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ci: remove empty directories from CI bundles

Ben Boeckel requested to merge ben.boeckel/cmb-superbuild:ci-bundle-no-empty-dirs into master

Empty directories left behind in the bundle may end up getting detected as "namespace packages" if they are under PYTHONPATH. This ends up causing confusion when such a namespace package is found and prevents loading of a real package's inner modules later in PYTHONPATH. Remove these directories to avoid such confusion.

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