In different ways, depending how you want to go:
1) Saperny option is to write procedures, additional tables, etc. total to make version control for MySQL.
2) write a bash script which would copy the structure, and the emergence of new tables, etc. was called a bash script that made a copy of the structure...all the same Saperny option, but easier implemented than 1, and much more flexible.
3) Look for the MySQL forks in which this mechanism is implemented.