New setting "logPlayerCommands" (default true) which can be disabled to prevent player commands from being logged.

src/com/massivecraft/factions/P.java

@@ -172,6 +172,12 @@ public class P extends MPlugin
 		Conf.save();
 	}
 
+	@Override
+	public boolean logPlayerCommands()
+	{
+		return Conf.logPlayerCommands;
+	}
+
 	@Override
 	public boolean handleCommand(CommandSender sender, String commandString, boolean testOnly)
 	{