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Singularity 2.3 compatibility

Diego Davila Foyo requested to merge gh-4ab3277a/26/rynge/master into master

Created by: rynge

2.3 changed --containall to also include cleaning of the environment. This PR breaks up the --containall to the pieces we used under 2.2.1 (--contain --pid --ipc). We have also added a test to verify that the environment has not been cleaned.

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