I’ve got some raw BD files. What tools can I use to convert them into a more familiar format?

So I’ve got a rip of the Japanese Blu Ray of Evangelion, and I’d like to turn it from a jumble of numbered .mts files into something more useable. How do I get started going about that process? As an example, if I download a raw CD rip, I can use cuetools to turn it into a list of .flac tracks ready for listening. Is there...