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With MySQL 5.6 every run of automysqlbackup will generate the following warning (and potentially an error email):

Warning: Using a password on the command line interface can be insecure.

This is because automysqlbackup uses username and password directly on the mysql command for the connection.

Here the problem has been solved:
http://www.redeo.nl/2013/11/automysqlbackup-warning-using-password-command-line-interface-can-insecure/

But I don't know if this is the cleanest solution.

When dumping tables, mysqldump will take the entire table in memory before actually dumping the content. This can be problematic for large tables. The use of the --quick option will prevent this behaviour.

The --quick options is enabled when using the default --opt option, but when using --single-transaction, it must be enabled manualy. I would be great to make it a configurable option in the same way as --single-transaction is.