mkclean (command line tool to clean and optimize Matroska)

mkclean is a command line tool to clean and optimize Matroska files
(.mkv / .mka / .mks / .mk3d) and WebM files (.webm / .weba) that
have already been muxed. It reorders the elements with the Cues
at the front, so your Matroska files are ready to be streamed
efficiently over the web.

It also removes elements not found in the Matroska specs and the extra
Meta Seek list of Clusters that some program add to their file. It can
also optionally remux the Cluster blocks to start each boundary with
a keyframe and the matching audio/subtitle blocks for that keyframe.

Also comes with mkWDclean to modify files in a way they can play in
broken/incomplete players.