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Making the setup.sh script generated by AtlasCMake a bit more robust

Attila Krasznahorkay requested to merge akraszna/atlasexternals:CDPATHFixes_20170227 into master

As we learned from Mark Sutton, the cd path/;pwd formalism may not work well when using the CDPATH environment variable.

This formalism, together with making sure that we are not hit by a user's alias for cd or pwd should make the setup scripts a bit more robust.

My local tests were successful with this formalism, so in the end I think this should be an uncontroversial update.

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