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For tracking purposes google adds unique fields at container level to mp4 files downloaded from youtube:
https://superuser.com/questions/503868/how-i-can-remove-all-google-data-from-youtube-video-downloads
I think youtube-dl should by default create reproducible downloads: if several people from different countries using different platforms execute at different time same youtube-dl commands for same urls they should get exactly the same files. Now md5sum for mp4 files from youtube changes after simple redownloading file from same system and location, because gs* entries are changed.
The most obvious and trivial workaround is to simply remux:
avconv -i _video.mp4 -c copy -flags bitexact video.mp4.-flags bitexactis required, because else info about ffmpeg/libav versions will be added to fileP.S. With matroska files bitexact option works fine too.