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The best that I can tell is that this code traces back to David Schmitt. It has been forked many times since then :)
1. you cannot add databases to an instance that has a root password
2. you have to specify username as USER@BLAH or it cannot be found
3. mysql_grant does not complain if user does not exist
4. Needs support for pre-seeding on debian
5. the types may need to take user/password
6. rather or not to configure /etc/.my.cnf should be configurable