Fixed Makefile to work with Melzi2 boards on arduino-1.6.x

- also by default use ${HOME}/Arduino as install directory which may be more
sane, especially with arduino packages provided by distributions
- bump arduino version to 106 (this seems to be useless)
- program firmware through the USB serial which is more comfortable way how
to program the firmware
- use 57600 programing speed by default which seems to be more reliable
with arduino bootloaders (at least with those shipped with the Melzi2 boards)

Signed-off-by: Jaroslav Škarvada <jskarvad@redhat.com>