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I want to merge two video files to a single video file. (No concating)

Via the vlc GUI, I can achieve this: vlc menu bar -> Media -> Convert/Save -> Show more options -> Play another media synchronously.

How to do this via the CLI?

I am not searching for this solution https://superuser.com/a/537482 because I want two separated video streams / windows.

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VLC GUI actually shows you the CLI equivalent!

When you check "Play another media synchronously" and choose the media file, the field "Options" above gets updated to include :input-slave=file:///Path/To/Media/file.ext etc.

The same command line option is also documented in VLC command-line help and vlc -H:

  --input-slave=<string>     Input slave (experimental)
      This allows you to play from several inputs at the same time. This
      feature is experimental, not all formats are supported. Use a '#'
      separated list of inputs.

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