I've released MKVToolNix 6.0.0. It packs quite a punch: several new features, a couple of bugfixes. The new features include a reader for the FlashVideo file format (.flv -- yes, for those YouTube videos), splitting by frame/field numbers, splitting by chapter numbers, splitting into parts by frame/field numbers, reading VobSubs from MP4 files and the ability to save additional command line options as default options in mmg.
Then there's a major change regarding one of the most controversial features in MKVToolNix: header removal compression has been turned off by default in both mkvmerge and mmg.
The list of fixed bugs is even longer than the one for new features, so please look at the ChangeLog for the details.