Update Makefile to newer arduino and fix upload issues

This patch updates the Makefile allowing 'make upload' to work more
reliably by using 'wiring' rather then 'arduino' as a programmer.

Additionally it sets more common arduino files/location for non windows
users.

Windows users tend to use _do_make.bat which overrides these values
anyway.

Fixes Ultimaker/Ultimaker2Marlin#44

Signed-off-by: Olliver Schinagl <o.schinagl@ultimaker.com>