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Currently i'm using MKVToolNix for my needs which is fine but i would prefer some CLI also. As far as i know ffmpeg supports chapters management.
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Firstly, install the mkvmerge command by installing the mkvtoolnix package. Now use mkvmerge to add that to your mkv file (this will remove any existing chapters in the file). Wait for the processing to complete (shou'dn't take long), and now you will be able to use your video-player's buttons to skip between chapters.
Launch Handbrake, import the MP4 file and add the chapter file. Click on Start Encode to add chapters to MP4.
Select a video file and click OK. The file is played in the VLC media player. Select Chapter in the Playback menu to view the list of chapters. Select a chapter of your choice.
The ffmetadata format allows you to add chapters to a file.
Have a look at https://ffmpeg.org/ffmpeg-formats.html#Metadata-1 for an example.
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