This matches the flash-command and is generally a bit easier to work
with.
This commit also prepares for allowing multiple formats to be used in
the emulator command, which is necessary for the esp32.
Instead of specifying the emulator command in atmega328p.json, specify
it in the two boards based on it (arduino and arduino-nano). This makes
the configuration consistent with the machine package, which only
defines the CPUFrequency function in the board files (and not in
machine_atmega328p.json).