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[ATR-28760] Correct the use of CloneAndReplace in trigger muon signature

Tim Martin requested to merge tamartin/athena:MuonCAFix into main

The function returns a copy of the flag container with the modification.

The behaviour of the job is unchanged as the ID code contains a fall-back to call CloneAndReplace itself if not done by the signature code. Hence not flagging as bugfix.

cc @vippolit, @yoyamagu

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