBNTAA_CaloCluster("CBNT_CaloClusterTopo")','theCBNT_CaloClusterTopo.MaxCaloCluster = 2000']
 
diff --git a/Calorimeter/CaloExample/CaloRecEx/share/CaloRecEx_RTT_physics_0091900_cosmics.py b/Calorimeter/CaloExample/CaloRecEx/share/CaloRecEx_RTT_physics_0091900_cosmics.py
index 64601c72a9cc5d7d34516c4c20b643e8f12a0b6a..ebbd3749985e400747ede1aaf6dfac843c4e626c 100644
--- a/Calorimeter/CaloExample/CaloRecEx/share/CaloRecEx_RTT_physics_0091900_cosmics.py
+++ b/Calorimeter/CaloExample/CaloRecEx/share/CaloRecEx_RTT_physics_0091900_cosmics.py
@@ -35,7 +35,7 @@ runArgs.trigStream = 'IDCosmic'
 runArgs.preExec = ['from RecExConfig.RecFlags  import rec','rec.doMonitoring=False','rec.doInDet=False','rec.doMuon=False','rec.doMuonCombined=False','rec.doEgamma=False','rec.doTau=False','rec.doTrigger=False','doTopoClusterCBNT=True','rec.doFloatingPointException=False']
 
 # Configuration fragment for DPD.
-runArgs.preInclude = ['RecExCommon/RecoUsefulFlags.py', 'RecExCommission/RecExCommissionRepro.py', 'RecExCommission/MinimalCommissioningSetup.py', 'RecJobTransforms/UseOracle.py']
+runArgs.preInclude = ['RecExCommon/RecoUsefulFlags.py', 'RecExCommission/RecExCommissionRepro.py', 'RecExCond/MinimalCommissioningSetup.py', 'RecJobTransforms/UseOracle.py']
 
 runArgs.postExec = ['from CaloRec.CaloRecConf import CBNTAA_CaloCluster','theCBNT_CaloClusterTopo=CBNTAA_CaloCluster("CBNT_CaloClusterTopo")','theCBNT_CaloClusterTopo.MaxCaloCluster = 2000']
 
diff --git a/Calorimeter/CaloExample/CaloRecEx/share/CaloRecEx_RTT_physics_MinBias.py b/Calorimeter/CaloExample/CaloRecEx/share/CaloRecEx_RTT_physics_MinBias.py
index 9909ad379f4211823f7fc668eca026fd022dac22..1155d1440061117d175383dc8d7f031c57c62317 100755
--- a/Calorimeter/CaloExample/CaloRecEx/share/CaloRecEx_RTT_physics_MinBias.py
+++ b/Calorimeter/CaloExample/CaloRecEx/share/CaloRecEx_RTT_physics_MinBias.py
@@ -36,7 +36,7 @@ runArgs.trigStream = 'MinBias'
 runArgs.preExec = ['from RecExConfig.RecFlags  import rec','rec.doMonitoring=False','rec.doInDet=False','rec.doMuon=False','rec.doMuonCombined=False','rec.doEgamma=False','rec.doTau=False','rec.doTrigger=False','from LArROD.LArRODFlags import larRODFlags','larRODFlags.readDigits.set_Value_and_Lock(False)','doTopoClusterCBNT=True']
 
 # Configuration fragment for DPD.
-runArgs.preInclude = ['RecExCommon/RecoUsefulFlags.py', 'RecExCommission/RecExCommissionRepro.py', 'RecExCommission/MinimalCommissioningSetup.py', 'RecJobTransforms/UseOracle.py']
+runArgs.preInclude = ['RecExCommon/RecoUsefulFlags.py', 'RecExCommission/RecExCommissionRepro.py', 'RecExCond/MinimalCommissioningSetup.py', 'RecJobTransforms/UseOracle.py']
 
 # Configuration fragment for DPD.
 #runArgs.postInclude = ['RecJobTransforms/reducedRegionSelectorPostConfig.py']
diff --git a/Calorimeter/CaloExample/CaloRecEx/share/CaloRecEx_RTT_physics_cosmics.py b/Calorimeter/CaloExample/CaloRecEx/share/CaloRecEx_RTT_physics_cosmics.py
index b24860976b101a02b0b3f68a18f2551aed336c78..09489ca70b20cf6b271bbf5ac18d8a9f239772b0 100755
--- a/Calorimeter/CaloExample/CaloRecEx/share/CaloRecEx_RTT_physics_cosmics.py
+++ b/Calorimeter/CaloExample/CaloRecEx/share/CaloRecEx_RTT_physics_cosmics.py
@@ -34,7 +34,7 @@ runArgs.preExec = ['from RecExConfig.RecFlags  import rec','rec.doMonitoring=Fal
 #runArgs.preExec = ['from RecExConfig.InputFilePeeker import inputFileSummary','inputFileSummary.stream_names=StreamESD']
 
 # Configuration fragment for DPD.
-runArgs.preInclude = ['RecExCommon/RecoUsefulFlags.py', 'RecExCommission/RecExCommissionRepro.py', 'RecExCommission/MinimalCommissioningSetup.py', 'RecJobTransforms/UseOracle.py']
+runArgs.preInclude = ['RecExCommon/RecoUsefulFlags.py', 'RecExCommission/RecExCommissionRepro.py', 'RecExCond/MinimalCommissioningSetup.py', 'RecJobTransforms/UseOracle.py']
 
 runArgs.postExec = ['from CaloRec.CaloRecConf import CBNTAA_CaloCluster','theCBNT_CaloClusterTopo=CBNTAA_CaloCluster("CBNT_CaloClusterTopo")','theCBNT_CaloClusterTopo.MaxCaloCluster = 2000']
 
diff --git a/Database/IOVDbSvc/share/IOVRecExCommission.py b/Database/IOVDbSvc/share/IOVRecExCommission.py
deleted file mode 100644
index f1e69355b0977b321c417c42907f76dd86a8ca7d..0000000000000000000000000000000000000000
--- a/Database/IOVDbSvc/share/IOVRecExCommission.py
+++ /dev/null
@@ -1,10 +0,0 @@
-# IOVRecExCommission.py - setup IOVDbSvc for RecExCommission
-# commissioning with real data
-
-log.warning("IOVDbSvc/IOVRecExCommission.py - This file is obselete; conditions DB access should automatically be configured from detector geometry")
-
-from AthenaCommon.GlobalFlags import globalflags
-if (globalflags.DetGeo()=='commis' and globalflags.DataSource()=='data'):
-    from IOVDbSvc.CondDB import conddb
-else:
-    raise RuntimeError,'IOVRecExCommission.py included but geometry is not commis / real data'
diff --git a/Database/IOVDbSvc/share/IOVRecExCommissionMC.py b/Database/IOVDbSvc/share/IOVRecExCommissionMC.py
deleted file mode 100644
index 107bab00a4bac343899bc9472d47f0c4b5e9f29f..0000000000000000000000000000000000000000
--- a/Database/IOVDbSvc/share/IOVRecExCommissionMC.py
+++ /dev/null
@@ -1,10 +0,0 @@
-# IOVRecExCommission.py - setup IOVDbSvc for RecExCommissionMC
-# commissioning with Monte Carlo
-
-log.warning("IOVDbSvc/IOVRecExCommissionMC.py - This file is obselete; conditions DB access should automatically be configured from detector geometry")
-
-from AthenaCommon.GlobalFlags import globalflags
-if (globalflags.DetGeo()=='commis' and globalflags.DataSource()!='data'):
-    from IOVDbSvc.CondDB import conddb
-else:
-    raise RuntimeError,'IOVRecExCommissionMC.py included but geometry is not commis / Monte Carlo'
diff --git a/Database/IOVDbSvc/share/IOVRecExCommissionSR1.py b/Database/IOVDbSvc/share/IOVRecExCommissionSR1.py
deleted file mode 100644
index 2c536f0fb08314bba560061f720afaa74a4d559b..0000000000000000000000000000000000000000
--- a/Database/IOVDbSvc/share/IOVRecExCommissionSR1.py
+++ /dev/null
@@ -1,17 +0,0 @@
-# IOVRecExCommissionSR1.py - setup IOVDbSvc for ID commissioning in SR1
-# commissioning with real data, but temporarily using COOL1.2.x CMCPROD db
-# setup for sqlite replica expected to be found in sqlite130/CMCPROD.db
-#
-
-include.block ( "IOVDbSvc/IOVRecExCommissionSR1.py" )
-
-IOVCoolDBTech="sqlite"
-IOVCoolDBProd="CMCPROD"
-IOVCoolDBUser="ATLAS_COOL_READER"
-IOVCoolDBPwd="COOLRED4PRO"
-#
-include("IOVDbSvc/IOVCondDB.py")
-
-# include comcond catalog via DATAPATH
-PoolSvc = Service( "PoolSvc" )
-PoolSvc.ReadCatalog+= [ "prfile:poolcond/PoolCat_comcond.xml" ]
diff --git a/ForwardDetectors/LUCID/LUCID_Monitoring/share/args.ESDtoAOD.lucid.py b/ForwardDetectors/LUCID/LUCID_Monitoring/share/args.ESDtoAOD.lucid.py
index a92cb9ab1db321dc3f7453c6adebb301ec81c5aa..be7ea706f4997515105765b9291d0422953c3bd0 100755
--- a/ForwardDetectors/LUCID/LUCID_Monitoring/share/args.ESDtoAOD.lucid.py
+++ b/ForwardDetectors/LUCID/LUCID_Monitoring/share/args.ESDtoAOD.lucid.py
@@ -21,7 +21,7 @@ runArgs.maxEvents = -1
 
 runArgs.inputESDFile = ['myESD.pool.root']
 
-runArgs.preInclude = ['RecExCommon/RecoUsefulFlags.py', 'RecExCommission/MinimalCommissioningSetup.py', 'RecJobTransforms/UseOracle.py', 'RecJobTransforms/debugConfig.py']
+runArgs.preInclude = ['RecExCommon/RecoUsefulFlags.py', 'RecExCond/MinimalCommissioningSetup.py', 'RecJobTransforms/UseOracle.py', 'RecJobTransforms/debugConfig.py']
 
 runArgs.outputAODFile = 'myAOD.pool.root'
 
