I am looking for a very simple explanation/tutorial on what flags are. I understand that flags work indicate a command what to do. For example:
rm -Rf test
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In your own C program you can process command line options in any way you see fit. Command line parameters in C come in the parameters of the main(int argc, char *argv[]) method as strings.
And if you'd like to process command line parameters in a way similar to most UNIX commands, the function you're probably looking for is getopt()
Good luck!