Fix RDOtoRDO_TRIG skeleton flag order

Fix RDOtoRDO_TRIG skeleton flag order. Input files should be set as early as possible.

Should fix ATR-28655.

/cc @martindl

Reconstruction/RecJobTransforms/python/RDOtoRDO_TRIG_Skeleton.py

-# Copyright (C) 2002-2023 CERN for the benefit of the ATLAS collaboration
+# Copyright (C) 2002-2024 CERN for the benefit of the ATLAS collaboration
 
 from PyJobTransforms.TransformUtils import processPreExec, processPreInclude, processPostExec, processPostInclude
 from TriggerJobOpts import runHLT
@@ -18,8 +18,6 @@ def configureFlags(runArgs):
     flags = initConfigFlags()
     from PyJobTransforms.CommonRunArgsToFlags import commonRunArgsToFlags
     commonRunArgsToFlags(runArgs, flags)
-    from RecJobTransforms.RecoConfigFlags import recoRunArgsToFlags
-    recoRunArgsToFlags(runArgs, flags)
 
     # Set standard flags for HLT jobs
     runHLT.set_flags(flags)
@@ -33,6 +31,9 @@ def configureFlags(runArgs):
         flags.Output.RDOFileName = runArgs.outputRDO_TRIGFile
         log.info("---------- Configured RDO_TRIG output")
 
+    from RecJobTransforms.RecoConfigFlags import recoRunArgsToFlags
+    recoRunArgsToFlags(runArgs, flags)
+
     from AthenaConfiguration.Enums import ProductionStep
     flags.Common.ProductionStep=ProductionStep.Reconstruction