diff --git a/InnerDetector/InDetExample/InDetTrigRecExample/CMakeLists.txt b/InnerDetector/InDetExample/InDetTrigRecExample/CMakeLists.txt
index b0e6f63e30b9741dddf4ca2c5ed83cde05e25d9a..23611ae2aa85f42346b0da38d63cfacc3eea431e 100644
--- a/InnerDetector/InDetExample/InDetTrigRecExample/CMakeLists.txt
+++ b/InnerDetector/InDetExample/InDetTrigRecExample/CMakeLists.txt
@@ -6,5 +6,3 @@ atlas_subdir( InDetTrigRecExample )
 # Install files from the package:
 atlas_install_python_modules( python/*.py )
 atlas_install_joboptions( share/*.py )
-atlas_install_scripts( share/RTT_NoBField_transform.sh )
-
diff --git a/InnerDetector/InDetExample/InDetTrigRecExample/share/RTT_NoBField_transform.sh b/InnerDetector/InDetExample/InDetTrigRecExample/share/RTT_NoBField_transform.sh
deleted file mode 100755
index bf9ea6862393b11657ca59057f5f96b627d7c71f..0000000000000000000000000000000000000000
--- a/InnerDetector/InDetExample/InDetTrigRecExample/share/RTT_NoBField_transform.sh
+++ /dev/null
@@ -1,13 +0,0 @@
-export STAGE_SVCCLASS=atlasgroupdisk
-Reco_trf.py \
-    inputBSFile_r2r=rfio:/castor/cern.ch/grid/atlas/DAQ/2009/00121513/physics_IDCosmic/data09_cos.00121513.physics_IDCosmic.daq.RAW._lb0000._SFO-1._0001.data,rfio:/castor/cern.ch/grid/atlas/DAQ/2009/00121513/physics_IDCosmic/data09_cos.00121513.physics_IDCosmic.daq.RAW._lb0000._SFO-1._0002.data,rfio:/castor/cern.ch/grid/atlas/DAQ/2009/00121513/physics_IDCosmic/data09_cos.00121513.physics_IDCosmic.daq.RAW._lb0000._SFO-1._0003.data,rfio:/castor/cern.ch/grid/atlas/DAQ/2009/00121513/physics_IDCosmic/data09_cos.00121513.physics_IDCosmic.daq.RAW._lb0000._SFO-1._0004.data,rfio:/castor/cern.ch/grid/atlas/DAQ/2009/00121513/physics_IDCosmic/data09_cos.00121513.physics_IDCosmic.daq.RAW._lb0000._SFO-1._0005.data,rfio:/castor/cern.ch/grid/atlas/DAQ/2009/00121513/physics_IDCosmic/data09_cos.00121513.physics_IDCosmic.daq.RAW._lb0000._SFO-1._0006.data,rfio:/castor/cern.ch/grid/atlas/DAQ/2009/00121513/physics_IDCosmic/data09_cos.00121513.physics_IDCosmic.daq.RAW._lb0000._SFO-1._0007.data,rfio:/castor/cern.ch/grid/atlas/DAQ/2009/00121513/physics_IDCosmic/data09_cos.00121513.physics_IDCosmic.daq.RAW._lb0000._SFO-1._0008.data,rfio:/castor/cern.ch/grid/atlas/DAQ/2009/00121513/physics_IDCosmic/data09_cos.00121513.physics_IDCosmic.daq.RAW._lb0000._SFO-1._0009.data \
-    outputBSFile='raw.data._0001.data'     \
-    outputHIST_TRIGEXPERTFile=trig-expert.root     \
-    maxEvents=-1     \
-    trigStream=IDCosmic \
-    autoConfiguration=FieldAndGeo,BeamType,ConditionsTag   \
-    preInclude=RecExCommission/RecExCommissionRepro.py,RecExCommission/MinimalCommissioningSetup.py,RecJobTransforms/TrigConfigForCosmic08RerunHLTRepro.py\
-    preExec='HLTMonDoOfflineTauTTP=False; doMonitoring=False'   \
-    outputESDFile=data09_cosmag.00121513.ESD.pool.root          \
-    outputCBNT=myCBNT.ntuple.root     \
-    --ignoreunknown
diff --git a/MuonSpectrometer/MuonValidation/MuonDQA/MuonDQAMonitoring/share/MuonDQAMonitoring_CommRunsTier0.py b/MuonSpectrometer/MuonValidation/MuonDQA/MuonDQAMonitoring/share/MuonDQAMonitoring_CommRunsTier0.py
deleted file mode 100644
index da8d4924900f3923a78754eb9b834fb5c984f8ac..0000000000000000000000000000000000000000
--- a/MuonSpectrometer/MuonValidation/MuonDQA/MuonDQAMonitoring/share/MuonDQAMonitoring_CommRunsTier0.py
+++ /dev/null
@@ -1,525 +0,0 @@
-#======================================================================
-__doc__ = """This is an example steering jobOption file for RecExCommission run on MuonSystem in Release 14.X.Y.
-It sets default values for muonRecFlags, recFlags, globalflags, DetFlags."""
-#======================================================================
-# Example JobOPt to monitor Muon Technical(Px) and Commissioning(Mx) Runs
-# Last modified Nectarios.Chr. Benekos (UIUC) <Nectarios.Benekos@cern.ch>
-#======================================================================
-# this version is for the setup we will use for M6 Feb run reprocessing!
-#======================================================================
-#####
-### athena.py -c "CollData=True" -b ../share/MuonDQAMonitoring_CommRunsTier0.py > log_collisions | tee
-#####
-include( "RecExCommission/RecExCommissionFlags_jobOptions.py" )
-#======================================================================
-import os
-from AthenaCommon.JobProperties import jobproperties
-from AthenaCommon.AthenaCommonFlags import athenaCommonFlags
-from RecExConfig.RecFlags import jobproperties, rec
-from AthenaCommon.BFieldFlags import jobproperties
-from AthenaCommon.BeamFlags import jobproperties
-from AthenaCommon.AlgSequence import AlgSequence
-topSequence = AlgSequence()
-#======================================================================
-from AthenaCommon.DetFlags import DetFlags
-DetFlags.ID_setOff()
-DetFlags.detdescr.ID_setOn()
-DetFlags.Calo_setOff()
-DetFlags.detdescr.Calo_setOn()
-DetFlags.Muon_setOn()
-# --- printout
-DetFlags.Print()
-#======================================================================
-from RecExConfig.RecFlags import rec as recFlags 
-recFlags.Commissioning=True
-recFlags.oldRecExCommissionConfig = False
-recFlags.oldFlagTopSteering = False
-recFlags.ScopingLevel = 4 
-#======================================================================
-# choose what detector to turn on:
-recFlags.doInDet = False
-recFlags.doLArg  = False
-recFlags.doTile  = False
-#======================================================================
-# Only Muons
-recFlags.doMuon                 = True 
-recFlags.doMuonCombined         = False
-recFlags.doHist                 = True
-#======================================================================
-recFlags.doInDet                = False
-recFlags.doCalo                 = False
-recFlags.doLArg                 = False
-recFlags.doTile                 = False
-recFlags.readESD                = False
-recFlags.doESD                  = True
-recFlags.doWriteESD             = True
-recFlags.doCBNT                 = False
-recFlags.doWriteAOD             = False
-recFlags.doWriteTAG             = False
-recFlags.doJiveXML              = False
-recFlags.doAOD                  = False
-recFlags.doAODall               = False
-recFlags.doTrigger              = False
-recFlags.doPerfMon              = False
-recFlags.doHeavyIon             = False
-recFlags.doEgamma               = False
-recFlags.doTau                  = False
-recFlags.doHeavyIon             = False
-recFlags.doJetMissingETTag      = False
-recFlags.doPersint              = False
-recFlags.doMonitoring           = True
-#======================================================================
-#If True monitor software performance, see https://twiki.cern.ch/twiki/bin/view/Atlas/PerfMonComps
-recFlags.doPerfMon=True 
-recFlags.doDetailedPerfMon=True
-rec.lock_JobProperties()
-#======================================================================
-# Set default recAlgsFlags
-#======================================================================
-from RecExConfig.RecAlgsFlags import recAlgs as recAlgsFlags
-recAlgsFlags.doMuonIDStandAlone = False # extrapolate Moore tracks to the IP
-recAlgsFlags.doMuonIDCombined   = False # combined reconstruction with MuIDCombined
-recAlgsFlags.doStaco            = False # combined reconstruction with Staco
-recAlgsFlags.doMuTag            = False # muon identification with MuTag (requires Muonboy and Staco)
-recAlgsFlags.doMuGirl           = False # muon identification with MuGirl
-recAlgsFlags.doTrigger          = False
-recAlgsFlags.doTrackRecordFilter = True # filter truth muons getting into the spectrometer
-recAlgsFlags.doTileMuID         = False
-recAlgsFlags.doCaloTrkMuId      = False
-recAlgsFlags.doMissingET        = False
-recAlgsFlags.doObjMissingET     = False
-recAlgsFlags.doMissingETSig     = False
-recAlgsFlags.doEFlow            = False
-recAlgsFlags.doEFlowJet         = False
-recAlgsFlags.doAtlfast          = False
-#======================================================================
-# Set default globalflags
-#======================================================================
-from AthenaCommon.GlobalFlags import globalflags
-globalflags.DetGeo      = 'commis'
-globalflags.DataSource.set_Value_and_Lock('data')
-globalflags.InputFormat = 'bytestream' 
-globalflags.Luminosity  = 'zero'
-#==========  Switch to the desired algorithms =========================
-ATLASCosmicFlags.doLVL1Calo=False
-ATLASCosmicFlags.doCTPMon = False
-ATLASCosmicFlags.doHLT  = False
-ATLASCosmicFlags.doCombinedFit = False
-ATLASCosmicFlags.doDQMonitoring = False
-## hack to turn off hlt met monitoring
-HLTMonDoMET = False
-ATLASCosmicFlags.UseDCS = False
-ATLASCosmicFlags.doFilteredESD = False  
-ATLASCosmicFlags.OnlineJiveXML = False
-ATLASCosmicFlags.AtlantisGeometry = False
-ATLASCosmicFlags.CaloDetailedJiveXML = False 
-ATLASCosmicFlags.doPersint = False
-#======================================================================
-# Setup Internal flags for the Muon DQA Monitoring (defaults values)
-from MuonDQAMonFlags.MuonDQAFlags import MuonDQAFlags as MuonDQAFlags
-from AthenaCommon import CfgMgr
-from AthenaMonitoring.DQMonFlags import DQMonFlags
-DQMonFlags.doGlobalMon = False
-DQMonFlags.doLVL1CaloMon = False
-DQMonFlags.doCTPMon = False
-DQMonFlags.doHLTMon = False
-DQMonFlags.doPixelMon = False
-DQMonFlags.doSCTMon = False
-DQMonFlags.doTRTMon = False
-DQMonFlags.doInDetGlobalMon = False
-DQMonFlags.doInDetAlignMon = False
-DQMonFlags.doInDetPerfMon = False
-DQMonFlags.doTileMon = False
-DQMonFlags.doLArMon = False
-DQMonFlags.doEgammaMon = False
-DQMonFlags.doMissingEtMon = False
-DQMonFlags.doTauMon = False
-DQMonFlags.doJetMon = False
-DQMonFlags.doJetTagMon = False
-DQMonFlags.doMuonCombinedMon = False
-#-----------------------------------------------------------------
-DQMonFlags.doMuonRawMon = True
-DQMonFlags.doMuonTrackMon = True
-DQMonFlags.doMuonSegmentMon = True
-DQMonFlags.doMuonAlignMon = True
-DQMonFlags.doMuonPhysicsMon = False
-
-# --- Callgrind Tool
-MuonDQAFlags.doCallgrind = False #False 
-
-# --- CPU and txt files
-MuonDQAFlags.doCpuMuonMon = True
-MuonDQAFlags.doMuonDQAPerfMonitoring = True
-#----------------------------------------------------------------- 
-##if you want to run Hephaestus Tool
-### https://twiki.cern.ch/twiki/bin/view/Atlas/UsingHephaestus
-MuonDQAFlags.doMuonDQAHephTool = False
-#----------------------------------------------------------------- 
-MuonDQAFlags.doAuditor = True
-MuonDQAFlags.doFinalCPU = False  
-MuonDQAFlags.doDumpFile = False
-MuonDQAFlags.doSimpleFile = True
-
-# --- Muon Monitoring options
-MuonDQAFlags.doMuonMonitoring = True
-ATLASCosmicFlags.doMuonMon = True
-
-# --- Muon EventInfo Monitoring option
-MuonDQAFlags.doMuonEvtMon = True
-ATLASCosmicFlags.doMuonEvtMon = True
-
-# --- Muon Hit Monitoring options
-ATLASCosmicFlags.doMuonHitMon = True
-# --- for each subdetector
-ATLASCosmicFlags.doMDTMon = True
-ATLASCosmicFlags.doRPCMon = True
-ATLASCosmicFlags.doRPCL1Mon = True
-ATLASCosmicFlags.doMDTRPCMon = True
-ATLASCosmicFlags.doTGCMon = True
-ATLASCosmicFlags.doTGCL1Mon = True
-ATLASCosmicFlags.doMDTTGCL1Mon = True   
-# --- Temporary for M8---------------
-ATLASCosmicFlags.doCSCMon = False
-MuonDQAFlags.doCSCMon = False
-# --- Temporary for M8---------------
-
-## --- Muon Segment Monitoring options
-ATLASCosmicFlags.doMuonSegmMon = True
-#
-## --- MuonTrk Monitoring options
-ATLASCosmicFlags.doMuonTrackMon = True
-## --- MuonTrk Trigger Aware Monitoring options
-MuonDQAFlags.MuonTrkMonDoTrigger = False
-#
-## --- Muon Trk Alignement Monitoring
-MuonDQAFlags.doMuonTrkAlignMon = True
-ATLASCosmicFlags.doMuonTrkAlignMon = True
-#
-## --- MuonTrk Monitoring options
-ATLASCosmicFlags.doMuonPhysMon = False
-#======================================================================
-
-if not 'Field' in dir():
-    Field = False
-if not 'noField' in dir():
-    noField = False
-if not 'BeamGas' in dir():
-    BeamGas = False
-if not 'BeamHalo' in dir():
-    BeamHalo = False
-if not 'SimBeamGas' in dir():
-    SimBeamGas = False
-if not 'SimBeamHalo' in dir():
-    SimBeamHalo = False
-if not 'CollData' in dir():
-    CollData = False   
-#======================================================================
-# Muon Monitoring Hist output
-if not 'MuonSystem' in dir():
-    MuonSystem = "ALL"        
-#======================================================================    
-#if BeamHalo or BeamGas or SimBeamHalo or SimBeamGas:
-#    jobproperties.Beam.beamType.set_Value_and_Lock("singlebeam")
-#else:
-#    jobproperties.Beam.beamType.set_Value_and_Lock("cosmics")
-#
-#if SimBeamHalo or SimBeamGas:
-#    globalflags.DataSource = 'geant4'
-#    globalflags.InputFormat = 'pool'
-#======================================================================
-#-----------------------------------------------------------------
-# Setup Internal flags for the Muon Spectrometer (defaults values)
-#-----------------------------------------------------------------
-from MuonRecExample.MuonRecFlags import muonRecFlags
-muonRecFlags.doMoore = True
-muonRecFlags.doMuonboy = True
-muonRecFlags.doCSCs=False
-#======================================================================
-# Set properly beam type, DataSource, InputFormat, Detector Description, Conditions Tag
-if globalflags.DataSource() == 'data':
-    recFlags.doTruth = False
-    jobproperties.Beam.beamType.set_Value_and_Lock("singlebeam")
-    globalflags.InputFormat.set_Value_and_Lock('bytestream')
-    globalflags.DetDescrVersion.set_Value_and_Lock('ATLAS-GEO-04-00-00')
-    globalflags.ConditionsTag.set_Value_and_Lock('COMCOND-ES1C-000-00')
-else :
-    globalflags.DetDescrVersion.set_Value_and_Lock('ATLAS-GEO-02-01-00')
-    globalflags.ConditionsTag.set_Value_and_Lock('OFLCOND-SIM-00-00-00')
-
-if globalflags.DataSource() == 'data' and globalflags.InputFormat == 'bytestream':
-    if muonRecFlags.doCSCs():
-        athenaCommonFlags.BSRDOInput.set_Value_and_Lock(['/castor/cern.ch/grid/atlas/DAQ/2008/91897/physics_TGCwBeam/daq.ATLAS.0091897.physics.TGCwBeam.LB0001.SFO-1._0001.data'])
-    else:
-        athenaCommonFlags.BSRDOInput.set_Value_and_Lock(['/castor/cern.ch/grid/atlas/DAQ/2008/87863/physics_BPTX/daq.NoTag.0087863.physics.BPTX.LB0000.SFO-1._0001.data'])
-
-if SimBeamHalo:
-    globalflags.DetDescrVersion ='ATLAS-CSC-02-02-00'
-    athenaCommonFlags.PoolRDOInput = ["rfio:/castor/cern.ch/user/d/dellacqu/beamHalo_digits.pool.root"]
-    ATLASCosmicFlags.IOVDbSvcGlobalTagSim = 'OFLCOND-CSC-00-01-07'
-    ATLASCosmicFlags.IOVDbSvcGlobalTagSimOverride = True
-if SimBeamGas:
-    globalflags.DetDescrVersion ='ATLAS-CSC-01-02-00'
-    athenaCommonFlags.PoolRDOInput = ["/afs/cern.ch/user/g/gencomm/w0/RTT_INPUT_DATA/BeamGas/hijing.O.digit._00430.pool.root"]
-    jobproperties.BField.solenoidOn=True
-    jobproperties.BField.barrelToroidOn=True
-    jobproperties.BField.endcapToroidOn=True        
-if BeamGas:
-    ATLASCosmicFlags.CosmicSetup = "M8"
-    globalflags.DetDescrVersion = 'ATLAS-Comm-09-00-00'
-    ATLASCosmicFlags.IOVDbSvcGlobalTagData = 'COMCOND-006-01'
-    athenaCommonFlags.BSRDOInput = [
-        "/castor/cern.ch/user/m/muoncomm/SingleBeam/run87764/run87764.MBTS_BCM_LUCID.LB0000.SFO-1.0001.data",
-        "/castor/cern.ch/user/m/muoncomm/SingleBeam/run87764/run87764.MBTS_BCM_LUCID.LB0000.SFO-1.0005.data",
-        "/castor/cern.ch/user/m/muoncomm/SingleBeam/run87764/run87764.MBTS_BCM_LUCID.LB0000.SFO-1.0007.data",
-        "/castor/cern.ch/user/m/muoncomm/SingleBeam/run87764/run87764.MBTS_BCM_LUCID.LB0000.SFO-1.0017.data",
-        "/castor/cern.ch/user/m/muoncomm/SingleBeam/run87764/run87764.MBTS_BCM_LUCID.LB0000.SFO-1.0022.data",
-        "/castor/cern.ch/user/m/muoncomm/SingleBeam/run87764/run87764.MBTS_BCM_LUCID.LB0000.SFO-1.0023.data",
-        "/castor/cern.ch/user/m/muoncomm/SingleBeam/run87764/run87764.MBTS_BCM_LUCID.LB0000.SFO-2.0017.data",
-        "/castor/cern.ch/user/m/muoncomm/SingleBeam/run87764/run87764.MBTS_BCM_LUCID.LB0000.SFO-2.0018.data",
-        "/castor/cern.ch/user/m/muoncomm/SingleBeam/run87764/run87764.MBTS_BCM_LUCID.LB0000.SFO-2.0019.data",
-        "/castor/cern.ch/user/m/muoncomm/SingleBeam/run87764/run87764.MBTS_BCM_LUCID.LB0000.SFO-3.0004.data",
-        "/castor/cern.ch/user/m/muoncomm/SingleBeam/run87764/run87764.MBTS_BCM_LUCID.LB0000.SFO-3.0007.data",
-        "/castor/cern.ch/user/m/muoncomm/SingleBeam/run87764/run87764.MBTS_BCM_LUCID.LB0000.SFO-3.0008.data",
-        "/castor/cern.ch/user/m/muoncomm/SingleBeam/run87764/run87764.MBTS_BCM_LUCID.LB0000.SFO-4.0008.data",
-        "/castor/cern.ch/user/m/muoncomm/SingleBeam/run87764/run87764.MBTS_BCM_LUCID.LB0000.SFO-4.0009.data",
-        "/castor/cern.ch/user/m/muoncomm/SingleBeam/run87764/run87764.MBTS_BCM_LUCID.LB0000.SFO-5.0005.data",
-        "/castor/cern.ch/user/m/muoncomm/SingleBeam/run87764/run87764.MBTS_BCM_LUCID.LB0000.SFO-5.0006.data",
-        "/castor/cern.ch/user/m/muoncomm/SingleBeam/run87764/run87764.MBTS_BCM_LUCID.LB0000.SFO-5.0007.data",
-        "/castor/cern.ch/user/m/muoncomm/SingleBeam/run87764/run87764.MBTS_BCM_LUCID.LB0000.SFO-5.0010.data",
-        "/castor/cern.ch/user/m/muoncomm/SingleBeam/run87764/run87764.MBTS_BCM_LUCID.LB0000.SFO-5.0021.data"
-        ]    
-    jobproperties.BField.solenoidOn=False
-    jobproperties.BField.barrelToroidOn=True
-    jobproperties.BField.endcapToroidOn=True
-
-MuonDQAFlags.doM8=True
-if MuonDQAFlags.doM8:
-    ATLASCosmicFlags.CosmicSetup = "ATLAS"
-    ATLASCosmicFlags.doMasking=False
-    include ("RecExCommission/GetInputFiles.py")
-    if CollData:
-        if not 'RunNumberList' in dir():
-            RunNumberList = [ 87863 ] 
-        if not 'FilePrefix' in dir():
-            FilePrefix = "daq.NoTag" 
-        if not 'Partition' in dir():
-            Partition      = "BPTX"
-        if not 'Trigger' in dir():
-            Trigger = "*.physics."+Partition
-        if not 'InputDir' in dir():
-            InputDir = "/castor/cern.ch/grid/atlas/DAQ/2008/"+str(RunNumberList[0])+"/physics_"+Partition	
-        BSRDOInput = []
-        for RunNumber in RunNumberList:
-            InputFiles = GetInputFilesFromTokens(InputDir,RunNumber,FilePrefix,Trigger)
-        print "Input files:"
-        athenaCommonFlags.BSRDOInput.set_Value_and_Lock(InputFiles)
-        print athenaCommonFlags.BSRDOInput
-        ATLASCosmicFlags.NumFile = []
-        # Detector description #jamie, use version with field (even though solenoid is off)
-        globalflags.DetDescrVersion.set_Value_and_Lock('ATLAS-GEO-04-00-00')
-        globalflags.ConditionsTag.set_Value_and_Lock('COMCOND-ES1C-000-00')
-        # for running over data with field on need this to be setto true
-        from AthenaCommon.BFieldFlags import jobproperties
-        jobproperties.BField.solenoidOn.set_Value_and_Lock(False)
-        jobproperties.BField.barrelToroidOn.set_Value_and_Lock(True)
-        jobproperties.BField.endcapToroidOn.set_Value_and_Lock(True)
-    if Field:
-        globalflags.DetDescrVersion ='ATLAS-Comm-09-00-00'
-        ATLASCosmicFlags.IOVDbSvcGlobalTagData = 'COMCOND-006-00'  #Database
-        ATLASCosmicFlags.Magnet = False
-        ATLASCosmicFlags.MagnetToroid = True
-        jobproperties.BField.solenoidOn = False
-        jobproperties.BField.barrelToroidOn = True
-        jobproperties.BField.endcapToroidOn = True
-        if not 'RunNumberList' in dir():
-            RunNumberList = [ 82075 ] # for M8 ###====LIST of GOOD M7 runs====> /afs/cern.ch/atlas/project/tzero/prod1/goodruns and https://twiki.cern.ch/twiki/bin/view/Atlas/M7MuonRunList
-        if not 'FilePrefix' in dir():
-            FilePrefix = "daq.ATLAS" # for M8
-        if not 'Partition' in dir():
-            Partition      = "HLT_Cosmics_MU3"   # for M7,M8 | physics.HLT_Cosmics_MU3 | physics.HLT_Cosmics
-        if not 'Trigger' in dir():
-            Trigger = "*.physics."+Partition
-        if not 'InputDir' in dir():
-            InputDir = "/castor/cern.ch/grid/atlas/DAQ/2008/"+str(RunNumberList[0])+"/physics_"+Partition # for M8	
-        BSRDOInput = []
-        for RunNumber in RunNumberList:
-            InputFiles = GetInputFilesFromTokens(InputDir,RunNumber,FilePrefix,Trigger)
-        print "Input files:"
-        athenaCommonFlags.BSRDOInput=InputFiles
-        print athenaCommonFlags.BSRDOInput
-        ATLASCosmicFlags.NumFile = []
-    if noField:
-        globalflags.DetDescrVersion = 'ATLAS-CommNF-09-00-00'      # Detector description
-        ATLASCosmicFlags.IOVDbSvcGlobalTagData = 'COMCOND-006-00'  #Database
-        jobproperties.BField.solenoidOn = False
-        jobproperties.BField.barrelToroidOn = False
-        jobproperties.BField.endcapToroidOn = False
-        if not 'RunNumberList' in dir():
-            RunNumberList = [ 77168 ] # for M8 ###====LIST of GOOD M7 runs====> /afs/cern.ch/atlas/project/tzero/prod1/goodruns and https://twiki.cern.ch/twiki/bin/view/Atlas/M7MuonRunList
-        if not 'FilePrefix' in dir():
-            FilePrefix = "daq.ATLAS" # for M8
-        if not 'Partition' in dir():
-            Partition      = "HLT_Cosmics_MU3"   # for M7,M8 | physics.HLT_Cosmics_MU3 | physics.HLT_Cosmics
-        if not 'Trigger' in dir():
-            Trigger = "*.physics."+Partition
-        if not 'InputDir' in dir():
-            InputDir = "/castor/cern.ch/grid/atlas/DAQ/2008/"+str(RunNumberList[0])+"/physics_"+Partition # for M8	
-        BSRDOInput = []
-        for RunNumber in RunNumberList:
-            InputFiles = GetInputFilesFromTokens(InputDir,RunNumber,FilePrefix,Trigger)
-        print "Input files:"
-        athenaCommonFlags.BSRDOInput=InputFiles
-        print athenaCommonFlags.BSRDOInput
-        ATLASCosmicFlags.NumFile = []
-
-###############################################################
-#
-#  Configuration jobOptions file
-#
-###############################################################  
-#=======================Output Files===================================
-if Field or noField or CollData:
-    DQMonFlags.histogramFile = MuonSystem+"MuonMonitoring_"+str(ATLASCosmicFlags.CosmicSetup)+"Setup_"+str(RunNumber)+".root"
-    athenaCommonFlags.PoolESDOutput = MuonSystem+"MuonMonitoringESD_"+str(ATLASCosmicFlags.CosmicSetup)+"_"+str(RunNumber)+".pool.root"
-    ATLASCosmicFlags.FilteredESDOutputFile = MuonSystem+"MuonMonitoringESD_Filtered"+str(ATLASCosmicFlags.CosmicSetup)+"_"+str(RunNumber)+".pool.root"
-    
-if BeamHalo or BeamGas:
-    recFlags.RootHistoOutput = MuonSystem+"MuonMonitoring_BeamHalo.root"
-    athenaCommonFlags.PoolESDOutput = MuonSystem+"MuonMonitoringESD_BeamHalo.pool.root"
