What are mysql-bin.000001, mysql-bin.000002…

By default whenever you make a change to a MySQL database it creates a log of the query and stores it in a file simlare to ‘mysql-bin.000001’ . The MySQL database does this so that you can recover or replicate a database. Most applications this is a good things to have enabled just like doing regular backups.

If you want to disable MySQL from creating these binary logs

1. Open "my.ini"
2. Search for this line "log-bin=mysql-bin"
3. Comment this line out "# log-bin=mysql-bin"
4. Save and restart the MySQL database

You can now safely delete these files from that directory.

For more information see Binary logs in the MySQL documentation