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Sorry, Beyond Compare for Linux scripting requires X-Window. It will not run as a console shell script or as a cron job. Removing the X-Window requirement for scripts on Linux is on our todo list but doesn't have a scheduled release date.
You could consider running Xvfb, an X server that runs and 'displays' completely in memory, so it doesn't need video hardware to run. You could start Xvfb as a second X server on your machine, have beyond compare connect to that X server, and run its scripts.
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