-    ATLASCosmicFlags.FilteredESDOutputFile = MuonSystem+"MuonMonitoringESD_Filtered_BeamHalo.pool.root"
-
-if SimBeamHalo or SimBeamGas:
-    recFlags.RootHistoOutput = MuonSystem+"MuonMonitoring_SimBeamHalo.root"
-    athenaCommonFlags.PoolESDOutput = MuonSystem+"MuonMonitoringESD_SimBeamHalo.pool.root"
-    ATLASCosmicFlags.FilteredESDOutputFile = MuonSystem+"MuonMonitoringESD_Filtered_SimBeamHalo.pool.root"
- 
-#======================================================================
-#Steering flags
-#======================================================================
-athenaCommonFlags.EvtMax.set_Value_and_Lock(10)
-athenaCommonFlags.SkipEvents.set_Value_and_Lock(0)
-#======================================================================
-if 'doAuditors' in dir():
-    from RecExConfig.RecFlags  import jobproperties
-    jobproperties.Rec.doNameAuditor.set_Value(True)
-#====================================================================== 
-#=BEGINNN=====================================================================
-# the main jobOpt
-if BeamGas:
-    include( "RecExCommission/RecExCommission_SingleBeamtopOptions.py" )
-else:
-    include( "RecExCommission/RecExCommission.py" )
-    include ("RecExCommon/RecExCommon_topOptions.py")
-#==ENDDDDD====================================================================
- 
-####Change Collections####################
-#if MuonDQAFlags.doMuonTrackMon:
-#    ToolSvc += CfgMgr.MuonMonTrkSummary(MuonTrackCollections=["MooreTrackParticles" ,"MuonboyTrackParticles"])
-#    ToolSvc += CfgMgr.MuonTrackValidation(MuonTrackCollections=["MooreTrackParticles" ,"MuonboyTrackParticles"])
-#    ToolSvc += CfgMgr.MuonAlignMonGenericTracks(MuonTrackCollections=["MooreTrackParticles" ,"MuonboyTrackParticles"])     
-
-###############################################################
-#
-#  Configuration jobOptions file
-#
-###############################################################
-#--------------------------------------------------------------
-# Performace monitoring (CPU and Memory)
-#--------------------------------------------------------------
-if MuonDQAFlags.doCpuMuonMon:
-    include("MuonDQAMonitoring/MuonDQAMonitoring_CpuPerfMon.py")
-    jobproperties.PerfMonFlags.OutputFile = MuonSystem+"muondqa.perfmon.pmon.gz"
-    
-#if recFlags.doPerfMon:
-#    from PerfMonComps.PerfMonFlags import jobproperties
-#    jobproperties.PerfMonFlags.doPerEvtLeakCheck = True
-
-if MuonDQAFlags.doMuonDQAPerfMonitoring and MuonDQAFlags.doMuonDQAHephTool:
-    from PerfMonComps.PerfMonFlags import jobproperties
-    jobproperties.PerfMonFlags.doPerEvtLeakCheck = True
-#--------------------------------------------------------------
-# Valgrind- Callgrind
-#--------------------------------------------------------------
-if MuonDQAFlags.doCallgrind:
-     from Valkyrie.ValkyrieConf import ValgrindSvc
-     valgrindSvc = ValgrindSvc( OutputLevel = VERBOSE )
-     if ATLASCosmicFlags.doMuonHitMon:
-         valgrindSvc.ProfiledAlgs += MuonDQAFlags.CallgrindHitAlgs
-         valgrindSvc.IgnoreFirstNEvents = MuonDQAFlags.CallgrindSkip      # to start instrumentation after the second event only
-     if ATLASCosmicFlags.doMuonTrackMon:
-         valgrindSvc.ProfiledAlgs += MuonDQAFlags.CallgrindTrkAlgs
-         valgrindSvc.IgnoreFirstNEvents = MuonDQAFlags.CallgrindSkip      # to start instrumentation after the second event only
-     if ATLASCosmicFlags.doMuonSegmMon:
-         valgrindSvc.ProfiledAlgs += MuonDQAFlags.CallgrindSegmAlgs
-         valgrindSvc.IgnoreFirstNEvents = MuonDQAFlags.CallgrindSkip      # to start instrumentation after the second event only          
-     # Add service and turn on auditing
-     svcMgr += valgrindSvc
-     theApp.CreateSvc += [svcMgr.ValgrindSvc.getFullJobOptName()]
-     theApp.AuditAlgorithms = True
-     theApp.AuditTools      = True
-     theApp.AuditServices   = True
-# -------------------------------------------------------------
-#Output level
-# -------------------------------------------------------------
-# --------------For RawData Monitoring----------------------------
-if MuonDQAFlags.doMuonHitMon:
-    #ToolSvc += CfgMgr.MDTRawDataBSValAlg(OutputLevel = INFO)
-    #ToolSvc += CfgMgr.MDTRawDataESDValAlg(OutputLevel = INFO)
-    #ToolSvc += CfgMgr.RPCRawDataValAlg(OutputLevel = INFO)
-    #ToolSvc += CfgMgr.MDTvsRPCRawDataValAlg(OutputLevel = INFO)
-    #ToolSvc += CfgMgr.RPCLV1RawDataValAlg(OutputLevel = INFO)
-    #ToolSvc += CfgMgr.TGCRawDataESDValAlg(OutputLevel = INFO)
-    #ToolSvc += CfgMgr.TGCLV1RawDataESDValAlg(OutputLevel = INFO)
-    #ToolSvc += CfgMgr.MDTvsTGCRawDataESDValAlg(OutputLevel = INFO)
-    if MuonDQAFlags.doCSCMon:
-        #ToolSvc += CfgMgr.CSCPrdValAlg(OutputLevel = INFO)
-        #ToolSvc += CfgMgr.CSCRdoValAlg(OutputLevel = INFO)
-        #ToolSvc += CfgMgr.CSCClusterTree(OutputLevel = INFO)
-        #ToolSvc += CfgMgr.CSCClusterValAlg(OutputLevel = INFO)
-# --------------For MuonSegment Monitoring------------------------    
-if MuonDQAFlags.doMuonSegmMon:
-    #ToolSvc += CfgMgr.MuonSegmValidation(OutputLevel = INFO)
-# --------------For MuonTrk Alignment Monitoring------------------------    
-if MuonDQAFlags.doMuonTrkAlignMon:
-    #ToolSvc += CfgMgr.MuonAlignValidation(OutputLevel = INFO)
-# --------------For MuonTrk Monitoring----------------------------
-# --------------For No Trigger MuonTrk Monitoring-----------------
-if MuonDQAFlags.doMuonTrackMon and not MuonDQAFlags.MuonTrkMonDoTrigger:
-    #ToolSvc += CfgMgr.MuonSelectedTracksMon(OutputLevel = INFO) 
-    #ToolSvc += CfgMgr.MuonGenericTracksMon(OutputLevel = INFO) 
-# --------------For TriggerAware MuonTrk Monitoring---------------
-if MuonDQAFlags.doMuonTrackMon and MuonDQAFlags.MuonTrkMonDoTrigger:
-    ### UseTriggerVector =True
-    #ToolSvc += CfgMgr.MuonSelectedTracksMon_Trig(OutputLevel = INFO) 
-    #ToolSvc += CfgMgr.MuonGenericTracksMon_Trig(OutputLevel = INFO)     
-    ### UseTriggerVector = False
-    #ToolSvc += CfgMgr.MuonSelectedTracksMon_trigmu10(OutputLevel = INFO) 
-    #ToolSvc += CfgMgr.MuonSelectedTracksMon_trigmu20(OutputLevel = INFO)         
-    #ToolSvc += CfgMgr.MuonSelectedTracksMon_trigmu40(OutputLevel = INFO) 
-    #ToolSvc += CfgMgr.MuonSelectedTracksMon_trig2mu10(OutputLevel = INFO)
-    #ToolSvc += CfgMgr.MuonGenericTracksMon_trigmu10(OutputLevel = INFO)
-    #ToolSvc += CfgMgr.MuonGenericTracksMon_trigmu20(OutputLevel = INFO)
-    #ToolSvc += CfgMgr.MuonGenericTracksMon_trigmu40(OutputLevel = INFO)
-    #ToolSvc += CfgMgr.MuonGenericTracksMon_trig2mu10(OutputLevel = INFO)     
-# --------------For MuonEventInfo Monitoring----------------------------
-if MuonDQAFlags.doMuonEvtMon:
-    #ToolSvc += CfgMgr.MuonDQA__MuonEventInfoMonTool(OutputLevel = INFO)  
-#--------------------------------------------------------------------------- 
-Service( "THistSvc" ).OutputLevel = WARNING
-#--------------------------------------------------------------------------- 
-# THIS IS TEMPORY HACK TO GET RID OF MUON ERRORS BEING PRINTED FOR EVERY EVENT
-# NEED A REAL FIX 
-#--------------------------------------------------------------------------- 
-Algorithm("TgcRdoToTgcPrepData").OutputLevel = ERROR
-#--------------------------------------------------------------------------- 
-print "List all DLL"
-print theApp.Dlls
-print "List all ExtSvc"
-print theApp.ExtSvc
-print "List of all top algorithms"
-print theApp.TopAlg
-#--------------------------------------------------------------------------- 
-print topSequence
-print ServiceMgr
-print #ToolSvc
-#======================================================================
diff --git a/PhysicsAnalysis/PrimaryDPDMaker/share/bstodpd_data.py b/PhysicsAnalysis/PrimaryDPDMaker/share/bstodpd_data.py
deleted file mode 100644
index af3a04e7fb8ec7aeb7e991987631cef750978fab..0000000000000000000000000000000000000000
--- a/PhysicsAnalysis/PrimaryDPDMaker/share/bstodpd_data.py
+++ /dev/null
@@ -1,53 +0,0 @@
-##=============================================================================
-## Name:        bstodpd_data.py
-##
-## Author:      David Cote (DESY)
-## Created:     November 2008
-##
-## Description: This is the starting script to produce a DPD from RAW.
-##=============================================================================
-
-from RecExConfig.RecFlags  import rec
-from AthenaCommon.BeamFlags import jobproperties
-from AthenaCommon.AthenaCommonFlags import athenaCommonFlags
-from AthenaCommon.GlobalFlags import globalflags
-from PrimaryDPDMaker.PrimaryDPDFlags import primDPD
-
-#Input
-globalflags.InputFormat.set_Value_and_Lock('bytestream')
-athenaCommonFlags.BSRDOInput.set_Value_and_Lock(['/castor/cern.ch/grid/atlas/DAQ/2008/87863/physics_BPTX/daq.NoTag.0087863.physics.BPTX.LB0000.SFO-1._0001.data'])
-athenaCommonFlags.EvtMax=5
-
-#Default configuration
-rec.doAOD=False
-rec.doWriteAOD=False
-rec.doWriteTAG=False	
-rec.doWriteTAGCOM=False
-rec.doMonitoring=False
-rec.doCBNT=False
-rec.doESD=True
-
-#auto-configuration
-rec.triggerStream="BPTX"
-rec.AutoConfiguration.append('FieldAndGeo')
-rec.AutoConfiguration.append('BeamType')
-rec.AutoConfiguration.append('ConditionsTag')
-
-#data configuration
-include( "RecExCommission/RecExCommissionFlags_jobOptions.py" )
-#ATLASCosmicFlags.doFilteredESD=False 
-include("RecExCommission/MinimalCommissioningSetup.py")
-
-#DPD (skimmed bytestream)
-rec.doDPD.set_Value_and_Lock( True )
-rec.DPDMakerScripts.append("PrimaryDPDMaker/PrimaryDPDMaker.py")
-from PrimaryDPDMaker.PrimaryDPDFlags import primDPD
-#skimmed bytestream
-primDPD.WriteRAW_IDPROJCOMM=True
-primDPD.RAW_IDPROJCOMMName="mySkimmedBS"
-
-#ESD (optional)
-rec.doWriteESD=True
-athenaCommonFlags.PoolESDOutput="myESD.pool.root"
-
-include("RecExCommon/RecExCommon_topOptions.py")
diff --git a/Reconstruction/RecExample/RecExCommission/CMakeLists.txt b/Reconstruction/RecExample/RecExCommission/CMakeLists.txt
deleted file mode 100644
index a2b2d4f2ba5666f617cdc40861e4679bcdc72784..0000000000000000000000000000000000000000
--- a/Reconstruction/RecExample/RecExCommission/CMakeLists.txt
+++ /dev/null
@@ -1,12 +0,0 @@
-################################################################################
-# Package: RecExCommission
-################################################################################
-
-# Declare the package name:
-atlas_subdir( RecExCommission )
-
-# Install files from the package:
-atlas_install_python_modules( python/*.py )
-atlas_install_joboptions( share/*.py )
-atlas_install_scripts( share/RecExCommissionData_links.sh share/RecExCommission_links.sh share/RecExCommissionData_links.csh )
-
diff --git a/Reconstruction/RecExample/RecExCommission/python/__init__.py b/Reconstruction/RecExample/RecExCommission/python/__init__.py
deleted file mode 100644
index a299a56aac03200c5c2005034e19a941eff828b3..0000000000000000000000000000000000000000
--- a/Reconstruction/RecExample/RecExCommission/python/__init__.py
+++ /dev/null
@@ -1,7 +0,0 @@
-# Copyright (C) 2002-2017 CERN for the benefit of the ATLAS collaboration
-
-# File RecExCommission/python/__init__.py
-# Author: jamie.boyd@cern.ch
-
-__author__="Jamie Boyd"
-__all__= ["RecExCommission_MagneticFieldConfig"]
diff --git a/Reconstruction/RecExample/RecExCommission/scripts/ec_mon.sh b/Reconstruction/RecExample/RecExCommission/scripts/ec_mon.sh
deleted file mode 100755
index ecc42623225af78681587710b242b43d5f993193..0000000000000000000000000000000000000000
--- a/Reconstruction/RecExample/RecExCommission/scripts/ec_mon.sh
+++ /dev/null
@@ -1,191 +0,0 @@
-#!/bin/bash
-#
-# script to run monitoring on phase 1 commissioning files.
-#
-# 30. Jan. 06   R. Seuster adopt it for online farm
-# 10. Jan. 06   R. Seuster make it run on kit and at CERN
-# 06. Jan. 06   R. Seuster, K. Voss
-#
-# After setting variables depending on the installation of
-# the atlas software, the enviroment and variables steering
-# the job are set in the first part.
-#
-# Next, a short python file with all variables for this job is
-# created.
-#
-# The job is run in its own run directory in the third part.
-#
-
-if [ $# -gt 4 ] ; then
-   echo "Script does not accept more than three parameters!"
-   echo ""
-   echo "usage: ec_mon.sh [runnumber [evtno [ gain [jobOptions.py]]]]"
-   echo "       runnumber     of the file to process (default 18720)"
-   echo "       gain          of the file to process (default HIGH)"
-   echo "       jobOptions.py of the algorithms to run (default RecExCommission_LAr_EC_INSTALLATION_jobOptions.py)"
-   return
-   exit
-fi
-
-##############################################################
-#          first part, general installation setup            #
-#                variables like runnumber                    #
-##############################################################
-
-# this is where your athena release is installed
-#export BASEPATH="/atlas/slc3"
-# at CERN this would be
-export BASEPATH="/afs/cern.ch/atlas/software"
-# P1:
-# export BASEPATH="/space/sw/offline_test"
-
-# which release to run
-ATLAS_RELEASE="11.2.0"
-
-# this is the run directory of the job, please give the absolute path !
-# RUNPATH=${HOME}/Athena/11.2.0-MON
-RUNPATH=${PWD}
-
-# the runnumber to process
-RUNNUMBER="1020"
-
-# the location of the datafiles disc or castor
-DATPATH="/castor/cern.ch/atlas/LargFec/EC_Installation"
-
-#
-EVTNO="10000000"
-
-# the gain of the noisefile
-GAIN=HIGH
-
-# the main joboptions file
-JOBOPTIONFILE=RecExCommission_LAr_EC_INSTALLATION_jobOptions.py
-
-# overwrite, if given on command line
-if [ $# -ge 1 ]; then
- RUNNUMBER="$1"
- shift
-fi
-
-# overwrite, if given on command line
-if [ $# -ge 1 ]; then
- EVTNO="$1"
- shift
-fi
-
-# overwrite, if given on command line
-if [ $# -ge 1 ]; then
- GAIN="$1"
- shift
-fi
-
-# overwrite, if given on command line
-if [ $# -eq 1 ]; then
- JOBOPTIONFILE=$1
- shift
-fi
-
-# construct string containing runnumber including leading 0's
-RUNSTR="`expr substr 0000000 1 \( 7 - length $RUNNUMBER \)`$RUNNUMBER"
-
-# name of logfile
-LOGFILE=logfile.$RUNSTR
-
-# do some basic cross checks, existance of directories and files
-if [ ! -d $RUNPATH ]; then
- echo Your run directory does not exist !!
- echo Please create one with
- echo \"mkdir $RUNPATH \"
- return
- exit
-fi
-
-
-# FILEPATH="${DATPATH}daq_EB-C_${GAIN}_InstPed_${RUNSTR}_file01.data"
-
-# if [ ! -e $FILEPATH ]; then
-#  echo Your datafile does not exist !!
-#  echo Looking for $FILEPATH
-# # return
-# # exit
-# fi
-
-# print out the setup:
-echo "Setting up for"
-echo "Atlas Release : $ATLAS_RELEASE"
-echo " installed in : $BASEPATH"
-echo ""
-echo "The run directory is    : $RUNPATH"
-echo "The data directory is   : $DATPATH"
-echo "The run number is       : $RUNSTR"
-echo "The number of events    : $EVTNO"
-echo "The gain of this run is : $GAIN"
-echo "The main jobOptions are : $JOBOPTIONFILE"
-echo ""
-echo "The output will be in   : $LOGFILE"
-
-# setup the athena enviroment
-
-#if [ ! -e $BASEPATH/$ATLAS_RELEASE/setup.sh ]; then
-#    echo "This AtlasRelease does not exist in this configuration !"
-#    echo $BASEPATH/$ATLAS_RELEASE
-##    return
-##    exit
-#fi
-
-# running at CERN ?
-if [ $BASEPATH = "/afs/cern.ch/atlas/software" ]; then
- source ~/Athena/cmthome/setup.sh -tag=$ATLAS_RELEASE,groupArea
- source ${BASEPATH}/dist/${ATLAS_RELEASE}/Control/AthenaRunTime/*/cmt/setup.sh
-else
- # basic setup and distribution dependent variables
- # source ${BASEPATH}/${ATLAS_RELEASE}/setup.sh
- source ${BASEPATH}/${ATLAS_RELEASE}-MON/setup.sh
- export CMTPATH=${RUNPATH}:${CMTPATH}
- # multiple releases in installation directory ?
- # source ${BASEPATH}/${ATLAS_RELEASE}/dist/${ATLAS_RELEASE}/Control/AthenaRunTime/*/cmt/setup.sh
- source ${BASEPATH}/${ATLAS_RELEASE}-MON/dist/${ATLAS_RELEASE}/Control/AthenaRunTime/*/cmt/setup.sh
- # source ${BASEPATH}/kits/dist/${ATLAS_RELEASE}/Control/AthenaRunTime/*/cmt/setup.sh
-fi
-
-# variables to access the CVS repository at CERN (via ssh)
-# P1:
-# export CVSROOT=:ext:atlas-sw.cern.ch:/atlascvs
-# export CVS_RSH=ssh
-
-
-
-if [ `basename $0` = "ec_mon.sh" ]; then
-
- if [ ! -e $JOBOPTIONFILE ]; then
-  echo No $JOBOPTIONFILE yet !
-  echo Getting it for you
-  get_files $JOBOPTIONFILE
- else
-  echo Using $JOBOPTIONFILE in your run directory !
- fi
- 
- MONDIR=~/scratch0/monitor.run.$RUNSTR
- TOPOPT=myTopOptions.py
- HEREDIR=`pwd` 
-
-
- mkdir -p $MONDIR
- cd $MONDIR
-
-cat <<EOF > $TOPOPT
-
-RunNumber = $RUNNUMBER
-LArDigitKey = "$GAIN"
-EvtNo=$EVTNO
-InputDir = "$DATPATH"
-
-EOF
-
- # now run athena
- echo starting athena
- athena.py -bs $TOPOPT $HEREDIR/$JOBOPTIONFILE >& $LOGFILE
-else
- echo just setting up the enviroment
-fi
-
diff --git a/Reconstruction/RecExample/RecExCommission/scripts/runmon.sh b/Reconstruction/RecExample/RecExCommission/scripts/runmon.sh
deleted file mode 100755
index 36896fafc39a32c55f5ee8291da0ce2cda9ae0d7..0000000000000000000000000000000000000000
--- a/Reconstruction/RecExample/RecExCommission/scripts/runmon.sh
+++ /dev/null
@@ -1,196 +0,0 @@
-#!/bin/bash
-#
-# script to run monitoring on phase 1 commissioning files.
-#
-# 30. Jan. 06   R. Seuster adopt it for online farm
-# 10. Jan. 06   R. Seuster make it run on kit and at CERN
-# 06. Jan. 06   R. Seuster, K. Voss
-#
-# After setting variables depending on the installation of
-# the atlas software, the enviroment and variables steering
-# the job are set in the first part.
-#
-# Next, a short python file with all variables for this job is
-# created.
-#
-# The job is run in its own run directory in the third part.
-#
-
-if [ $# -gt 4 ] ; then
-   echo "Script does not accept more than three parameters!"
-   echo ""
-   echo "usage: runmon.sh [runnumber [evtno [ gain [jobOptions.py]]]]"
-   echo "       runnumber     of the file to process (default 18720)"
-   echo "       gain          of the file to process (default HIGH)"
-   echo "       jobOptions.py of the algorithms to run (default RecExCommission_LAr_EXPERT-WEEK_jobOptions.py)"
-   return
-   exit
-fi
-
-##############################################################
-#          first part, general installation setup            #
-#                variables like runnumber                    #
-##############################################################
-
-# this is where your athena release is installed
-#export BASEPATH="/atlas/slc3"
-# at CERN this would be
-export BASEPATH="/afs/cern.ch/atlas/software"
-# P1:
-# export BASEPATH="/space/sw/offline_test"
-
-# which release to run
-ATLAS_RELEASE="11.2.0"
-
-# this is the run directory of the job, please give the absolute path !
-RUNPATH=${HOME}/scratch0/LArMonRun
-
-# the runnumber to process
-RUNNUMBER="1020"
-
-# the location of the datafiles disc or castor
-# DATPATH="/atlas/LargFec/Installation/"
-DATPATH="/castor/cern.ch/atlas/LargFec/ExpertWeek01"
-# P1:
-# DATPATH="/atlas-home/larmon/hma/data/"
-
-#
-EVTNO="10000000"
-
-# the gain of the noisefile
-GAIN=HIGH
-
-# the main joboptions file
-# JOBOPTIONFILE=RecExCommission_LArPhase1_jobOptions.py
-JOBOPTIONFILE=RecExCommission_LAr_EXPERT-WEEK_jobOptions.py
-
-# overwrite, if given on command line
-if [ $# -ge 1 ]; then
- RUNNUMBER="$1"
- shift
-fi
-
-# overwrite, if given on command line
-if [ $# -ge 1 ]; then
- EVTNO="$1"
- shift
-fi
-
-# overwrite, if given on command line
-if [ $# -ge 1 ]; then
- GAIN="$1"
- shift
-fi
-
-# overwrite, if given on command line
-if [ $# -eq 1 ]; then
- JOBOPTIONFILE=$1
- shift
-fi
-
-# construct string containing runnumber including leading 0's
-RUNSTR="`expr substr 0000000 1 \( 7 - length $RUNNUMBER \)`$RUNNUMBER"
-
-# name of logfile
-LOGFILE=logfile.$RUNSTR
-
-# do some basic cross checks, existance of directories and files
-if [ ! -d $RUNPATH ]; then
- echo Your run directory does not exist !!
- echo Please create one with
- echo \"mkdir $RUNPATH \"
- return
- exit
-fi
-
-if [ ! -d $DATPATH ]; then
- echo Your data directory does not exist !!
- echo $DATPATH
-# return
-# exit
-fi
-
-# FILEPATH="${DATPATH}daq_ROS-1_${GAIN}_InstPed_${RUNSTR}_file01.data"
-
-# if [ ! -e $FILEPATH ]; then
-#  echo Your datafile does not exist !!
-#  echo Looking for $FILEPATH
-# # return
-# # exit
-# fi
-
-# print out the setup:
-echo "Setting up for"
-echo "Atlas Release : $ATLAS_RELEASE"
-echo " installed in : $BASEPATH"
-echo ""
-echo "The run directory is    : $RUNPATH"
-echo "The data directory is   : $DATPATH"
-echo "The run number is       : $RUNSTR"
-echo "The number of events    : $EVTNO"
-echo "The gain of this run is : $GAIN"
-echo "The main jobOptions are : $JOBOPTIONFILE"
-echo ""
-echo "The output will be in   : $LOGFILE"
-
-# setup the athena enviroment
-
-#if [ ! -e $BASEPATH/$ATLAS_RELEASE/setup.sh ]; then
-#    echo "This AtlasRelease does not exist in this configuration !"
-#    echo $BASEPATH/$ATLAS_RELEASE
-##    return
-##    exit
-#fi
-
-# running at CERN ?
-if [ $BASEPATH = "/afs/cern.ch/atlas/software" ]; then
- source ~/cmthome/setup.sh -tag=$ATLAS_RELEASE,groupArea
- source ${BASEPATH}/dist/${ATLAS_RELEASE}/Control/AthenaRunTime/*/cmt/setup.sh
-else
- # basic setup and distribution dependent variables
- # source ${BASEPATH}/${ATLAS_RELEASE}/setup.sh
- source ${BASEPATH}/${ATLAS_RELEASE}-MON/setup.sh
- export CMTPATH=${RUNPATH}:${CMTPATH}
- # multiple releases in installation directory ?
- # source ${BASEPATH}/${ATLAS_RELEASE}/dist/${ATLAS_RELEASE}/Control/AthenaRunTime/*/cmt/setup.sh
- source ${BASEPATH}/${ATLAS_RELEASE}-MON/dist/${ATLAS_RELEASE}/Control/AthenaRunTime/*/cmt/setup.sh
- # source ${BASEPATH}/kits/dist/${ATLAS_RELEASE}/Control/AthenaRunTime/*/cmt/setup.sh
-fi
-
-# variables to access the CVS repository at CERN (via ssh)
-# P1:
-# export CVSROOT=:ext:atlas-sw.cern.ch:/atlascvs
-# export CVS_RSH=ssh
-
-if [ `basename $0` = "runmon.sh" ]; then
-
- if [ ! -e $JOBOPTIONFILE ]; then
-  echo No $JOBOPTIONFILE yet !
-  echo Getting it for you
-  get_files $JOBOPTIONFILE
- else
-  echo Using $JOBOPTIONFILE in your run directory !
- fi
- 
- MONDIR=monitor.run.$RUNSTR
- TOPOPT=myTopOptions.py
- 
- mkdir -p $MONDIR
- cd $MONDIR
-
-cat <<EOF > $TOPOPT
-
-RunNumber = $RUNNUMBER
-LArDigitKey = "$GAIN"
-EvtNo=$EVTNO
-InputDir = "$DATPATH"
-
-EOF
-
- # now run athena
- echo starting athena
- athena.py -bs $TOPOPT ../$JOBOPTIONFILE >& $LOGFILE
-else
- echo just setting up the enviroment
-fi
-
diff --git a/Reconstruction/RecExample/RecExCommission/share/Collisions_ATN.py b/Reconstruction/RecExample/RecExCommission/share/Collisions_ATN.py
deleted file mode 100644
index 8423966e91b09f75ee425f8ee39be7aa8a8a52d8..0000000000000000000000000000000000000000
--- a/Reconstruction/RecExample/RecExCommission/share/Collisions_ATN.py
+++ /dev/null
