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fix for race condition in merge_files.py

Charles Leggett requested to merge leggett/Gaudi:dev/merge_files into master

semi-regularly, Atlas has build failures due to race conditions from merge_files.py:

https://its.cern.ch/jira/browse/ATEAM-151

https://its.cern.ch/jira/browse/GAUDI-1079

here is the fix proposed by Scott and implemented by Rolf.

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