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I just got around to using MediaTomb, and I love it.
I have all my videos in .mkv format, and I like to keep the original video and audio streams. Unfortunately, some of my devices cannot play, for example dts or truehd audio (giving me a dreaded "unsuppoerted audio" message).
I would like mediatomb to transcode the audio track in those videos to either PCM or FLAC (if that means transcoding the entire video with something similar to "vcodec copy", that is fine). I found information about fourcc in the documentation, but as far as I understand, that pertains to .avi files, and after two days of googleing, I wasn't able to find an enlightning example.
I have figured out how to enable transcoding, but not how to make it work with matroska (I.e. I only get a black screen with no audio on the player), and not how to only trigger it if some specific audio codec is found. I offer a reward of 10 billion "Thank you!" to anyone who can help me or give me some pointers. :-)