@@ -1,312 +0,0 @@
-from RecExConfig.RecFlags  import rec
-from AthenaCommon.BeamFlags import jobproperties
-from AthenaCommon.AthenaCommonFlags import athenaCommonFlags
-from AthenaCommon.GlobalFlags import globalflags
-
-if not 'RTTdata' in dir():
-    RTTdata=False
-
-if not 'RTTsim' in dir():
-    RTTsim=False
-
-if not 'ATNsim' in dir():
-        ATNsim=False
-
-if ATNsim:
-    RTTsim=True
-        
-rec.readRDO=False
-
-
-
-#uncomment if read BS
-rec.readRDO=True
-#uncomment if read AOD
-#rec.readAOD=True
-#uncomment if read ESD (note that cosmics DPD are best treated as ESD)
-#rec.readESD=True
-
-# uncomment if reading from TAG (for commissioning one of rec.readESD or rec.readRDO should be true)
-#rec.readTAG=True
-# note that a PoolFileCatalog with the files to navigate to should be available in the run directory
-# note that there is problem 
-
-
-#uncomment if want JiveXML file
-#rec.doJiveXML=True
-
-
-if RTTdata:
-    Input = 'data'
-    
-if RTTsim:    
-    Input = 'simrdo'
-
-if RTTdata or RTTsim:
-    Debug = False
-
-
-
-
-if not 'Input' in dir():
-    # uncomment if input is real data
-    Input='data'
-    # uncomment if input is simulation BS
-    # Input='simbs'
-    # uncomment if input is simulation RDO
-    # Input='simrdo'
-
-if not 'Debug' in dir():
-    Debug=True  # change to True to have printout information
-
-
-#specify beam type (default is "collisions", other values "cosmics" "singlebeam"
-# pick the correct one
-jobproperties.Beam.beamType = 'cosmics'
-# singlebeam not tested recently
-#jobproperties.Beam.beamType = 'singlebeam'
-
-
-
-
-
-
-# input configuration (lock to prevent override)
-# note that if reading from TAG, the input file spec is ignored,
-#   however the flag settings should still be consistent 
-if Input=='data':
-    if rec.readTAG():
-        # read TAG, navigate to ESD
-        athenaCommonFlags.PoolTAGInput=['../cosm/myTAGCOMM.root']
-        athenaCommonFlags.PoolInputQuery.set_Value_and_Lock("TRTTracks>0")
-    if rec.readRDO(): 
-       if jobproperties.Beam.beamType() == 'cosmics':
-           if RTTdata:
-               # this is ignored if TAG are read
-               athenaCommonFlags.BSRDOInput.set_Value_and_Lock(['/castor/cern.ch/grid/atlas/DAQ/2008/91900/physics_IDCosmic/daq.ATLAS.0091900.physics.IDCosmic.LB0001.SFO-1._0001.data',
-                                                                '/castor/cern.ch/grid/atlas/DAQ/2008/91900/physics_IDCosmic/daq.ATLAS.0091900.physics.IDCosmic.LB0001.SFO-1._0002.data',
-                                                                '/castor/cern.ch/grid/atlas/DAQ/2008/91900/physics_IDCosmic/daq.ATLAS.0091900.physics.IDCosmic.LB0001.SFO-1._0003.data',
-                                                                '/castor/cern.ch/grid/atlas/DAQ/2008/91900/physics_IDCosmic/daq.ATLAS.0091900.physics.IDCosmic.LB0001.SFO-2._0001.data',
-                                                                '/castor/cern.ch/grid/atlas/DAQ/2008/91900/physics_IDCosmic/daq.ATLAS.0091900.physics.IDCosmic.LB0001.SFO-2._0002.data',
-                                                                '/castor/cern.ch/grid/atlas/DAQ/2008/91900/physics_IDCosmic/daq.ATLAS.0091900.physics.IDCosmic.LB0001.SFO-2._0003.data',
-                                                                '/castor/cern.ch/grid/atlas/DAQ/2008/91900/physics_IDCosmic/daq.ATLAS.0091900.physics.IDCosmic.LB0001.SFO-3._0001.data',
-                                                                '/castor/cern.ch/grid/atlas/DAQ/2008/91900/physics_IDCosmic/daq.ATLAS.0091900.physics.IDCosmic.LB0001.SFO-3._0002.data',
-                                                                '/castor/cern.ch/grid/atlas/DAQ/2008/91900/physics_IDCosmic/daq.ATLAS.0091900.physics.IDCosmic.LB0001.SFO-3._0003.data',
-                                                                '/castor/cern.ch/grid/atlas/DAQ/2008/91900/physics_IDCosmic/daq.ATLAS.0091900.physics.IDCosmic.LB0001.SFO-4._0001.data',
-                                                                '/castor/cern.ch/grid/atlas/DAQ/2008/91900/physics_IDCosmic/daq.ATLAS.0091900.physics.IDCosmic.LB0001.SFO-4._0002.data',
-                                                                '/castor/cern.ch/grid/atlas/DAQ/2008/91900/physics_IDCosmic/daq.ATLAS.0091900.physics.IDCosmic.LB0001.SFO-4._0003.data',
-                                                                '/castor/cern.ch/grid/atlas/DAQ/2008/91900/physics_IDCosmic/daq.ATLAS.0091900.physics.IDCosmic.LB0001.SFO-5._0001.data',
-                                                                '/castor/cern.ch/grid/atlas/DAQ/2008/91900/physics_IDCosmic/daq.ATLAS.0091900.physics.IDCosmic.LB0001.SFO-5._0002.data',
-                                                                '/castor/cern.ch/grid/atlas/DAQ/2008/91900/physics_IDCosmic/daq.ATLAS.0091900.physics.IDCosmic.LB0001.SFO-5._0003.data',
-                                                                '/castor/cern.ch/grid/atlas/DAQ/2008/91900/physics_IDCosmic/daq.ATLAS.0091900.physics.IDCosmic.LB0002.SFO-1._0001.data',
-                                                                '/castor/cern.ch/grid/atlas/DAQ/2008/91900/physics_IDCosmic/daq.ATLAS.0091900.physics.IDCosmic.LB0002.SFO-1._0002.data',
-                                                                '/castor/cern.ch/grid/atlas/DAQ/2008/91900/physics_IDCosmic/daq.ATLAS.0091900.physics.IDCosmic.LB0002.SFO-1._0003.data',
-                                                                '/castor/cern.ch/grid/atlas/DAQ/2008/91900/physics_IDCosmic/daq.ATLAS.0091900.physics.IDCosmic.LB0002.SFO-2._0001.data',
-                                                                '/castor/cern.ch/grid/atlas/DAQ/2008/91900/physics_IDCosmic/daq.ATLAS.0091900.physics.IDCosmic.LB0002.SFO-2._0002.data',
-                                                                '/castor/cern.ch/grid/atlas/DAQ/2008/91900/physics_IDCosmic/daq.ATLAS.0091900.physics.IDCosmic.LB0002.SFO-2._0003.data',
-                                                                '/castor/cern.ch/grid/atlas/DAQ/2008/91900/physics_IDCosmic/daq.ATLAS.0091900.physics.IDCosmic.LB0002.SFO-3._0001.data',
-                                                                '/castor/cern.ch/grid/atlas/DAQ/2008/91900/physics_IDCosmic/daq.ATLAS.0091900.physics.IDCosmic.LB0002.SFO-3._0002.data',
-                                                                '/castor/cern.ch/grid/atlas/DAQ/2008/91900/physics_IDCosmic/daq.ATLAS.0091900.physics.IDCosmic.LB0002.SFO-3._0003.data',
-                                                                '/castor/cern.ch/grid/atlas/DAQ/2008/91900/physics_IDCosmic/daq.ATLAS.0091900.physics.IDCosmic.LB0002.SFO-4._0001.data',
-                                                                '/castor/cern.ch/grid/atlas/DAQ/2008/91900/physics_IDCosmic/daq.ATLAS.0091900.physics.IDCosmic.LB0002.SFO-4._0002.data',
-                                                                '/castor/cern.ch/grid/atlas/DAQ/2008/91900/physics_IDCosmic/daq.ATLAS.0091900.physics.IDCosmic.LB0002.SFO-4._0003.data',
-                                                                '/castor/cern.ch/grid/atlas/DAQ/2008/91900/physics_IDCosmic/daq.ATLAS.0091900.physics.IDCosmic.LB0002.SFO-5._0001.data',
-                                                                '/castor/cern.ch/grid/atlas/DAQ/2008/91900/physics_IDCosmic/daq.ATLAS.0091900.physics.IDCosmic.LB0002.SFO-5._0002.data',
-                                                                '/castor/cern.ch/grid/atlas/DAQ/2008/91900/physics_IDCosmic/daq.ATLAS.0091900.physics.IDCosmic.LB0002.SFO-5._0003.data',
-                                                                '/castor/cern.ch/grid/atlas/DAQ/2008/91900/physics_IDCosmic/daq.ATLAS.0091900.physics.IDCosmic.LB0003.SFO-1._0001.data'])
-           else:
-               athenaCommonFlags.BSRDOInput.set_Value_and_Lock(['/afs/cern.ch/user/g/gencomm/w0/RTT_INPUT_DATA/CosmicATN/daq.ATLAS.0091900.physics.IDCosmic.LB0001.SFO-1._0001.10EVTS.data'])
-
-           globalflags.DetDescrVersion.set_Value_and_Lock('ATLAS-GEO-03-00-00')
-           globalflags.ConditionsTag.set_Value_and_Lock('COMCOND-REPC-001-00')
-           # for running over data with field on need this to be setto true
-           from AthenaCommon.BFieldFlags import jobproperties
-           jobproperties.BField.solenoidOn.set_Value_and_Lock(True)
-           jobproperties.BField.barrelToroidOn.set_Value_and_Lock(True)
-           jobproperties.BField.endcapToroidOn.set_Value_and_Lock(True)
-
-        
-       else:
-           # this is ignored if tag are read
-           athenaCommonFlags.BSRDOInput.set_Value_and_Lock([
-            '/castor/cern.ch/grid/atlas/DAQ/2008/87863/physics_BPTX/daq.NoTag.0087863.physics.BPTX.LB0000.SFO-1._0001.data'])
-           # Detector description #jamie, use version with field (even though solenoid is off)
-
-           globalflags.DetDescrVersion.set_Value_and_Lock('ATLAS-GEO-04-00-00')
-           globalflags.ConditionsTag.set_Value_and_Lock('COMCOND-REPC-001-00')
-           # for running over data with field on need this to be setto true
-           from AthenaCommon.BFieldFlags import jobproperties
-           jobproperties.BField.solenoidOn.set_Value_and_Lock(False)
-           jobproperties.BField.barrelToroidOn.set_Value_and_Lock(True)
-           jobproperties.BField.endcapToroidOn.set_Value_and_Lock(True)
-        
-       globalflags.InputFormat.set_Value_and_Lock('bytestream')
-
-
-
-    if rec.readAOD():    
-       if rec.readTAG():
-           raise "Cannot have both readAOD and readTAG true"
-       athenaCommonFlags.PoolAODInput.set_Value_and_Lock(["../cosm/myAOD.pool.root"])
-       rec.doWriteAOD=False
-       rec.doWriteESD=False 
-
-    if rec.readESD():    #lxplus225
-        ####L1CaloEM
-        # this is ignored if tags are read
-        athenaCommonFlags.PoolESDInput.set_Value_and_Lock(["../cosm/myESD.pool.root"])
-        rec.doWriteESD=False
-
-    if rec.readESD() or rec.readAOD():
-        globalflags.InputFormat.set_Value_and_Lock('pool')
-        globalflags.DetDescrVersion.set_Value_and_Lock('ATLAS-GEO-03-00-00')
-        globalflags.ConditionsTag.set_Value_and_Lock('COMCOND-REPC-001-00')
-        from AthenaCommon.BFieldFlags import jobproperties
-        jobproperties.BField.solenoidOn.set_Value_and_Lock(True)
-        jobproperties.BField.barrelToroidOn.set_Value_and_Lock(True)
-        jobproperties.BField.endcapToroidOn.set_Value_and_Lock(True)
-
-
-
-elif Input=='overlay':
-    # not tested recently
-    from LArConditionsCommon.LArCondFlags import larCondFlags
-    larCondFlags.useShape=True
-
-    athenaCommonFlags.PoolRDOInput.set_Value_and_Lock([
-            'singleMuon100plusCosmics.RDO.020162._00002.pool.root'])
-
-    globalflags.DetDescrVersion.set_Value_and_Lock('ATLAS-GEO-03-00-00')
-    globalflags.ConditionsTag.set_Value_and_Lock('COMCOND-REPC-001-00')
-
-    from AthenaCommon.BFieldFlags import jobproperties
-    jobproperties.BField.solenoidOn.set_Value_and_Lock(True)
-    jobproperties.BField.barrelToroidOn.set_Value_and_Lock(True)
-    jobproperties.BField.endcapToroidOn.set_Value_and_Lock(True)
-
-    globalflags.InputFormat.set_Value_and_Lock('pool')
-    
-else:
-    if Input=='simbs':
-        #beware there might be sthg wrong in these BS files wrt ID cabling
-        athenaCommonFlags.BSRDOInput.set_Value_and_Lock(
-            ["/afs/cern.ch/user/g/gencomm/w0/jboyd/900Gev/BS/daq.0951001._0001.data",
-             "/afs/cern.ch/user/g/gencomm/w0/jboyd/900Gev/BS/daq.0951001._0002.data"])
-        globalflags.InputFormat.set_Value_and_Lock('bytestream')
-        globalflags.DetDescrVersion.set_Value_and_Lock('ATLAS-GEO-02-01-00')
-        globalflags.ConditionsTag.set_Value_and_Lock('OFLCOND-SIM-00-00-00')
-        doTileCosmicsTrigger=False
-    elif Input=='simrdo':
-
-        if jobproperties.Beam.beamType() == 'cosmics':
-            globalflags.DetDescrVersion.set_Value_and_Lock('ATLAS-Comm-02-00-00')
-            athenaCommonFlags.PoolRDOInput.set_Value_and_Lock( ["/afs/cern.ch/atlas/maxidisk/d17/dig.trtbarrel_ma_B100.root"])
-            from AthenaCommon.BFieldFlags import jobproperties
-            jobproperties.BField.solenoidOn=True
-            jobproperties.BField.barrelToroidOn=True
-            jobproperties.BField.endcapToroidOn=True
-            SpecialTileConfigHack=True
-            globalflags.ConditionsTag.set_Value_and_Lock('OFLCOND-CSC-01-00-00')
-
-        if jobproperties.Beam.beamType() == 'singlebeam':
-            athenaCommonFlags.PoolRDOInput.set_Value_and_Lock( ["/afs/cern.ch/user/g/gencomm/w0/RTT_INPUT_DATA/BeamGas/hijing.O.digit._00430.pool.root"])
-            globalflags.DetDescrVersion.set_Value_and_Lock('ATLAS-CSC-01-02-00')
-            from AthenaCommon.BFieldFlags import jobproperties
-            jobproperties.BField.solenoidOn=True
-            jobproperties.BField.barrelToroidOn=True
-            jobproperties.BField.endcapToroidOn=True
-            
-        else:
-            athenaCommonFlags.PoolRDOInput.set_Value_and_Lock(
-                ["castor:/castor/cern.ch/user/i/ivivarel/900GeVminbias/RDO.024944._00001.pool.root.1",
-                 "castor:/castor/cern.ch/user/i/ivivarel/900GeVminbias/RDO.024944._00002.pool.root.1",
-                 "castor:/castor/cern.ch/user/i/ivivarel/900GeVminbias/RDO.024944._00003.pool.root.1",    
-                 "castor:/castor/cern.ch/user/i/ivivarel/900GeVminbias/RDO.024944._00004.pool.root.1",
-                 "castor:/castor/cern.ch/user/i/ivivarel/900GeVminbias/RDO.024944._00005.pool.root.1",
-                 "castor:/castor/cern.ch/user/i/ivivarel/900GeVminbias/RDO.024944._00006.pool.root.1",
-                 "castor:/castor/cern.ch/user/i/ivivarel/900GeVminbias/RDO.024944._00007.pool.root.1",
-                 "castor:/castor/cern.ch/user/i/ivivarel/900GeVminbias/RDO.024944._00008.pool.root.1",
-                 "castor:/castor/cern.ch/user/i/ivivarel/900GeVminbias/RDO.024944._00009.pool.root.1",
-                 "castor:/castor/cern.ch/user/i/ivivarel/900GeVminbias/RDO.024944._000010.pool.root.1"])         
-
-            globalflags.InputFormat.set_Value_and_Lock('pool')
-#            globalflags.DetDescrVersion.set_Value_and_Lock('ATLAS-GEO-02-01-00')
-#            globalflags.ConditionsTag.set_Value_and_Lock('OFLCOND-SIM-00-00-00')
-        # crashing :  No valid proxy for object TileTTL1CosmicsCnt  of type TileTTL1Container(CLID 2933)
-            doTileCosmicsTrigger=False
-
-    else:
-      raise RuntimeError,"Wrong Input value"
-
-    globalflags.DataSource.set_Value_and_Lock('geant4')    
-    #doTileCosmicsTrigger=False
-
-#hardcoded output specification (corresponds to optional flags from runArgs in transform skeleton)
-rec.RootNtupleOutput.set_Value_and_Lock("commission.ntuple.root")
-athenaCommonFlags.PoolESDOutput.set_Value_and_Lock("commissionESD.pool.root")
-rec.RootHistoOutput.set_Value_and_Lock("monitoring.root")
-if RTTdata or RTTsim:
-    if not ATNsim:
-        athenaCommonFlags.EvtMax.set_Value_and_Lock(500)
-    else:
-        athenaCommonFlags.EvtMax.set_Value_and_Lock(10)
-        
-else:
-    athenaCommonFlags.EvtMax.set_Value_and_Lock(10)
-#athenaCommonFlags.SkipEvents = 0
-
-
-if RTTsim:
-    rec.doHist=False
-else:
-    rec.doHist = True
-
-rec.doWriteTAG.set_Value_and_Lock(False)	
-rec.doWriteAOD=False
-rec.doAOD=False
-if RTTsim or Input=='overlay' or rec.readAOD():
-    rec.doMonitoring.set_Value_and_Lock(False)
-else:
-    rec.doMonitoring.set_Value_and_Lock(True)    
-
-if Input=='overlay':
-   topSequence.LArRawChannelBuilder.DataLocation = "LArDigitContainer_MC_Thinned"
-   topSequence.CBNT_AthenaAware.CBNTAA_LArDigits.ContainerKey = "LArDigitContainer_MC_Thinned"
-   ServiceMgr.MboySvc.UseAllSegments=0 # standard way to run Muonboy on collisions
-   topSequence.LArDigitThinner.Enable = False
-   topSequence.TileDigitsFilter.Enable = False
-
-if Debug:
-    # DEBUG/VERBOSE options
-    rec.doNameAuditor=True
-    rec.doPerfMon=True
-    rec.doDetailedPerfMon=True
-    rec.doDumpProperties=True
-    rec.doDumpTES=True
-    # rec.OutputLevel = INFO
-
-
-include("RecExCommission/RecExCommissionRepro.py")                
-
-# filtered ESD calib and tracking ntuple if from RDO
-if rec.readRDO():
-    from AthenaMonitoring.DQMonFlags import DQMonFlags
-    DQMonFlags.histogramFile.set_Value_and_Lock( "myMonitoring.root" )
-
-    #crashing in 14.5.X VAL 2 3 Feb
-    include("TrigT1CTMonitoring/CTPFlags.py")
-    CTPFlags.doCTRDO=False
-
-if RTTsim:
-    rec.doTrigger=False
-
-#FIXME very temporary, crashing
-#if rec.doJiveXML():
-#    include.block("TrigJiveXML/TrigJiveXML_DataTypes.py")
-
-
-include("RecExCommon/RecExCommon_topOptions.py")                
-
-if Debug:
-    from IOVDbSvc.CondDB import conddb
-    conddb.dumpFolderTags('iovfolderlist.txt',True)
diff --git a/Reconstruction/RecExample/RecExCommission/share/CombinedMuonFit_jobOptions.py b/Reconstruction/RecExample/RecExCommission/share/CombinedMuonFit_jobOptions.py
deleted file mode 100644
index 0fbf5498db6d3776037ccbc8e93faef780e542c9..0000000000000000000000000000000000000000
--- a/Reconstruction/RecExample/RecExCommission/share/CombinedMuonFit_jobOptions.py
+++ /dev/null
@@ -1,49 +0,0 @@
-from TrkGlobalChi2Fitter.TrkGlobalChi2FitterConf import Trk__GlobalChi2Fitter
-GlobalChi2FitterComb=Trk__GlobalChi2Fitter(name='GlobalChi2FitterComb',
-                                       StraightLine=not jobproperties.BField.solenoidOn(),
-                                       ExtrapolationTool=InDetExtrapolator,
-                                       NavigatorTool = InDetNavigator,
-                                       PropagatorTool = InDetPropagator,
-                                       RotCreatorTool = InDetRotCreator,
-                                       OutlierCut = 5.,
-                                       ExternalMat = True,
-                                       sortingReferencePoint = [0,25000,0])
-
-ToolSvc += GlobalChi2FitterComb
-
-print(GlobalChi2FitterComb)
-
-from CombinedMuonRefit.CombinedMuonRefitConf import ReFitMuon
-MuonReFitTrack2 = ReFitMuon (name = "CombMuonRefit",
-                             FitterTool     = GlobalChi2FitterComb,
-                             Cosmics=True,
-                             IDTrackName="Tracks",
-                             MSTrackName="MooreTracks",
-                             matEffects=0,
-                             runOutlier=False,
-                             NewTrackName="Combined_Tracks",
-                             OutputLevel=3)
-
-topSequence += MuonReFitTrack2
-print(MuonReFitTrack2)
-
-#GlobalChi2FitterBarrel.OutputLevel=1
-#GlobalChi2FitterBarrel.NumericalDerivs=True
-#MdtDriftCircleOnTrackCreator = Service( "ToolSvc.Muon::MdtDriftCircleOnTrackCreator" )
-#MdtDriftCircleOnTrackCreator.CreateTubeHit = True
-#MdtDriftCircleOnTrackCreator.OutputLevel=1
-#MdtTubeHitOnTrackCreator = Service( "ToolSvc.Muon::MdtTubeHitOnTrackCreator" )
-#MdtTubeHitOnTrackCreator.CreateTubeHit = True
-#MdtTubeHitOnTrackCreator.OutputLevel=1
-
-
-#mooretotracktool=Service("ToolSvc.Muon::MooreToTrackTool")
-#mooretotracktool.OutputLevel=1
-
-#ToolSvc.TrackFitter.OutputLevel=1
-#ToolSvc.GlobalChi2FitterBarrel.LayerCreatorTool="Trk::MuidDynamicLayerCreator/MuidDynamicLayerCreator"
-#ToolSvc.GlobalChi2FitterBarrel.ExternalMat=True
-#ToolSvc.GlobalChi2FitterBarrel.Momentum=5000
-#ToolSvc.MuidDynamicLayerCreator.Cosmics=True
-#MuonReFitTrack2.OutputLevel=1
-
diff --git a/Reconstruction/RecExample/RecExCommission/share/CosmicSimulationRecoSetup-HLT.py b/Reconstruction/RecExample/RecExCommission/share/CosmicSimulationRecoSetup-HLT.py
deleted file mode 100644
index 6a6c1e12d9b4f75f992979ea2246fb15a17c6243..0000000000000000000000000000000000000000
--- a/Reconstruction/RecExample/RecExCommission/share/CosmicSimulationRecoSetup-HLT.py
+++ /dev/null
@@ -1,56 +0,0 @@
-LArDigitKey='FREE'
-
-from AthenaCommon.GlobalFlags import globalflags
-globalflags.DetGeo = 'commis'
-globalflags.DataSource.set_Value_and_Lock('geant4')
-
-from RecExConfig.RecFlags import rec
-rec.Commissioning.set_Value_and_Lock(True)
-rec.oldFlagTopSteering.set_Value_and_Lock(False)
-#rec.doTruth.set_Value_and_Lock(False)
-#rec.doJiveXML.set_Value_and_Lock(True)
-
-if rec.readRDO :
-    rec.doTrigger.set_Value_and_Lock(True)
-    from TriggerJobOpts.TriggerFlags import TriggerFlags as tf
-    #####for l1 simulation configuration
-    tf.doCosmicSim.set_Value_and_Lock(True)
-    #############
-    tf.readLVL1configFromXML.set_Value_and_Lock(True)
-    tf.readHLTconfigFromXML.set_Value_and_Lock(True)
-
-    tf.triggerMenuSetup.set_Value_and_Lock('cosmic_default')
-
-
-# for running over data with field on need this to be setto true
-from AthenaCommon.BFieldFlags import jobproperties
-
-# set the field properties based on DetDescrVersion
-if globalflags.DetDescrVersion.get_Value().find('ATLAS-GEONSF-') >= 0 :
-    jobproperties.BField.solenoidOn.set_Value_and_Lock(False)
-    jobproperties.BField.barrelToroidOn.set_Value_and_Lock(True)
-    jobproperties.BField.endcapToroidOn.set_Value_and_Lock(True)
-    globalflags.ConditionsTag.set_Value_and_Lock('OFLCOND-SIMCT-00-00-00')
-    print('configuring reco with solenoid off, toroid on from DetDescrVersion:',globalflags.DetDescrVersion.get_Value())
-    
-if globalflags.DetDescrVersion.get_Value().find('ATLAS-GEO-') >= 0 :
-    jobproperties.BField.solenoidOn.set_Value_and_Lock(True)
-    jobproperties.BField.barrelToroidOn.set_Value_and_Lock(True)
-    jobproperties.BField.endcapToroidOn.set_Value_and_Lock(True)
-    globalflags.ConditionsTag.set_Value_and_Lock('OFLCOND-SIMCST-00-00-00')
-    print('configuring reco with solenoid on, toroid on from DetDescrVersion:',globalflags.DetDescrVersion.get_Value())
-    
-if globalflags.DetDescrVersion.get_Value().find('ATLAS-GEONF-') >= 0 :
-    jobproperties.BField.solenoidOn.set_Value_and_Lock(False)
-    jobproperties.BField.barrelToroidOn.set_Value_and_Lock(False)
-    jobproperties.BField.endcapToroidOn.set_Value_and_Lock(False)
-    globalflags.ConditionsTag.set_Value_and_Lock('OFLCOND-SIMC-00-00-00')
-    print('configuring reco with solenoid off, toroid off from DetDescrVersion:',globalflags.DetDescrVersion.get_Value())
-        
-if globalflags.DetDescrVersion.get_Value().find('ATLAS-GEONTF-') >= 0 :
-    jobproperties.BField.solenoidOn.set_Value_and_Lock(True)
-    jobproperties.BField.barrelToroidOn.set_Value_and_Lock(False)
-    jobproperties.BField.endcapToroidOn.set_Value_and_Lock(False)
