I don't think it'd make a difference if Haali's source was available or not. The code that can be ported from it is just the matroska parsing stuff, for which there's libmatroska, or for demux_mkv behind mplayer. The main part of Haali is a directshow filter, which can't be ported anyway. Also, the directory searching code used for segment linking is unportable and would be useless.
I don't think there'll be support for ordered chapters in any of the main linux player releases for quite a while anyway. Not because it's difficult to code, but because developers can't be arsed with all the privacy, security concerns and making it cross-platform. Best opting for LoneShadow's patch if need be.
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