bugfix on read behavior: start at 0 w bin & blank

- change so read command starts at buffer 0 when --bin is specified
  or when the contents of memory are blank.
improve stderr print, shift print to atmel.c

- better status / error printing from atmel.c than command.c
- improved erase, read and program messages
- add back print of usage % at the end of program

STATUS: looks like there is a page error for program thought
this had already been fixed
Merge branch 'development' into avr32bootconfig