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[ATR-19328] Set empty Collections when running with athenaHLT.py

[ATR-19328] Set empty Collections when running with athenaHLT.py
tamartin/athena:setEmptyCollections into master
Merged Tim Martin requested to merge tamartin/athena:setEmptyCollections into master

Prevents crashes from this flag attempting to auto-configure when running athenaHLT.py

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