MKVCleaver is a front end (GUI) for MKVExtract.exe (from MKVToolNix package by Moritz Bunkus) which extracts data from MKV files.
MKVExtract is a command line tool and is capable of extracting tracks, attachments, tags, subtitles and other information from an MKV file, but it can only work with one file at a time. And many times if you are dealing with TV shows they come as many separate MKV files.
So if you wanted to modify stream data (video, audio, subtitles) inside of an MKV file you would need to extract data first (could be a subtitle track to fix display issues, for example), adjust it and then mux it back together.
Now imagine doing this process one by one on dozens and sometimes hundreds of files ! Way too much time and work.
So that’s what MKVCleaver does: it allows you to automate the extraction process to the point where you can set it up and walk away then come back and work on the extracted files.