www.makemkv.com

Some blu-ray movies have an option where you can watch a movie with a video of commentary as pop-up picture-in-picture (Groundhog Day) or even little trivia and facts about the movie (Back to the Future). This is done through Java and at specified timestamps during the movie, the Java code will tell the blu-ray player to grab another small video file and overlay it on top of the main movie as far as I understand.

Is there any hope of somehow using MakeMKV to rip the main movie, then rip all of these little video files, extract all of the timestamps for when these little videos are to be displayed and somehow remux everything back together so you end up with one movie file with the pop-up picture-in-picture baked in?

EDIT: Now that I think more about it, this would require encoding and be out-of-scope for MakeMKV.

The Matroska specs have their own "scripting language" in the chapter system. Unfortunately at the moment it consists of nothing more than one single command "go to ChapterUID X". Even more unfortunately the Matroska Specs aren't so much "Specs" as they are a bunch of vague notes that for the most part add up to nothing but gibberish. The support for the current Matroska feature set is pretty much non-existent in both hardware and software playback circles and it's impossible to know if that's caused by an unwillingness by developers to complicate their playback code in order to support Matroska features or if it's caused by them simply not being able to figure out how the damn thing is supposed to work. Anyway, the general lack of Matroska support is having the effect of giving the Matroska developers the excuses they need to not bother working on expanding or improving the thing to any great extent, or even properly implementing the features already in existence.

The worst thing is, they pretty much shot themselves in the foot by neglecting to specifically mention that players were supposed to completely ignore any element in the file they don't understand. Now they're too afraid to do anything, because every time they try a bunch of players start crashing when they try to play back the files with these extra elements.

Basically, Matroska isn't in a happy state at the moment and I can't see it getting better any time soon.