Sorry, but such a feature will never be implemented. There are excellent shells out there that can do this easily. For example, with a bash you could convert all .avi files into Matroska with these commands:
Quote:
find -type f -name '*.avi' | { while read filename ; do mkvmerge -o /path/to/output/dir/"`basename "$filename" .avi`.mkv" "$filename" ; done ; }
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I know that using shells is not everyone's thing. However, implementing a powerful and flexible batch remuxer requires countless hours of work. If I cut down on the hours then either the flexibility or the number of features would be severely reduced and therefore the work would not be worth it because too few people could actually use it in such a state.
The short version is that it's waaaaay too much work and that I don't have that amount of free time. So.... no. Sorry.