Replace getopt_long_only with getopt_long

It seems that in the past, the intention was to only use long options.
At some point short variants where added, implemented as long options.
This patch cleans up the implementation and uses getopt_long that allows
parsing of both long and short options improving readability.

Signed-off-by: Olliver Schinagl <o.schinagl@ultimaker.com>