Remove old flag system

[LauPM]

Replace old flag system as there are better, cleaner and optimized way of doing this. Have a look at argparse which is a Parser for command-line options, arguments and subcommands:

• Divide initialize_macros in two: we need to maintain the user_input dictionary as it is used along SCINT functions and the questions if no flags are provided. The way we provide the flags is the thing to optimize here