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Fix issue with S3 handler not being included in the PyInstaller binary.

This was because PyInstaller actually crawls import statements when looking for modules to include. Because the S3 modules were imported dynamically (module sourced from the config), PyInstaller wouldn't pick them up. This is solved by adding the modules to PyInstaller's `hiddenimports` directive.

Also added some more smoke testing to the Linux binary to make sure it can do basic actions (download repo, check it out).

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