atmel: checkpatch.pl cleanups

Before: 881 errors, 265 warnings, 4507 lines checked
After:  114 errors, 273 warnings, 4548 lines checked

This was mostly "space required after that ',' (ctx:VxV)".
Also a fair number of whitespace, code indent, and C99 comment cleanups.

New warnings introduced are all "line over 80 character"

md5sums are identical, as I skipped any fixes which may have altered the resulting binary.
Signed-off-by: John Daiker <daikerjohn@gmail.com>
Signed-off-by: John W. Linville <linville@tuxdriver.com>