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When using the new command line feature of arduino 1.5.2 the --board argument can be used to set the board. However, if the board has custom menus such as the Nano entry, it is not possible to select a custom option on command line. This makes it impossible to build many of the boards by command line, such as a Nano 168.
Current workaround is to create manually new board entries by combining the board and custom entries. I don't think this was indended.