MakeMKV

Great software. Use it. :)

See: http://www.makemkv.com/forum2/viewtopic.php?f=5&t=1053 for key

You can use MakeMKV on CLI, though the syntax is so confusing, I don't recommend it.

See http://www.makemkv.com/developers/usage.txt

To backup into directory “test”:

makemkvcon backup --decrypt disc:/mnt/bluray/

That will decrypt and dump the entire disc, in original M2TS format.

Backup main titles to MKV

makemkvcon mkv disc:0 all .