remove direct reset command make it default start

the device should 'always' be reset after a dfu program because
certain settings for the bootloader will still be present on
the device if no reset is performed.  if start --no-reset is
the default behavior this could make for some very tricking
debugging down the road.

with the --no-reset flag, at least the user is a bit more aware
of whay they are doing when they start their app.

files with changes include :arguments.[ch], commands.c, main.c
clarify start & reset function calls

atmel start and reset both start the device only start calls a jump
instead of resetting the device (which can lead to problems with bugs
associated with initial device state not matching datasheet or device
state after normal reset).  update code to highly similarities of
these commands. there is no functional change here, only change names.

also add atmel command sheet for uc3 devices
add cscope and ctags out to gitignore
Merge branch 'master' into changeargs
add taghighlight settings to gitignore
Merge branch 'master' into changeargs
begin adding debug info
Merge branch 'implementuser' into add_debug

Conflicts:
	src/atmel.h
finished adding debug comments