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Fix EvtMax and SkipEvents setting

Stewart Martin-Haugh requested to merge smh/athena:fix_evtMax_skipEvents into master

@tamartin and I discovered this serious bug in runbatch.py - it was only setting EvtMax and SkipEvents when they were provided at the command line. Any attempt to set them in athenaCommonFlags was ignored.

Additionally, add code to TrigMT_Reco_tf.py to set athenaCommonFlags properly.

Lots of test references will need updating...

EDIT: not sure this is the best way to proceed, see ATEAM-541

Edited by Stewart Martin-Haugh

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