-    globalflags.ConditionsTag.set_Value_and_Lock('OFLCOND-SIMCS-00-00-00')
-    print('configuring reco with solenoid on, toroid off from DetDescrVersion:',globalflags.DetDescrVersion.get_Value())
- 
diff --git a/Reconstruction/RecExample/RecExCommission/share/CosmicSimulationRecoSetup.py b/Reconstruction/RecExample/RecExCommission/share/CosmicSimulationRecoSetup.py
deleted file mode 100644
index 0065ac4c43541643a9ecac53527ffbccb9512af1..0000000000000000000000000000000000000000
--- a/Reconstruction/RecExample/RecExCommission/share/CosmicSimulationRecoSetup.py
+++ /dev/null
@@ -1,63 +0,0 @@
-LArDigitKey='FREE'
-
-from AthenaCommon.GlobalFlags import globalflags
-globalflags.DetGeo = 'commis'
-globalflags.DataSource.set_Value_and_Lock('geant4')
-
-from RecExConfig.RecFlags import rec
-rec.Commissioning.set_Value_and_Lock(True)
-rec.oldFlagTopSteering.set_Value_and_Lock(False)
-#rec.doTruth.set_Value_and_Lock(False)
-#rec.doJiveXML.set_Value_and_Lock(True)
-
-if rec.readRDO :
-    rec.doTrigger.set_Value_and_Lock(True)
-    from TriggerJobOpts.TriggerFlags import TriggerFlags as tf
-    #####for l1 simulation configuration
-    tf.doCosmicSim.set_Value_and_Lock(True)
-    #############
-    tf.readLVL1configFromXML.set_Value_and_Lock(True)
-    tf.readHLTconfigFromXML.set_Value_and_Lock(True)
-
-    tf.triggerMenuSetup.set_Value_and_Lock('Cosmic2009_v1')
-
-    # This will need to be changed when things work better
-    tf.inputLVL1configFile.set_Value_and_Lock('TriggerMenuXML/LVL1config_Cosmic2009_v1_7-bit_trigger_types.xml')
-
-globalflags.DetDescrVersion.set_Value_and_Lock('ATLAS-GEO-07-00-00')
-#globalflags.ConditionsTag.set_Value_and_Lock('OFLCOND-CSC-01-00-00')
-
-# for running over data with field on need this to be setto true
-from AthenaCommon.BFieldFlags import jobproperties
-
-# set the field properties based on DetDescrVersion
-if globalflags.DetDescrVersion=='ATLAS-GEONSF-07-00-00':
-    jobproperties.BField.solenoidOn.set_Value_and_Lock(False)
-    jobproperties.BField.barrelToroidOn.set_Value_and_Lock(True)
-    jobproperties.BField.endcapToroidOn.set_Value_and_Lock(True)
-    globalflags.ConditionsTag.set_Value_and_Lock('OFLCOND-SIMCT-00-00-00')
-    print('configuring reco with solenoid off, toroid on from DetDescrVersion: ATLAS-GEONSF-07-00-00')
-    
-if globalflags.DetDescrVersion=='ATLAS-GEO-07-00-00':
-    jobproperties.BField.solenoidOn.set_Value_and_Lock(True)
-    jobproperties.BField.barrelToroidOn.set_Value_and_Lock(True)
-    jobproperties.BField.endcapToroidOn.set_Value_and_Lock(True)
-    globalflags.ConditionsTag.set_Value_and_Lock('OFLCOND-SIMCST-00-00-00')
-    print('configuring reco with solenoid on, toroid on from DetDescrVersion: ATLAS-GEO-07-00-00')
-    
-if globalflags.DetDescrVersion=='ATLAS-GEONF-07-00-00':
-    jobproperties.BField.solenoidOn.set_Value_and_Lock(False)
-    jobproperties.BField.barrelToroidOn.set_Value_and_Lock(False)
-    jobproperties.BField.endcapToroidOn.set_Value_and_Lock(False)
-    globalflags.ConditionsTag.set_Value_and_Lock('OFLCOND-SIMC-00-00-00')
-    print('configuring reco with solenoid off, toroid off from DetDescrVersion: ATLAS-GEONF-07-00-00')
-        
-if globalflags.DetDescrVersion=='ATLAS-GEONTF-07-00-00':
-    jobproperties.BField.solenoidOn.set_Value_and_Lock(True)
-    jobproperties.BField.barrelToroidOn.set_Value_and_Lock(False)
-    jobproperties.BField.endcapToroidOn.set_Value_and_Lock(False)
-    globalflags.ConditionsTag.set_Value_and_Lock('OFLCOND-SIMCS-00-00-00')
-    print('configuring reco with solenoid on, toroid off from DetDescrVersion: ATLAS-GEONTF-07-00-00')
-                            
-
-                                                
diff --git a/Reconstruction/RecExample/RecExCommission/share/Cosmics_ATN.py b/Reconstruction/RecExample/RecExCommission/share/Cosmics_ATN.py
deleted file mode 100644
index ef982d6c550caf4caa97c0e7a7cf01fac3e1f039..0000000000000000000000000000000000000000
--- a/Reconstruction/RecExample/RecExCommission/share/Cosmics_ATN.py
+++ /dev/null
@@ -1,5 +0,0 @@
-from AthenaCommon.BeamFlags import jobproperties
-jobproperties.Beam.beamType.set_Value_and_Lock("cosmics")
-# the main jobOpt
-include("RecExCommission/Collisions_ATN.py")                
-
diff --git a/Reconstruction/RecExample/RecExCommission/share/GetInputFiles.py b/Reconstruction/RecExample/RecExCommission/share/GetInputFiles.py
deleted file mode 100644
index a1528d067bc3949e2daaa25fa69679cce279128f..0000000000000000000000000000000000000000
--- a/Reconstruction/RecExample/RecExCommission/share/GetInputFiles.py
+++ /dev/null
@@ -1,24 +0,0 @@
-from os import popen
-
-def GetInputFiles(inputPath,filePattern):
-    print("Searching for files with pattern '",filePattern,"' in ",inputPath)
-    fileList=[]
-    if (inputPath[0:8]=='/castor/'):
-        cmd='nsls'
-    else:
-        cmd='ls -1'
-
-    for f in popen("%(cmd)s %(path)s | grep '%(pattern)s'" \
-                   % {'cmd':cmd,'path':inputPath,'pattern':filePattern}):
-        if f[len(f)-1:]=='\n':
-            f=f[0:len(f)-1]
-        fileList+=[inputPath+'/'+f]
-    print("Found ",len(fileList), " files")
-    return fileList
-    
-
-def GetInputFilesFromTokens(inputPath,runnumber,prefix=".*",trigger=".*"):
-    #pattern=prefix+"\.00"+str(runnumber)+"\..*"
-    pattern="%(prefix)s.*%(rn)07d.%(trig)s.*" % {'prefix' : prefix ,'rn' : runnumber,'trig' : trigger}
-    
-    return GetInputFiles(inputPath,pattern)
diff --git a/Reconstruction/RecExample/RecExCommission/share/NoRandomTrig.py b/Reconstruction/RecExample/RecExCommission/share/NoRandomTrig.py
deleted file mode 100644
index 39ef526a7ce5ad14ac95a060c2a104b5693a14cc..0000000000000000000000000000000000000000
--- a/Reconstruction/RecExample/RecExCommission/share/NoRandomTrig.py
+++ /dev/null
@@ -1,5 +0,0 @@
-#Random trigger off for reproducibility
-from TrigSteering.TrigSteeringConfig import ScalerSvc
-ScalerSvc = ScalerSvc()
-ScalerSvc.DefaultType = "HLT::PeriodicScaler"
-
diff --git a/Reconstruction/RecExample/RecExCommission/share/RecExCommission.py b/Reconstruction/RecExample/RecExCommission/share/RecExCommission.py
deleted file mode 100644
index 9bdbdae43cdd53235ff7a6cd5a48aa33322aa30f..0000000000000000000000000000000000000000
--- a/Reconstruction/RecExample/RecExCommission/share/RecExCommission.py
+++ /dev/null
@@ -1,21 +0,0 @@
-include("RecExCommission/MinimalCommissioningSetup.py")
-
-# not needed anymore (RS, Dec. 6th 2010)
-# needed to get TRT track extension working
-# from TrkDetDescrSvc.TrkDetDescrJobProperties import TrkDetFlags
-# TrkDetFlags.TRT_BuildStrawLayers.set_Value(True)
-
-# setup trigger reading from COOL (obo Clemencia)
-if rec.doTrigger():
-    from TriggerJobOpts.TriggerFlags import TriggerFlags as tf
-    tf.configForStartup="HLTonline"
-    tf.configForStartup.lock()
-
-from RecExConfig.RecFlags  import rec
-rec.ScopingLevel.set_Value_and_Lock(1)
-# done in the trf
-# rec.Production=True
-
-#from LArConditionsCommon.LArCondFlags import larCondFlags
-#larCondFlags.LArCoolChannelSelection.set_Value_and_Lock("3:238,306,313,319,325,331,338,344,350,1001:1012,1021,1022")
-#larCondFlags.OFCShapeFolder.set_Value_and_Lock('5samples3bins17phases') 
diff --git a/Reconstruction/RecExample/RecExCommission/share/RecExCommissionCommonFlags_jobOptions.py b/Reconstruction/RecExample/RecExCommission/share/RecExCommissionCommonFlags_jobOptions.py
deleted file mode 100644
index d08ce74f2f95f2befd5268406faa51e63801e316..0000000000000000000000000000000000000000
--- a/Reconstruction/RecExample/RecExCommission/share/RecExCommissionCommonFlags_jobOptions.py
+++ /dev/null
@@ -1,200 +0,0 @@
-# ---------------------------------------------------------------------------
-# RecExCommon flags
-# ---------------------------------------------------------------------------
-
-include.block("RecExCommission/RecExCommissionCommonFlags_jobOptions.py")
-
-
-# ---------------------------------------------------------------------------
-# AthenaCommonFlags
-# ---------------------------------------------------------------------------
-
-# start using the new job properties
-from AthenaCommon.JobProperties import jobproperties
-
-# AthenaCommon flags
-from AthenaCommon.AthenaCommonFlags  import athenaCommonFlags
-
-# -----------------------------------------------------------------------
-# being general reconstruction flags
-# -----------------------------------------------------------------------
-from RecExConfig.RecFlags  import jobproperties, rec
-
-#Number of events to process or generate
-athenaCommonFlags.EvtMax=10
-# Number of events to skip when reading an input POOL file.
-athenaCommonFlags.SkipEvents = 0
-# The list of input POOL files containing collections of Raw data objects
-# ['myfile.pool.root'] : file in run directory
-# ['LFN:mylogicalfile.root']: logical file name as specified in PoolFileCatalog.cml
-# ['rfio:/castor/cern.ch/somepath/somefile.pool.root']:file on castor (at CERN)
-athenaCommonFlags.PoolRDOInput = ["/afs/cern.ch/atlas/maxidisk/d17/data/TileTest/dig.05AprProd-10000000.root"]
-# The list of input ByteStream files containing collections of Raw data objects
-#athenaCommonFlags.BSRDOInput = ["/castor/cern.ch/grid/atlas/t0/perm/DAQ/daq.m4_combined.0019783.Default.L1TT-b00000001.LB0001.SFO-1._0001.data"]
-athenaCommonFlags.BSRDOInput = ["/castor/cern.ch/grid/atlas/t0/perm/DAQ/daq.m4_combined.0020720.debug.L1TT-b00000001.LB0000.SFO-1._0001.data"]
-#athenaCommonFlags.BSRDOInput = ["/castor/cern.ch/grid/atlas/DAQ/M6/daq.NoTag.0043719.physics.HLT_Cosmic_AllTeIDSelected.LB0000.SFO-1._0001.data"]
-# The list of input POOL files containing collections of ESD objects
-athenaCommonFlags.PoolESDInput = ["castor:/castor/cern.ch/grid/atlas/t0/perm/M4reproc/0020720/FESD/M4.0020720.physics.L1TT-b00000010.FESD.v130026.part0001._lumi0002._0001.1"]
-# The name of the output POOL file containing collections of ESD objects
-athenaCommonFlags.PoolESDOutput = "ESD.root"
-# The list of input POOL files containing collections of TAGs
-#athenaCommonFlags.PoolTAGInput = "TAG.root"
-# The name of the output POOL file containing collections of TAGs
-athenaCommonFlags.PoolTAGOutput = "TAG.root" 
-rec.PoolTAGCOMOutput="TAGCOM.root"
-athenaCommonFlags.PoolInputQuery = "TRT_Cosmic_Tracks"
-#AllowIgnoreExistingDataObject
-#AllowIgnoreConfigError
-#athenaCommonFlags.AthenaCommonFlags
-
-# -----------------------------------------------------------------------
-# GlobalFlags
-# -----------------------------------------------------------------------
-
-# GlobalFlags 
-from AthenaCommon.GlobalFlags import globalflags
-
-# Which detector configuration : atlas, combined test beam or commisisoning
-# Commissioning: 'commis'
-globalflags.DetGeo = 'commis'
-# Detector geometry DB tag
-globalflags.DetDescrVersion="ATLAS-CommNF-04-00-00"
-# data source: Where does the data comes from : real data, geant3 or geant4
-# real data: data
-# simulation: 'geant4'
-globalflags.DataSource = 'data'
-# Input format:
-# to read from BS: 'bytestream'
-# to read from ESD, RDO Pool files = 'pool'
-globalflags.InputFormat = 'bytestream'
-
-# ---------------------------------------------------------------------------
-# Beam flags to define the 
-# ---------------------------------------------------------------------------
-# Type of data to reconstruct: 'singlebeam','cosmics'
-from AthenaCommon.BeamFlags import jobproperties
-#jobproperties.Beam.beamType.set_Value_and_Lock("cosmics")
-
-
-# ---------------------------------------------------------------------------
-# BField flags to define the
-# ---------------------------------------------------------------------------
-# Field configuration: solenoidOn()   barrelToroidOn() endcapToroidOn()
-from AthenaCommon.BFieldFlags import jobproperties
-jobproperties.BField.solenoidOn=False
-jobproperties.BField.barrelToroidOn=False
-jobproperties.BField.endcapToroidOn=False
-
-# -----------------------------------------------------------------------
-# flags to drive the general behaviour of Reconstruction configuration
-# -----------------------------------------------------------------------
-#from RecExConfig.RecConfFlags import recConfFlags
-
-
-#RecConfFlags.AllowDisable
-#RecConfFlags.AllowIgnoreConfigError	
-#RecConfFlags.AllowIgnoreExistingDataObject	
-#RecConfFlags.RecConfFlags
-
-rec.CBNTAthenaAware = True	
-rec.doAOD = False
-#rec.doAODall	
-#rec.doAODCaloCells	
-rec.doCBNT = True	
-#rec.doCheckDictionary	
-#rec.doCheckJOT	
-#rec.doDetailedAuditor	
-#rec.doDumpMC	
-#rec.doDumpPoolInputContent	
-#rec.doDumpProperties	
-#rec.doDumpTDS	
-#rec.doDumpTES	
-#rec.doEdmMonitor	
-#rec.doESD = True
-# rec.doFileMetaData TODO might replace doDetStatus???
-rec.doDetStatus = True
-#rec.doFloatingPointException	
-#rec.doHeavyIon	
-rec.doHist = True
-rec.doJiveXML = False	
-#rec.doLowPt	
-#rec.doMinimalRec	
-#rec.doNameAuditor	
-#rec.doPerfMon = False
-rec.doPersint = False	
-#rec.doRestrictedESD	
-#rec.doSGAuditor	
-#rec.doShowSizeStatistics	
-#rec.doTimeLimit	
-#rec.doTruth	
-rec.doWriteAOD = False
-#rec.doWriteBS
-# If True writes out ESD file
-rec.doWriteESD = True
-#rec.doWriteRDO
-# If True writes out TAG file
-rec.doWriteTAG = True	
-#rec.noESDTrigger	
-#rec.oldFlagCompatibility	
-#rec.oldFlagLandMine	
-#rec.oldFlagTopSteering
-# General msg output level ALL,VERBOSE,DEBUG,INFO,WARNING,ERROR,FATAL
-rec.OutputLevel	= INFO
-#rec.readAOD
-#If True runs on ESD file  
-rec.readESD = False	
-#rec.readRDO	
-#rec.readTAG	
-#rec.Rec	
-#rec.RecAlgs	
-rec.RootHistoOutput = "monitoring.root"	
-rec.RootNtupleOutput = "ntuple.root"	
-#rec.TAGFromRDO	
-#rec.UserAlgs
-
-rec.doTile = True
-rec.doLArg = True
-rec.doInDet = True
-rec.doMuon = True
-
-## Switch on/off Calibration Ntuple
-#from MuonRecExample.MuonRecFlags import muonRecFlags
-#from MuonCalibAlgs.MuonCalibFlags import muonCalibFlags
-#muonRecFlags.doCalib = True
-#muonCalibFlags.Mode = 'trackNtuple'
-#muonCalibFlags.EventTag = 'Moore'
-
-### Switch on/off Combined Algorithms
-from MuonCombinedRecExample.MuonCombinedRecFlags import muonCombinedRecFlags,muidFlags
-muonCombinedRecFlags.doMuGirl = False
-muonCombinedRecFlags.doCaloTrkMuId = True
-muonCombinedRecFlags.doStaco = False
-muonCombinedRecFlags.doMuTag = False
-muonCombinedRecFlags.doAODMuons = True  # switch off AOD making
-muonCombinedRecFlags.doMergeMuons = True # switch off merging for ESD
-muidFlags.SegmentTagger = 'MuTagIMO' # switch off  by ''
-#muidFlags.Extrapolated = 'MuidStandalone' # switch off  by ''
-muidFlags.Extrapolated = '' # switch off  by ''
-#muidFlags.Combined = 'MuidCombined' # NOW not run # switch off  by ''
-muidFlags.Combined = 'CombinedMuonFit' # switch off  by ''
-
-
-# ----------------------------------------------------------------------
-# being flags to switch algorithm on/off
-# ----------------------------------------------------------------------
-from RecExConfig.RecAlgsFlags  import recAlgs
-
-#recAlgs.doTrigger 
-
-#
-# hack...
-#
-from RecExConfig.RecFlags import rec
-if not 'InDetKeys' in dir():
-    #
-    # --- setup StoreGate keys (JobProperties!)
-    #
-    print("InDetRec_jobOptions: InDetKeys not set before - I import them now")
-    from InDetRecExample.InDetKeys import InDetKeys
-#    InDetKeys.lock_JobProperties()
-                                                                         
diff --git a/Reconstruction/RecExample/RecExCommission/share/RecExCommissionConDB_jobOptions.py b/Reconstruction/RecExample/RecExCommission/share/RecExCommissionConDB_jobOptions.py
deleted file mode 100644
index fcb88ffede38203045efd9d7fce9cbd76e4a631a..0000000000000000000000000000000000000000
--- a/Reconstruction/RecExample/RecExCommission/share/RecExCommissionConDB_jobOptions.py
+++ /dev/null
@@ -1,24 +0,0 @@
-if rec.doLArg() or rec.doTile():
-    if globalflags.DataSource()=='geant4':
-        include("LArConditionsCommon/LArIdMap_MC_jobOptions.py")
-        include("LArConditionsCommon/LArConditionsCommon_MC_jobOptions.py")
-    else :
-        include("LArConditionsCommon/LArIdMap_comm_jobOptions.py")
-        include("LArConditionsCommon/LArConditionsCommon_comm_jobOptions.py")
-
-    include( "LArIdCnv/LArIdCnv_joboptions.py" )
-    include ("CaloDetMgrDetDescrCnv/CaloDetMgrDetDescrCnv_joboptions.py")
- 
-if rec.doTile():
-    include( "TileIdCnv/TileIdCnv_jobOptions.py" )
-    include( "TileConditions/TileConditions_jobOptions.py" )        
-
-if rec.doMuon():
-    #MW/RN
-   
-    import MuonRecExample.MuonReadCalib
-    #    GeoModelSvc.MuonVersionOverride = "MuonSpectrometer-R.01.01.Initial.Light"
-    #if not globalflags.DataSource()=='geant4':
-    #    MuDetCosmicFlags.doCalibCOOLprod=True        
-    #    include("MuonCommRecExample/MuDetCosmicConDB_jobOptions.py")
-
diff --git a/Reconstruction/RecExample/RecExCommission/share/RecExCommissionData_links.csh b/Reconstruction/RecExample/RecExCommission/share/RecExCommissionData_links.csh
deleted file mode 100644
index 92e3e82a3b2b9e58706355868a79dc3eb663be8e..0000000000000000000000000000000000000000
--- a/Reconstruction/RecExample/RecExCommission/share/RecExCommissionData_links.csh
+++ /dev/null
@@ -1,12 +0,0 @@
-#!/bin/tcsh
-if ( -e sqlite200 )then
-    rm -r sqlite200
-endif
-
-ln -s /afs/cern.ch/atlas/project/database/DBREL/packaging/DBRelease/current/geomDB .
-ln -s /afs/cern.ch/atlas/conditions/poolcond/catalogue/poolcond .
-
-setenv STAGE_HOST castoratlas 
-setenv RFIO_USE_CASTOR_V2 YES 
-setenv STAGE_SVCCLASS atlcal
-
diff --git a/Reconstruction/RecExample/RecExCommission/share/RecExCommissionData_links.sh b/Reconstruction/RecExample/RecExCommission/share/RecExCommissionData_links.sh
deleted file mode 100644
index abab5dc3ec8b708fa9ab7f79338269dc30ce0459..0000000000000000000000000000000000000000
--- a/Reconstruction/RecExample/RecExCommission/share/RecExCommissionData_links.sh
+++ /dev/null
@@ -1,12 +0,0 @@
-if [ -e sqlite200 ]
-then
-    rm -r sqlite200
-fi
-
-ln -s /afs/cern.ch/atlas/project/database/DBREL/packaging/DBRelease/current/geomDB .
-ln -s /afs/cern.ch/atlas/conditions/poolcond/catalogue/poolcond .
-
-export STAGE_HOST=castoratlas 
-export RFIO_USE_CASTOR_V2=YES 
-export STAGE_SVCCLASS=atlcal
-
diff --git a/Reconstruction/RecExample/RecExCommission/share/RecExCommissionRepro.py b/Reconstruction/RecExample/RecExCommission/share/RecExCommissionRepro.py
deleted file mode 100644
index 82a65d7c95922e2c2b59e835d7bfa1181fe23e8a..0000000000000000000000000000000000000000
--- a/Reconstruction/RecExample/RecExCommission/share/RecExCommissionRepro.py
+++ /dev/null
@@ -1,73 +0,0 @@
-# general configuration for commissioning
-from RecExConfig.RecFlags  import rec
-from RecExConfig.RecAlgsFlags  import recAlgs
-from AthenaCommon.BeamFlags import jobproperties
-from AthenaCommon.AthenaCommonFlags import athenaCommonFlags
-from AthenaCommon.GlobalFlags import globalflags
-
-#Minimally required flags for commissioning
-rec.ScopingLevel.set_Value_and_Lock(2)
-include("RecExCommission/MinimalCommissioningSetup.py")
-
-#default
-
-#Commissioning Flags
-# include( "RecExCommission/RecExCommissionCommonFlags_jobOptions.py" )
-#include( "RecExCommission/RecExCommissionFlags_jobOptions.py" )
-#should not be there
-#from MuonCombinedRecExample.MuonCombinedRecFlags import muonCombinedRecFlags,muidFlags
-#muonCombinedRecFlags.doMuGirl = False
-#muonCombinedRecFlags.doCaloTrkMuId = True
-#muonCombinedRecFlags.doStaco = False
-#muonCombinedRecFlags.doMuTag = False
-#muonCombinedRecFlags.doAODMuons = True  # switch off AOD making
-#muonCombinedRecFlags.doMergeMuons = True # switch off merging for ESD
-#muidFlags.SegmentTagger = 'MuTagIMO' # switch off  by ''
-#muidFlags.Extrapolated = 'MuidStandalone' # switch off  by ''
-#muidFlags.Extrapolated = '' # switch off  by ''
-#muidFlags.Combined = 'MuidCombined' # NOW not run # switch off  by ''
-#muidFlags.Combined = 'CombinedMuonFit' # switch off  by ''
-
-
-   
-#if read from TAG, cannot write TAG at the same time
-#these lines should be in RecExCommon_flags.py
-if rec.readTAG():
-    rec.doWriteTAGCOM=False
-
-#rec.doTrigger=True
-#jet problem right now
-#from JetRec.JetRecFlags import jetFlags
-#jetFlags.Enabled.set_Value_and_Lock(False)
-recAlgs.doObjMissingET.set_Value_and_Lock(False)
-recAlgs.doMissingETSig.set_Value_and_Lock(False)
-
-
-#rec.doJetMissingETTag.set_Value_and_Lock(False)
-#from RecExConfig.RecAlgsFlags  import recAlgs
-#recAlgs.doMissingET.set_Value_and_Lock(True)
-#rec.doEgamma.set_Value_and_Lock(False)
-#rec.doTau.set_Value_and_Lock(False)
-#recAlgs.doMuonSpShower.set_Value_and_Lock(False)
-
-
-# For Trigger configuration during the reprocessing 08.
-# Will allow to read LVL1 thresholds from COOL instead of from hard-coded XML file.
-# For info: Sylvie Brunet, Joerg Stelzer
-from TriggerJobOpts.TriggerFlags import TriggerFlags as tf
-tf.configForStartup= "HLTonline"
-tf.configForStartup.lock()
-
-
-from LArConditionsCommon.LArCondFlags import larCondFlags
-larCondFlags.LArCoolChannelSelection.set_Value_and_Lock("3:238,306,313,319,325,331,338,344,350,1001:1012,1021,1022")
-#Option: Remove Conditions for HECC Quadrant with broken LV Power supply
-#larCondFlags.LArCoolChannelSelection.set_Value_and_Lock("3:238,306,313,325,331,338,344,350,1001:1012,1021,1022")
-larCondFlags.OFCShapeFolder.set_Value_and_Lock('5samples3bins17phases')
-larCondFlags.SingleVersion.set_Value_and_Lock(False)
-larCondFlags.useShape.set_Value_and_Lock(True)
-
-
-#Switch off EM-Topo cluster corrections for 2nd round of 2008 reprocessing
-from CaloClusterCorrection.CaloClusterCorrectionFlags import caloClusterCorrectionFlags
-caloClusterCorrectionFlags.CaloTopoEMWhichCorrection.set_Value ("none")
diff --git a/Reconstruction/RecExample/RecExCommission/share/RecExCommission_RemoveHLT_TrigTauRecMerged.py b/Reconstruction/RecExample/RecExCommission/share/RecExCommission_RemoveHLT_TrigTauRecMerged.py
deleted file mode 100644
index b51d8e2580d10c65f5fa95937e93dc6c99a51d58..0000000000000000000000000000000000000000
--- a/Reconstruction/RecExample/RecExCommission/share/RecExCommission_RemoveHLT_TrigTauRecMerged.py
+++ /dev/null
@@ -1,15 +0,0 @@
-# RecExCommission_RemoveHLT_TrigTauRecMerged
-# Emergency hack to remove HLT_TrigTauRecMerged containers from ESD
-# because of failure : ERROR CreateRep failed, key = HLT_TrigTauRecMerged
-# C. Mora, May 4th, 2009  based on W. Lampl
-
-from AthenaCommon.Logging import logging
-log_HLTTau = logging.getLogger( 'RemoveHLT_TrigTauRecMerged' )
-
-try:
-    from AthenaCommon.AppMgr import theApp
-    StreamESD = theApp.getOutputStream( "StreamESD" )
-    StreamESD.ItemList.remove("Analysis::TauJetContainer#HLT_TrigTauRecMerged")
-    log_HLTTau.info("Removing Analysis::TauJetContainer#HLT_TrigTauRecMerged from ESD ItemList")
