If there is not any difference, why having two server parameters to achieve one behavior?
From mysql documentation:
The --log-slow-queries option is deprecated and is removed (along with the log_slow_queries system variable) in MySQL 5.6. Instead, use the --slow_query_log option to enable the slow query log and the --slow_query_log_file=file_name option to set the slow query log file name.
See here: http://dev.mysql.com/doc/refman/5.5/en/server-options.html#option_mysqld_log-slow-queries
log_slow_queries
was deprecated in MySQL 5.1.29 by slow-query-log
.
The MySQL 5.1 Reference Manual has more details.
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