update write flash to use buffer structure

- pass buffer structure to flash program, remove all extra/ old
  params
- pass buffer structure to align buffer, remove olds
- move duplicated functionality from commands.c to atmel.c
update start command to launch and change doc

the start command is now back just as it always has been
the new command is launch, that way neither start or reset
functionality change
Consolidate flash command into one function

- move buffer info inside buffer_out / buffer_in to prevent
  init of almost identical array 2x
- consolidate command write functions