-except:
-    pass
diff --git a/Reconstruction/RecExample/RecExCommission/share/RecExCommission_RemoveTRTBSErr.py b/Reconstruction/RecExample/RecExCommission/share/RecExCommission_RemoveTRTBSErr.py
deleted file mode 100644
index 5a0d1d1b85dcd6893ef00602449ff8d90b04dbfe..0000000000000000000000000000000000000000
--- a/Reconstruction/RecExample/RecExCommission/share/RecExCommission_RemoveTRTBSErr.py
+++ /dev/null
@@ -1,22 +0,0 @@
-#RecExCommission_RemoveTRTBSERR
-# Emergency hack to remove TRT BS Error containers from ESD
-# because of unresonably large disk-space consumption
-# Walter Lampl, Dec 16th, 2008
-
-from AthenaCommon.Logging import logging
-log_TRT_BS_ERR = logging.getLogger( 'RemoveTRTBSErrFromESD' )
-
-# Setup the output sequence
-from AthenaCommon.AppMgr import theApp
-StreamESD = theApp.getOutputStream( "StreamESD" )
-
-try:
-    StreamESD.ItemList.remove("TRT_BSErrContainer#TRT_ByteStreamErrs")
-    log_TRT_BS_ERR.info("Removing TRT_BSErrContainer#TRT_ByteStreamErrs from ESD ItemList")
-except:
-    pass
-try:
-    StreamESD.ItemList.remove("TRT_BSIdErrContainer#TRT_ByteStreamIdErrs")
-    log_TRT_BS_ERR.info("Removing TRT_BSIdErrContainer#TRT_ByteStreamIdErrs from ESD ItemList")
-except:
-    pass
diff --git a/Reconstruction/RecExample/RecExCommission/share/RecExCommission_SingleBeamtopOptions.py b/Reconstruction/RecExample/RecExCommission/share/RecExCommission_SingleBeamtopOptions.py
deleted file mode 100755
index abb3de82dba86a0c370cb0ef5085e0b02652ff06..0000000000000000000000000000000000000000
--- a/Reconstruction/RecExample/RecExCommission/share/RecExCommission_SingleBeamtopOptions.py
+++ /dev/null
@@ -1,5 +0,0 @@
-from AthenaCommon.BeamFlags import jobproperties
-jobproperties.Beam.beamType.set_Value_and_Lock("singlebeam")
-
-include("RecExCommon/RecExCommon_topOptions.py")
-
diff --git a/Reconstruction/RecExample/RecExCommission/share/RecExCommission_fastRepro.py b/Reconstruction/RecExample/RecExCommission/share/RecExCommission_fastRepro.py
deleted file mode 100644
index d079e1485366427961590f117db4886f76a21d29..0000000000000000000000000000000000000000
--- a/Reconstruction/RecExample/RecExCommission/share/RecExCommission_fastRepro.py
+++ /dev/null
@@ -1,28 +0,0 @@
-include("RecExCommission/MinimalCommissioningSetup.py")
-
-
-## tempory fix to get TCT to run whil bug 51007 is being fixed
-#DQMonFlags.doMuonTrackMon.set_Value_and_Lock(False)
-#DQMonFlags.doMuonSegmentMon.set_Value_and_Lock(False)
-#DQMonFlags.doMuonAlignMon.set_Value_and_Lock(False)
-#DQMonFlags.doMuonPhysicsMon.set_Value_and_Lock(False)
-
-#Temprary workaround for bug 51068
-#DQMonFlags.doTauMon.set_Value_and_Lock(False) 
-
-# needed to get TRT track extension working
-from TrkDetDescrSvc.TrkDetDescrJobProperties import TrkDetFlags
-TrkDetFlags.TRT_BuildStrawLayers.set_Value(True)
-
-# setup trigger reading from COOL (obo Clemencia)
-from TriggerJobOpts.TriggerFlags import TriggerFlags as tf
-tf.configForStartup="HLTonline"
-tf.configForStartup.lock()
-
-from RecExConfig.RecFlags  import rec
-rec.ScopingLevel.set_Value_and_Lock(2)
-
-from LArConditionsCommon.LArCondFlags import larCondFlags
-larCondFlags.SingleVersion=False
-larCondFlags.LArCoolChannelSelection.set_Value_and_Lock("3:238,306,313,319,325,331,338,344,350,1001:1012,1021,1022")
-larCondFlags.OFCShapeFolder.set_Value_and_Lock('5samples3bins17phases') 
diff --git a/Reconstruction/RecExample/RecExCommission/share/RecExCommission_links.sh b/Reconstruction/RecExample/RecExCommission/share/RecExCommission_links.sh
deleted file mode 100755
index 5fca3dee361d88eff7e8535cd0d4ee2ce34c1471..0000000000000000000000000000000000000000
--- a/Reconstruction/RecExample/RecExCommission/share/RecExCommission_links.sh
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/bin/sh
-ln -s /afs/cern.ch/user/c/chriss/public/EndcapSoftware/InDetLayerMaterial-ATLAS-DC3-07.pool.root
-rm -rf sqlite200
-ln -s /afs/cern.ch/user/a/atlcond/coolrep/sqlite200
-ln -s /afs/cern.ch/atlas/project/database/DBREL/packaging/DBRelease/current/geomDB .
-
diff --git a/Reconstruction/RecExample/RecExCommission/share/RecoPixelStreamSetup.py b/Reconstruction/RecExample/RecExCommission/share/RecoPixelStreamSetup.py
deleted file mode 100644
index 3d3368596de2e232dd63d0a9e8fd24ad00f1a494..0000000000000000000000000000000000000000
--- a/Reconstruction/RecExample/RecExCommission/share/RecoPixelStreamSetup.py
+++ /dev/null
@@ -1,28 +0,0 @@
-from InDetRecExample.InDetJobProperties import InDetFlags
-InDetFlags.useBeamConstraint.set_Value_and_Lock(False)
-InDetFlags.selectSCTIntimeHits=False
-InDetFlags.doVtxLumi.set_Value_and_Lock(True)
-
-AODFlags.TrackParticleSlimmer=True
-
-from AthenaCommon.DetFlags import DetFlags
-DetFlags.Calo_setOff()
-DetFlags.Muon_setOff()
-DetFlags.ID_setOn()
-DetFlags.TRT_setOff()
-DetFlags.detdescr.TRT_setOn()
-DetFlags.makeRIO.TRT_setOff()
-
-rec.doTrigger.set_Value_and_Lock(True)
-rec.doCalo.set_Value_and_Lock(False)
-rec.doMuon.set_Value_and_Lock(False)
-rec.doJetMissingETTag.set_Value_and_Lock(False)
-rec.doMuonCombined.set_Value_and_Lock(False)
-rec.doEgamma.set_Value_and_Lock(False)
-rec.doTau.set_Value_and_Lock(False)
-
-from TrackD3PDMaker.VertexD3PDAnalysisFlags import VertexD3PDAnalysisFlags
-VertexD3PDAnalysisFlags.useBeamspot.set_Value_and_Lock(True)
-VertexD3PDAnalysisFlags.useTrigger.set_Value_and_Lock(False)
-VertexD3PDAnalysisFlags.useTriggerRaw.set_Value_and_Lock(True)
-
diff --git a/Reconstruction/RecExample/RecExCommission/share/RecoVtxSatellitesSetup.py b/Reconstruction/RecExample/RecExCommission/share/RecoVtxSatellitesSetup.py
deleted file mode 100644
index 9a1895dfef74f7466f0afad8ec4e21b6f0c0565f..0000000000000000000000000000000000000000
--- a/Reconstruction/RecExample/RecExCommission/share/RecoVtxSatellitesSetup.py
+++ /dev/null
@@ -1,70 +0,0 @@
-## preInlcude for Reco_trf.py for satellite bunches reconstruction
-## Runs extended |z| tracking with low-pT threshold
-## This is the porting to 17.2 of what was used in ATLAS-CONF-2011-049
-## Example usage (see also VtxSatellitesD3PD_trf_v1.txt):
-## Reco_trf.py maxEvents=-1 autoConfiguration=everything preInclude=PUStudies/VtxSatellitesD3PD_preInclude_v1.py inputBSFile=/eliza18/atlas/spagan/GBStudies/RAW/data12_8TeV.00201351.calibration_VdM.daq.RAW/data12_8TeV.00201351.calibration_VdM.daq.RAW._lb0000._SFO-3._2333.data outputESDFile=myESD.pool.root outputAODFile=myAOD.pool.root outputNTUP_IDVTXLUMIFile=myVTXD3PD.root
-
-#Set general reco settings
-from InDetRecExample.InDetJobProperties import InDetFlags
-InDetFlags.useBeamConstraint.set_Value_and_Lock(False)
-InDetFlags.doLowMuRunSetup.set_Value_and_Lock(True)
-InDetFlags.doTrackSegmentsPixel.set_Value_and_Lock(False)
-InDetFlags.doTrackSegmentsSCT.set_Value_and_Lock(False)
-InDetFlags.doTrackSegmentsTRT.set_Value_and_Lock(False)
-InDetFlags.selectSCTIntimeHits=False
-
-
-#Set algorithms to be run
-AODFlags.TrackParticleSlimmer=True
-
-from AthenaCommon.DetFlags import DetFlags
-DetFlags.Calo_setOff()
-DetFlags.Muon_setOff()
-DetFlags.ID_setOn()
-DetFlags.TRT_setOff()
-DetFlags.detdescr.TRT_setOn()
-DetFlags.makeRIO.TRT_setOff()
-
-rec.doTrigger.set_Value_and_Lock(False)
-rec.doCalo.set_Value_and_Lock(False)
-rec.doMuon.set_Value_and_Lock(False)
-rec.doJetMissingETTag.set_Value_and_Lock(False)
-rec.doMuonCombined.set_Value_and_Lock(False)
-rec.doEgamma.set_Value_and_Lock(False)
-rec.doTau.set_Value_and_Lock(False)
-
-from RecExConfig.RecAlgsFlags import recAlgs
-recAlgs.doEgammaBremReco.set_Value_and_Lock  (False)
-
-from TrackD3PDMaker.VertexD3PDAnalysisFlags import VertexD3PDAnalysisFlags
-VertexD3PDAnalysisFlags.useBeamspot.set_Value_and_Lock(True)
-
-#Change tracking reconstruction cuts (Increase maximum z of tracking accpetance)
-from InDetRecExample.ConfiguredNewTrackingCuts import ConfiguredNewTrackingCuts
-InDetNewTrackingCuts      = ConfiguredNewTrackingCuts("Offline")
-InDetNewTrackingCuts._ConfiguredNewTrackingCuts__maxZImpact = 1700.
-InDetNewTrackingCuts.printInfo()
-
-InDetNewTrackingCutsLowPt = ConfiguredNewTrackingCuts("LowPt")
-InDetNewTrackingCutsLowPt._ConfiguredNewTrackingCuts__maxZImpact = 1700.
-InDetNewTrackingCutsLowPt.printInfo()
-
-#Change vertex reconstruction cuts (Increase maximum z of tracking accpetance)
-from InDetRecExample.ConfiguredVertexingCuts import ConfiguredVertexingCuts
-InDetPrimaryVertexingCuts = ConfiguredVertexingCuts("LowPt")
-InDetPrimaryVertexingCuts._ConfiguredVertexingCuts__z0Max = 1700.
-InDetPrimaryVertexingCuts._ConfiguredVertexingCuts__IPz0Max = 1700.
-InDetPrimaryVertexingCuts._ConfiguredVertexingCuts__sigIPd0Max = 5.0
-InDetPrimaryVertexingCuts.printInfo()
-
-#Setup D3PD making options
-InDetFlags.doVertexFindingForMonitoring.set_Value_and_Lock(False)
-InDetFlags.doSplitVertexFindingForMonitoring.set_Value_and_Lock(False)
-
-from TrackD3PDMaker.VertexD3PDAnalysisFlags import VertexD3PDAnalysisFlags
-VertexD3PDAnalysisFlags.useAllVertexCollections.set_Value_and_Lock(False)
-VertexD3PDAnalysisFlags.useBeamspot.set_Value_and_Lock(True)
-# Disable tracking info to have small D3PDs
-#VertexD3PDAnalysisFlags.useTracks.set_Value_and_Lock(True)
-# The following is only available after TrackD3PDMaker-01-03-05
-#VertexD3PDAnalysisFlags.filterTightTruth.set_Value_and_Lock(True)
diff --git a/Reconstruction/RecExample/RecExCommission/share/SingleBeam_ATN.py b/Reconstruction/RecExample/RecExCommission/share/SingleBeam_ATN.py
deleted file mode 100644
index 1ba6f9157fa7a6c17c052c0ff3fee59dc880b18c..0000000000000000000000000000000000000000
--- a/Reconstruction/RecExample/RecExCommission/share/SingleBeam_ATN.py
+++ /dev/null
@@ -1,5 +0,0 @@
-from AthenaCommon.BeamFlags import jobproperties
-jobproperties.Beam.beamType.set_Value_and_Lock("singlebeam")
-# the main jobOpt
-include("RecExCommission/Collisions_ATN.py")                
-
diff --git a/Reconstruction/RecExample/RecExCommission/share/minimalRecoSplashSetup.py b/Reconstruction/RecExample/RecExCommission/share/minimalRecoSplashSetup.py
deleted file mode 100644
index ee370f546e93419f9fc8bc2df2139f3455ba2dc6..0000000000000000000000000000000000000000
--- a/Reconstruction/RecExample/RecExCommission/share/minimalRecoSplashSetup.py
+++ /dev/null
@@ -1,26 +0,0 @@
-from AthenaCommon.BeamFlags import jobproperties
-jobproperties.Beam.beamType.set_Value_and_Lock("singlebeam")
-
-## calo settings from Guillaume
-from CaloRec.CaloRecFlags import jobproperties
-jobproperties.CaloRecFlags.doEmCluster.set_Value_and_Lock(False)
-jobproperties.CaloRecFlags.doCaloTopoCluster.set_Value_and_Lock(False)
-jobproperties.CaloRecFlags.doCaloEMTopoCluster.set_Value_and_Lock(False)
-rec.doJetMissingETTag.set_Value_and_Lock(False)
-rec.doEgamma.set_Value_and_Lock(False)
-rec.doTau.set_Value_and_Lock(False)
-BTaggingFlags.Active=False
-
-## muon settings from Rosy
-#muonRecFlags.doMoore=False
-#muonCombinedRecFlags.doMuidMuonCollection=False 
-#muonRecFlags.doMuonboy=False
-#muonCombinedRecFlags.doStacoMuonCollection=False
-mooreFlags.doSegmentsOnly=True
-muonboyFlags.doSegmentsOnly=True
-muonRecFlags.doSegmentT0Fit = False
-muonCombinedRecFlags.Enabled = False
-
-## from Markus, Tony...
-from InDetRecExample.InDetJobProperties import InDetFlags
-InDetFlags.doMinimalReco      = True
diff --git a/Reconstruction/RecExample/RecExCommission/share/postInclude_ESDtoESD_MuonBoy.py b/Reconstruction/RecExample/RecExCommission/share/postInclude_ESDtoESD_MuonBoy.py
deleted file mode 100644
index 68c5da845ce60530138b978b5471e7b70c877882..0000000000000000000000000000000000000000
--- a/Reconstruction/RecExample/RecExCommission/share/postInclude_ESDtoESD_MuonBoy.py
+++ /dev/null
@@ -1,4 +0,0 @@
-from MuonboyAth.MuonboyAthConf import MboyRec
-theMboyRec = MboyRec()
-theMboyRec.AthPosOff = 1
-
diff --git a/Reconstruction/RecExample/RecExCommission/share/readbsusingtag.py b/Reconstruction/RecExample/RecExCommission/share/readbsusingtag.py
deleted file mode 100644
index e4dc99043ebe7fca7c59f9c8314b5230cc62acfe..0000000000000000000000000000000000000000
--- a/Reconstruction/RecExample/RecExCommission/share/readbsusingtag.py
+++ /dev/null
@@ -1,15 +0,0 @@
-# for reading BS events using TAG_COMM 
-# need to have the BS file in your file catalogue
-# either by using: catalogBytestreamFiles.sh
-# or by using dq2-ls -P
-
-from AthenaCommon.AthenaCommonFlags  import athenaCommonFlags
-athenaCommonFlags.FilesInput=['tagcomm.root']
-athenaCommonFlags.PoolInputQuery.set_Value_and_Lock("EventNumber==2317247")
-
-from RecExConfig.RecFlags import rec
-rec.readRDO.set_Value_and_Lock(True)
-rec.doAOD.set_Value_and_Lock(False)
-rec.doWriteAOD.set_Value_and_Lock(False)
-rec.doWriteTAG.set_Value_and_Lock(False)
-include ("RecExCommon/RecExCommon_topOptions.py")
diff --git a/Reconstruction/RecExample/RecExCommission/share/readesd.py b/Reconstruction/RecExample/RecExCommission/share/readesd.py
deleted file mode 100644
index d99a52482bb6a7d7b9e6b0edc52844df4efe57f2..0000000000000000000000000000000000000000
--- a/Reconstruction/RecExample/RecExCommission/share/readesd.py
+++ /dev/null
@@ -1,95 +0,0 @@
-from RecExConfig.RecFlags  import rec
-from AthenaCommon.BeamFlags import jobproperties
-from AthenaCommon.AthenaCommonFlags import athenaCommonFlags
-from AthenaCommon.GlobalFlags import globalflags
-
-
-# various configuration special to commissioning, needed for all jobs
-athenaCommonFlags.PoolESDInput.set_Value_and_Lock(['castor:/castor/cern.ch/grid/atlas/tzero/prod1/perm/data08_cosmag/physics_IDCosmic/0091900/data08_cosmag.00091900.physics_IDCosmic.recon.ESD.o4_f73/data08_cosmag.00091900.physics_IDCosmic.recon.ESD.o4_f73._lb0001._sfo01._0001.1'])
-
-rec.AutoConfiguration=['everything']
-
-
-# all of these should now be autoconfigured - but i leave here incase 
-#jobproperties.Beam.beamType.set_Value_and_Lock("cosmics")
-#globalflags.DetDescrVersion.set_Value_and_Lock('ATLAS-GEO-04-00-00')
-#globalflags.ConditionsTag.set_Value_and_Lock('COMCOND-ES1C-000-00')
-# for running over data with field on need this to be setto true
-#from AthenaCommon.BFieldFlags import jobproperties
-#jobproperties.BField.solenoidOn.set_Value_and_Lock(False)
-#jobproperties.BField.barrelToroidOn.set_Value_and_Lock(True)
-#jobproperties.BField.endcapToroidOn.set_Value_and_Lock(True)
-
-
-#hardcoded output specification (corresponds to optional flags from runArgs in transform skeleton)
-rec.RootNtupleOutput.set_Value_and_Lock("newcommission.ntuple.root")
-#rec.RootHistoOutput.set_Value_and_Lock("monitoring.root")
-athenaCommonFlags.EvtMax.set_Value_and_Lock(10)
-#athenaCommonFlags.SkipEvents = 0
-
-# run ID reconstruction
-#from InDetRecExample.InDetJobProperties import InDetFlags
-#jobproperties.InDetJobProperties.Enabled.set_Value_and_Lock(True)
-#For version < 14.4.0: it requires to set in RecExCond/RecExCommon_DetFlags.py
-# the following: DetFlags.makeRIO.ID_setOn()
-
-
-# run Muons reconstruction
-#from MuonRecExample.MuonRecFlags import muonRecFlags
-#jobproperties.MuonRec.Enabled.set_Value_and_Lock(True)
-
-# run combined muon reconstruction
-#from MuonCombinedRecExample.MuonCombinedRecFlags import muonCombinedRecFlags 
-#jobproperties.MuonCombinedRec.Enabled.set_Value_and_Lock(True)
-
-#uncomment to do egamma
-#rec.doEgamma.set_Value_and_Lock(True)
-#from egammaRec.egammaRecFlags import jobproperties
-#jobproperties.egammaRecFlags.Enabled.set_Value_and_Lock(True)
-
-#but not others
-rec.doJetMissingETTag.set_Value_and_Lock(False)
-from JetRec.JetRecFlags import jetFlags
-jetFlags.Enabled.set_Value_and_Lock(False)
-from RecExConfig.RecAlgsFlags  import recAlgs
-recAlgs.doMissingET.set_Value_and_Lock(False)
-rec.doTau.set_Value_and_Lock(False)
-recAlgs.doMuonSpShower.set_Value_and_Lock(False)
-
-
-
-rec.doHist.set_Value_and_Lock(True)
-rec.doCBNT.set_Value_and_Lock(True)
-rec.doWriteTAGCOM.set_Value_and_Lock(False)
-rec.doWriteTAG.set_Value_and_Lock(False)	
-rec.doWriteAOD.set_Value_and_Lock(False)
-rec.doAOD.set_Value_and_Lock(False)
-rec.doMonitoring.set_Value_and_Lock(True)
-
-rec.readESD.set_Value_and_Lock(True)
-rec.doESD.set_Value_and_Lock(False)
-rec.doWriteESD.set_Value_and_Lock(False)
-globalflags.InputFormat.set_Value_and_Lock('pool')
-
-if not 'Debug' in dir():
-    Debug=True  # change to True to have printout information
-
-if Debug:
-    # DEBUG/VERBOSE options
-    rec.doNameAuditor=True
-    rec.doPerfMon=True
-    rec.doDetailedPerfMon=True
-    rec.doDumpProperties=True
-    rec.doDumpTES=True
-    # rec.OutputLevel = INFO
-
-# the main jobOpt
-include("RecExCommission/RecExCommission.py")                
-
-
-from AthenaMonitoring.DQMonFlags import DQMonFlags
-DQMonFlags.monType='BS_ESD'
-DQMonFlags.histogramFile.set_Value_and_Lock( "myMonitoringESD.root" )
-include ("RecExCommon/RecExCommon_topOptions.py")
-
-
diff --git a/Reconstruction/RecExample/RecExCommission/share/readesdusingtag.py b/Reconstruction/RecExample/RecExCommission/share/readesdusingtag.py
deleted file mode 100644
index ce1479528eb2d8b7b702f938601b8db68a849119..0000000000000000000000000000000000000000
--- a/Reconstruction/RecExample/RecExCommission/share/readesdusingtag.py
+++ /dev/null
@@ -1,54 +0,0 @@
-from RecExConfig.RecFlags  import rec
-from AthenaCommon.BeamFlags import jobproperties
-from AthenaCommon.AthenaCommonFlags import athenaCommonFlags
-from AthenaCommon.GlobalFlags import globalflags
-
-#Minimally required flags for commissioning
-include("RecExCommission/MinimalCommissioningSetup.py")
-
-athenaCommonFlags.FilesInput=["TAG.root"]
-rec.Commissioning.set_Value_and_Lock(True)
-# choose what detector to turn on:
-rec.doInDet.set_Value_and_Lock(True)
-rec.doLArg.set_Value_and_Lock(True)
-rec.doTile.set_Value_and_Lock(True)
-rec.doMuon.set_Value_and_Lock(True)
-rec.doMuonCombined.set_Value_and_Lock(True)
-
-rec.doTrigger.set_Value_and_Lock(False)
-
-#hardcoded output specification (corresponds to optional flags from runArgs in transform skeleton)
-rec.RootNtupleOutput.set_Value_and_Lock("newcommission.ntuple.root")
-#rec.RootHistoOutput.set_Value_and_Lock("monitoring.root")
-athenaCommonFlags.EvtMax.set_Value_and_Lock(10)
-#athenaCommonFlags.SkipEvents = 0
-
-rec.doJiveXML.set_Value_and_Lock(True)
-athenaCommonFlags.PoolInputQuery.set_Value_and_Lock("PixelTracks==1&&SCTTracks==1&&TRTTracks==1&&TileMuonFitter>0&&MooreTracks>0&&ConvertedMBoyTracks>0&&NpixSPs>2")
-
-rec.doCBNT.set_Value_and_Lock(False)
-
-if not 'Debug' in dir():
-    Debug=False  # change to True to have printout information
-
-if Debug:
-    # DEBUG/VERBOSE options
-#    rec.doNameAuditor=True
-    rec.doPerfMon=True
-    rec.doDetailedPerfMon=True
-    rec.doDumpProperties=True
-#    rec.doDumpTES=True
-    rec.OutputLevel = DEBUG
-
-# the main jobOpt
-include("RecExCommission/RecExCommission.py")                
-
-
-from AthenaMonitoring.DQMonFlags import DQMonFlags
-DQMonFlags.monType='BS_ESD'
-DQMonFlags.histogramFile.set_Value_and_Lock( "myMonitoringESD.root" )
-include ("RecExCommon/RecExCommon_topOptions.py")
-
-
-svcMgr.EventSelector.CollectionType="ExplicitROOT"
-svcMgr.EventSelector.Query=athenaCommonFlags.PoolInputQuery()
diff --git a/Reconstruction/RecExample/RecExCommission/share/setuptrf_offline.sh b/Reconstruction/RecExample/RecExCommission/share/setuptrf_offline.sh
deleted file mode 100644
index 24c416a004224d591fb4264f15c0bb1cef07408b..0000000000000000000000000000000000000000
--- a/Reconstruction/RecExample/RecExCommission/share/setuptrf_offline.sh
+++ /dev/null
@@ -1,64 +0,0 @@
-#!/usr/bin/env zsh
-
-#########################################################################
-##
-##  Script for setting up ATLAS/Athena run-time environment via CMT
-##
-##  - input parameters:
-##     1) CMT version; e.g. 'v1r20p20080222'
-##     2) patch directory (CMT test area)
-##     3) transuses string, i.e. hyphen-separated 'project-release' string; 
-##        e.g. 'AtlasTier0-14.2.10.2'
-##     4) special setup to be sourced
-##
-## (C) Luc Goossens, Armin Nairz (July 2008)
-##
-#########################################################################
-
-if test $# -ne 4 ; then
-     echo "ERROR incorrect nr of args"
-     echo "USAGE:  setuptrf.sh CMTVERSION PATCHDIR TRANSUSES SPECIALSETUP"
-     echo
-     exit 1
-fi
-
-export CMTVERSION=$1
-export PATCHDIR=$2
-export TRANSUSES=$3
-export SPECIALSETUP=$4
-
-export PROJECT=`echo ${TRANSUSES} | awk -F '-' '{print $1}'`
-export RELEASE=`echo ${TRANSUSES} | awk -F '-' '{print $2}'`
-
-export WORKDIR=`pwd`
-
-# set AthenaPOOL output level
-#-------------------------------------------------------------------------------
-export POOL_OUTMSG_LEVEL=5
-
-
-# assemble CMT requirements file
-#-------------------------------------------------------------------------------
-cat > requirements << EOF
-set   CMTSITE  CERN
-set   SITEROOT /afs/cern.ch
-macro ATLAS_DIST_AREA \${SITEROOT}/atlas/software/dist                           
-macro ATLAS_TEST_AREA ${PATCHDIR}
-use AtlasLogin AtlasLogin-* \$(ATLAS_DIST_AREA)
-EOF
-
-# set up CMT version
-#-------------------------------------------------------------------------------
-source /afs/cern.ch/sw/contrib/CMT/${CMTVERSION}/mgr/setup.sh ""
-cmt config
-
-# set up run environment
-#-------------------------------------------------------------------------------
-source ${WORKDIR}/setup.sh -tag=${PROJECT},${RELEASE},32,oneTest,runtime
-
-# source special/custom setup
-#-------------------------------------------------------------------------------
-if test $SPECIALSETUP != 'none' ;
-then
-  source $SPECIALSETUP
-fi
diff --git a/Reconstruction/RecExample/RecExCommission/share/skipBadEvents.py b/Reconstruction/RecExample/RecExCommission/share/skipBadEvents.py
deleted file mode 100644
index 8a0760044019e2efd725b21dde8cfeb877cf4dad..0000000000000000000000000000000000000000
--- a/Reconstruction/RecExample/RecExCommission/share/skipBadEvents.py
+++ /dev/null
@@ -1,3 +0,0 @@
-from AthenaCommon.AppMgr import ServiceMgr
-if (rec.doWriteESD):
-    ServiceMgr.EventSelector.MaxBadEvents=1000
diff --git a/Reconstruction/RecExample/RecExCommon/share/RecExCommon_topOptions.py b/Reconstruction/RecExample/RecExCommon/share/RecExCommon_topOptions.py
index ac97aa0382bcea27f38fa9dcf62b43dc75441de7..f54bc4c6768dcee50d778c8e1fbfb049d5890530 100644
--- a/Reconstruction/RecExample/RecExCommon/share/RecExCommon_topOptions.py
+++ b/Reconstruction/RecExample/RecExCommon/share/RecExCommon_topOptions.py
@@ -1565,7 +1565,6 @@ if not rec.oldFlagCompatibility:
 # -------------------------------------------------------------
 pdr.flag_domain('tag')
 if rec.doWriteTAGCOM():
-    # include( "RecExCommission/RecExCommissionTAG_jobOptions.py" )
     logRecExCommon_topOptions.warning( "TAGCOM has been retired !! Please use doWriteTAG instead !!" )
 
