Use `getopt` to parse command line arguments.

[majjoha]

As we continuously add more options to the stack machine, it becomes cumbersome to handle each one, and we increase the risk of introducing errors related to array indices. This commit changes the way we parse command line arguments by using getopt instead.

It also changes the --verbose flag to -v, and the --manualstep flag to simply -m. The latter now sets both the verbose flag, and the manual step flag.

See more about getopt here: http://www.gnu.org/software/libc/manual/html_node/Example-of-Getopt.html

[engesgaard]

This is a much better way to handle optional arguments.