Generating MKV files from Blu-rays with "Seamless branching"

[foxmulder2]

There are quite a few Blu-rays with multiple versions of the same movie on one disc out there, for example the Blu-ray version of "Apocalypse Now" usually has both the Theatrical Cut and the Redux Cut on the same disc.
Now I, as many others before me I suppose, searched for a way to combine both versions in one file, as to not waste a lot of disk space. After searching the web and learning a lot about the Matroska format, the answer seems to be Editions and Ordered Chapters. And there actually is an application out the which seems to do exactly what I want: xin1generator.

But, this application hasn't been updated in years, wasn't ported to Linux which I use and relies on eac3to.

So, I guess my question to you is: do I have to/should I use xin1generator, or are there any other applications with similar functionality out there? What about doing it manually, are there any guides out there? I have searched for a long while, but couldn't come up with anything. Is there a different solution altogether out there?

Any help would be appreciated.