 try:
diff --git a/Reconstruction/RecExample/RecExCommission/share/MinimalCommissioningSetup.py b/Reconstruction/RecExample/RecExCond/share/MinimalCommissioningSetup.py
similarity index 100%
rename from Reconstruction/RecExample/RecExCommission/share/MinimalCommissioningSetup.py
rename to Reconstruction/RecExample/RecExCond/share/MinimalCommissioningSetup.py
diff --git a/Reconstruction/RecExample/RecExCond/share/RecExCommon_flags.py b/Reconstruction/RecExample/RecExCond/share/RecExCommon_flags.py
index f92301fd72ad413dc6e411c7808bb20a2033a93c..6b1b99e7cc0552b622dbad59d045a6c78ec32de9 100755
--- a/Reconstruction/RecExample/RecExCond/share/RecExCommon_flags.py
+++ b/Reconstruction/RecExample/RecExCond/share/RecExCommon_flags.py
@@ -233,10 +233,16 @@ if len(rec.AutoConfiguration())>0:
     from AthenaCommon.AppMgr import ServiceMgr as svcMgr
     svcMgr += AutoConfigConsistencyCheckSvc("AutoConfigConsistencyCheckSvc")
 
-
 #special commisioning job options
 if rec.Commissioning():
-   include("RecExCommission/RecExCommission.py")
+   include("RecExCond/MinimalCommissioningSetup.py")
+   # setup trigger reading from COOL
+   if rec.doTrigger():
+      from TriggerJobOpts.TriggerFlags import TriggerFlags as tf
+      tf.configForStartup="HLTonline"
+      tf.configForStartup.lock()
+
+   rec.ScopingLevel.set_Value_and_Lock(1)
 
