athenaHLT/runHLT: fix flag parsing

Ensure to parse the flags given on the command line, after we are setting the default values. This ensures that e.g. Beam.Type can be overwritten on the command line for the cosmics menu.

Relates to ATR-28733.

Trigger/TriggerCommon/TriggerJobOpts/python/runHLT.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
 """
 CA module to configure the (standalone) HLT for athena and athenaHLT.
 There is a separate entry point for each application to tailor some
@@ -120,6 +120,13 @@ def athenaHLTCfg(flags):
    # Set default flags for running HLT
    set_flags(flags)
 
+   # Decoding the flags from the command line is already done in athenaHLT.
+   # But we have to do it again in case some of the flags from set_flags
+   # get overwritten by the user.
+   from TrigPSC import PscConfig
+   for flag_arg in PscConfig.unparsedArguments:
+      flags.fillFromString(flag_arg)
+
    # Lock flags
    lock_and_restrict(flags)