Yes, if you find that it differs it qualifies as a bug.
I think I need to clarify:
Is $PWD always the same as $bamboo_build_working_directory?
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Sorry, I don't understand the answer. Yes it is always the same?
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Yes Bamboo changes working directory to a build working directory for the script task. You can use Bamboo variables to get build working directory (and more) injected into your script task.
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