These are scripts used to modify MKV-related files. You may use them as references.
merge-generator.sh - generates a merge.bat to merge video, audio and subtitles
merger.sh - an improved version of merge-generator.sh which process the files, merging the video, audio and subtitles directly while running
modify-default-subs.sh - changes the default subtitles using mkvpropinfo id tracks
remove-thumbs.sh - removes any images (jpeg & png) attached to the mkv which are usually used as cover photos