Not tested, but if you need a quick and dirty way, you could put a script like this in your WordPress folder and call it each time:
define( 'WP_USE_THEMES', false );
require('wp-blog-header.php');
global $wpdb;
$wpdb->query( "DELETE FROM $wpdb->options WHERE option_name LIKE '%\_transient\_%'" );
Not to be used on a production server.
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