 if rec.triggerStream().startswith('express'):
    logRecExCommon_flags.info('Disabling track slimming for express stream.')
@@ -594,12 +600,6 @@ except Exception:
 
 #load commissioning flags here (major cleanup needed)
 if rec.Commissioning():
-   #--------------------------------------------------------------
-   # Common flags with RecExCommon
-   #--------------------------------------------------------------
-   #if rec.readRDO:
-   #   include( "RecExCommission/RecExCommissionCommonFlags_jobOptions.py" )
-
 
    # ---------------------------------------------------------------------------
    # AthenaCommonFlags
diff --git a/Reconstruction/RecJobTransforms/python/ConfigUtils.py b/Reconstruction/RecJobTransforms/python/ConfigUtils.py
deleted file mode 100644
index fe7189dfba9304bc41941b0bcf6cfa3d386a2e56..0000000000000000000000000000000000000000
--- a/Reconstruction/RecJobTransforms/python/ConfigUtils.py
+++ /dev/null
@@ -1,82 +0,0 @@
-#!/usr/bin/env python
-
-# Copyright (C) 2002-2017 CERN for the benefit of the ATLAS collaboration
-
-# First define a list of functions
-# Then call them from PredefinedConfigFunctions(key,runArgs) at the end
-
-from __future__ import print_function
-def ConfigureFieldAndGeo(runArgs):
-    print("Method ConfigureFieldAndGeo...")
-    from PATJobTransforms.GeoConfig import GetRunNumber
-    RunNumber=GetRunNumber(runArgs)
-    print("Configuring geometry and field from RunNuber",RunNumber)
-    from RecExCommission.RecExCommission_MagneticFieldConfig import setFieldConfig
-    setFieldConfig(RunNumber)
-    return
-
-#------------------------
-def SetBeamType(runArgs):
-    print("Method SetBeamType...")
-    BeamType='NONE'
-    if hasattr(runArgs,"beamType"):
-        BeamType=runArgs.beamType
-    elif hasattr(runArgs,"outputESDFile") or hasattr(runArgs,"outputAODFile") or hasattr(runArgs,"inputESDFile") or hasattr(runArgs,"inputAODFile"):
-        print("Attempting to set beamType from outputESD or outputAOD file...")
-        print("known cosmics projects: data08_cos, data08_cosmag")
-        print("known single beam projects: data08_1beam, data08_1beammag")
-        print("know collisions projects: data08_coll900, data08 ")
-
-        if hasattr(runArgs,"outputESDFile"): fileName=runArgs.outputESDFile
-        elif hasattr(runArgs,"outputAODFile"): fileName=runArgs.outputAODFile
-        elif hasattr(runArgs,"inputESDFile"): fileName=runArgs.inputESDFile[0]
-        elif hasattr(runArgs,"inputAODFile"): fileName=runArgs.inputAODFile[0]
-        #base on a file named like this:
-        #run08_cos.00077585.physics_HLT_Cosmics_NIM4.recon.ESD.o4_r509_tid024433/ESD.024433._00001.pool.root.2
-        #or directly
-        #data08_cosmag.00090415.physics_CosmicMuons.recon.ESD.o4_f68._lb0001._sfo02._0001
-
-        #if several directories, take the first part
-        subNames=fileName.split('/')
-        firstName=subNames[0]
-        #from run08_cos.ESD.pool.root, split by dots and project is the first part
-        project = firstName.split('.')[0]
-        print('project = ',project)
-        if project=="data08_cos" or project=="data08_cosmag": BeamType='cosmics'
-        elif project=="data08_1beam" or project=="data08_1beammag": BeamType='singlebeam'
-        elif project=="data08" or project=="data08_coll900": BeamType='collisions'
-        else:
-            print("\n\nWARNING - unknown project name '%s'\n\n"%project)
-            print("Will try to guess project from 'data', '_cos', '_1beam', '_coll' keywords...")
-            if project.startswith('data'):
-                if project.rfind('_cos')>0: BeamType='cosmics'
-                elif project.rfind('_1beam')>0: BeamType='singlebeam'
-                elif project.rfind('_coll')>0: BeamType='collisions'                
-            if BeamType == 'NONE':
-                print("Unexpected project name. Maybe the project position is wrong?")
-                print("Trying to search the complete file name for known projects... [%s]"%fileName)
-                if fileName.rfind("data08_cos")>0 or fileName.rfind("data08_cosmag")>0: BeamType='cosmics'
-                elif fileName.rfind("data08_1beam")>0 or fileName.rfind("data08_1beammag")>0: BeamType='singlebeam'
-                elif fileName.rfind("data08.")>0 or fileName.rfind("data08_coll900")>0: BeamType='collisions'
-                else:
-                    raise RuntimeError("(2) Unable to determine beamType from file named '%s'"%fileName)
-            
-    if BeamType == 'NONE':
-        raise RuntimeError("(3) Unable to determine beamType from file name nor from direct argument")
-    else:
-        from AthenaCommon.BeamFlags import jobproperties
-        jobproperties.Beam.beamType.set_Value_and_Lock( BeamType )
-        print("The beamType is set to",BeamType)
-
-    return
-
-
-def PredefinedConfigFunctions(key,runArgs):
-    if key == "FieldAndGeo":
-        ConfigureFieldAndGeo(runArgs)
-    elif key == "BeamType":
-        SetBeamType(runArgs)
-    else:
-        raise RuntimeError("Unknown key '%s' in PredefinedConfigFunctions(key,runArgs)"%key)
-    return
-
diff --git a/Tools/Tier0ChainTests/scripts/tct_runAll.sh b/Tools/Tier0ChainTests/scripts/tct_runAll.sh
index fc2e8269793b329af04d7ee453242999f6384ca0..fbf5914aebb5a82808ed19ee9d71f55bf7d05a2d 100755
--- a/Tools/Tier0ChainTests/scripts/tct_runAll.sh
+++ b/Tools/Tier0ChainTests/scripts/tct_runAll.sh
@@ -87,7 +87,7 @@ do
   idx=`expr $idx + 1`
 done
 
-TRFARGS="preInclude=RecExCommission/MinimalCommissioningSetup.py --ignoreunknown"
+TRFARGS="preInclude=RecExCond/MinimalCommissioningSetup.py --ignoreunknown"
 
 ## merge aods
 INFILE=job_${TRIGSTR}_0.AOD.pool.root