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DS commands, messages and replies. Commands are used to control the DS and can be issued through the network or through the serial port. The DS replies to the commands- reply codes indicate the result of command execution. Messages are different in that they are not replied to. For more information see programming.
DS settings. Settings are permanent functioning parameters that are stored in the non-volatile memory (EEPROM) of the DS. Once programmed, they remain intact even when the DS is powered off. Many (but not all) settings require the DS to be rebooted for the new setting value to take effect. 
DS parameters and instructions. Parameters are temporary overrides for settings. Parameters are not saved into the EEPROM and take immediate effect (no rebooting required). Instructions are used to make the DS perform a certain action.