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atlas_build_run.sh Update, master branch (2020.04.24.)

Attila Krasznahorkay requested to merge akraszna/atlasexternals:BuildRunUpdate-master-20200424 into master

This MR was broken off of !664 (closed), to reduce the size of that MR a bit.

Updated atlas_build_run.sh(.in) to handle quoted commands correctly. Previously any complicated command fed through the script would break if it had quotes/spaces in it.

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