All config settings in messages.conf use the standard minecraft formatting codes except for Message Color.
This is the message displayed after after a clear has run. %d is the variable for the number of items.
Message Color only affects messages not defined in messages.conf. You can use any of the colors on this page. Make sure to check your spelling.
This is the part that comes before any messages from the plugin in-game. If you would like a space between the prefix and the message, add a space just before the end quote.
This setting is used when there is a minute or less until the clear. %d is the variable for seconds.
This setting is used when there is more than a minute until the clear. The first %d is for minutes. The second %d is for seconds.