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Ensure opts are passed into Open3.popen3

What does this Merge Request do?

This MR fixes a bug that was introduced in !1237 (merged) that meant running gdk update/reconfigure would not work outside of the GDK_ROOT.

Merge Request checklist

  • Tests added for new functionality. If not, please raise Issue to follow-up.
  • This change is backward compatible. If not, please include steps to communicate to our users.
  • Documentation added/updated, if needed.
  • gdk doctor test added, if needed.

Closes #946 (closed)

Edited by 🤖 GitLab Bot 🤖

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